Voice processing in monkey and human brains.

PubMed

Scott, Sophie K

2008-09-01

Studies in humans have indicated that the anterior superior temporal sulcus has an important role in the processing of information about human voices, especially the identification of talkers from their voice. A new study using functional magnetic resonance imaging (fMRI) with macaques provides strong evidence that anterior auditory fields, part of the auditory 'what' pathway, preferentially respond to changes in the identity of conspecifics, rather than specific vocalizations from the same individual.

Integrated Geophysical Investigation of Preferential Flow Paths at the Former Tyson Valley Powder Farm near Eureka, Missouri, May 2006

USGS Publications Warehouse

Burton, Bethany L.; Ball, Lyndsay B.; Stanton, Gregory P.; Hobza, Christopher M.

2009-01-01

In May 2006, the U.S. Geological Survey, in cooperation with the U.S. Army Corps of Engineers, conducted surface and borehole geophysical surveys at the former Tyson Valley Powder Farm near Eureka, Mo., to identify preferential pathways for potential contaminant transport along the bedrock surface and into dissolution-enhanced fractures. The Tyson Valley Powder Farm was formerly used as a munitions storage and disposal facility in the 1940s and 1950s, and the site at which the surveys were performed was a disposal area for munitions and waste solvents such as trichloroethylene and dichloroethylene. Direct-current resistivity and seismic refraction data were acquired on the surface; gamma, electromagnetic induction, and full waveform sonic logs were acquired in accessible boreholes. Through the combined interpretation of the seismic refraction tomographic and resistivity inversion results and borehole logs, inconsistencies in the bedrock surface were identified that may provide horizontal preferential flow paths for dense nonaqueous phase liquid contaminants. These results, interpreted and displayed in georeferenced three-dimensional space, should help to establish more effective monitoring and remediation strategies.

A stilbenoid-specific prenyltransferase utilizes dimethylallyl pyrophosphate from the plastidic terpenoid pathway

USDA-ARS?s Scientific Manuscript database

Prenylated stilbenoids found preferentially in a few legume plants exhibit phytoalexin properties and pharmacological activities with potential benefits to human health. Despite their importance, the biosynthetic pathways of these compounds remain to be elucidated. Peanut (Arachis hypogaea) hairy r...

Delayed Early Primary Visual Pathway Development in Premature Infants: High Density Electrophysiological Evidence

PubMed Central

Tremblay, Emmanuel; Vannasing, Phetsamone; Roy, Marie-Sylvie; Lefebvre, Francine; Kombate, Damelan; Lassonde, Maryse; Lepore, Franco; McKerral, Michelle; Gallagher, Anne

2014-01-01

In the past decades, multiple studies have been interested in developmental patterns of the visual system in healthy infants. During the first year of life, differential maturational changes have been observed between the Magnocellular (P) and the Parvocellular (P) visual pathways. However, few studies investigated P and M system development in infants born prematurely. The aim of the present study was to characterize P and M system maturational differences between healthy preterm and fullterm infants through a critical period of visual maturation: the first year of life. Using a cross-sectional design, high-density electroencephalogram (EEG) was recorded in 31 healthy preterms and 41 fullterm infants of 3, 6, or 12 months (corrected age for premature babies). Three visual stimulations varying in contrast and spatial frequency were presented to stimulate preferentially the M pathway, the P pathway, or both systems simultaneously during EEG recordings. Results from early visual evoked potentials in response to the stimulation that activates simultaneously both systems revealed longer N1 latencies and smaller P1 amplitudes in preterm infants compared to fullterms. Moreover, preterms showed longer N1 and P1 latencies in response to stimuli assessing the M pathway at 3 months. No differences between preterms and fullterms were found when using the preferential P system stimulation. In order to identify the cerebral generator of each visual response, distributed source analyses were computed in 12-month-old infants using LORETA. Source analysis demonstrated an activation of the parietal dorsal region in fullterm infants, in response to the preferential M pathway, which was not seen in the preterms. Overall, these findings suggest that the Magnocellular pathway development is affected in premature infants. Although our VEP results suggest that premature children overcome, at least partially, the visual developmental delay with time, source analyses reveal abnormal brain activation of the Magnocellular pathway at 12 months of age. PMID:25268226

Preferential Allele Expression Analysis Identifies Shared Germline and Somatic Driver Genes in Advanced Ovarian Cancer

PubMed Central

Halabi, Najeeb M.; Martinez, Alejandra; Al-Farsi, Halema; Mery, Eliane; Puydenus, Laurence; Pujol, Pascal; Khalak, Hanif G.; McLurcan, Cameron; Ferron, Gwenael; Querleu, Denis; Al-Azwani, Iman; Al-Dous, Eman; Mohamoud, Yasmin A.; Malek, Joel A.; Rafii, Arash

2016-01-01

Identifying genes where a variant allele is preferentially expressed in tumors could lead to a better understanding of cancer biology and optimization of targeted therapy. However, tumor sample heterogeneity complicates standard approaches for detecting preferential allele expression. We therefore developed a novel approach combining genome and transcriptome sequencing data from the same sample that corrects for sample heterogeneity and identifies significant preferentially expressed alleles. We applied this analysis to epithelial ovarian cancer samples consisting of matched primary ovary and peritoneum and lymph node metastasis. We find that preferentially expressed variant alleles include germline and somatic variants, are shared at a relatively high frequency between patients, and are in gene networks known to be involved in cancer processes. Analysis at a patient level identifies patient-specific preferentially expressed alleles in genes that are targets for known drugs. Analysis at a site level identifies patterns of site specific preferential allele expression with similar pathways being impacted in the primary and metastasis sites. We conclude that genes with preferentially expressed variant alleles can act as cancer drivers and that targeting those genes could lead to new therapeutic strategies. PMID:26735499

A density functional theory study on peptide bond cleavage at aspartic residues: direct vs cyclic intermediate hydrolysis.

PubMed

Sang-aroon, Wichien; Amornkitbamrung, Vittaya; Ruangpornvisuti, Vithaya

2013-12-01

In this work, peptide bond cleavages at carboxy- and amino-sides of the aspartic residue in a peptide model via direct (concerted and step-wise) and cyclic intermediate hydrolysis reaction pathways were explored computationally. The energetics, thermodynamic properties, rate constants, and equilibrium constants of all hydrolysis reactions, as well as their energy profiles were computed at the B3LYP/6-311++G(d,p) level of theory. The result indicated that peptide bond cleavage of the Asp residue occurred most preferentially via the cyclic intermediate hydrolysis pathway. In all reaction pathways, cleavage of the peptide bond at the amino-side occurred less preferentially than at the carboxy-side. The overall reaction rate constants of peptide bond cleavage of the Asp residue at the carboxy-side for the assisted system were, in increasing order: concerted < step-wise < cyclic intermediate.

Evidence of a sewer vapor transport pathway at the USEPA vapor intrusion research duplex

EPA Science Inventory

The role of sewer lines as preferential pathways for vapor intrusion is poorly understood. Although the importance of sewer lines for volatile organic compound (VOC) transport has been documented at a small number of sites with vapor intrusion, sewer lines are not routinely sampl...

Large-Scale 13C Flux Profiling Reveals Conservation of the Entner-Doudoroff Pathway as a Glycolytic Strategy among Marine Bacteria That Use Glucose

PubMed Central

Klingner, Arne; Bartsch, Annekathrin; Dogs, Marco; Wagner-Döbler, Irene; Jahn, Dieter; Simon, Meinhard; Brinkhoff, Thorsten; Becker, Judith

2015-01-01

Marine bacteria form one of the largest living surfaces on Earth, and their metabolic activity is of fundamental importance for global nutrient cycling. Here, we explored the largely unknown intracellular pathways in 25 microbes representing different classes of marine bacteria that use glucose: Alphaproteobacteria, Gammaproteobacteria, and Flavobacteriia of the Bacteriodetes phylum. We used 13C isotope experiments to infer metabolic fluxes through their carbon core pathways. Notably, 90% of all strains studied use the Entner-Doudoroff (ED) pathway for glucose catabolism, whereas only 10% rely on the Embden-Meyerhof-Parnas (EMP) pathway. This result differed dramatically from the terrestrial model strains studied, which preferentially used the EMP pathway yielding high levels of ATP. Strains using the ED pathway exhibited a more robust resistance against the oxidative stress typically found in this environment. An important feature contributing to the preferential use of the ED pathway in the oceans could therefore be enhanced supply of NADPH through this pathway. The marine bacteria studied did not specifically rely on a distinct anaplerotic route, but the carboxylation of phosphoenolpyruvate (PEP) or pyruvate for fueling of the tricarboxylic acid (TCA) cycle was evenly distributed. The marine isolates studied belong to clades that dominate the uptake of glucose, a major carbon source for bacteria in seawater. Therefore, the ED pathway may play a significant role in the cycling of mono- and polysaccharides by bacterial communities in marine ecosystems. PMID:25616803

The Bcl-2-Beclin 1 interaction in (-)-gossypol-induced autophagy versus apoptosis in prostate cancer cells.

PubMed

Lian, Jiqin; Karnak, David; Xu, Liang

2010-11-01

Bcl-2 is a key dual regulator of autophagy and apoptosis, but how the level of Bcl-2 influences the cellular decision between autophagy and apoptosis is unclear. The natural BH3-mimetic (-)-gossypol preferentially induces autophagy in androgen-independent (AI) prostate cancer cells that have high levels of Bcl-2 and are resistant to apoptosis, whereas apoptosis is preferentially induced in androgen-dependent or -independent cells with low Bcl-2. (-)-Gossypol induces autophagy via blocking Bcl-2-Beclin 1 interaction at the endoplasmic reticulum (ER), together with downregulating Bcl-2, upregulating Beclin 1 and activating the autophagic pathway. Furthermore, (-)-gossypol-induced autophagy is Beclin 1- and Atg5-dependent. These results provide new insights into the mode of cell death induced by Bcl-2 inhibitors, which could facilitate the rational design of clinical trials by selecting patients who are most likely to benefit from the Bcl-2-targeted molecular therapy.

ICOS and Bcl6-dependent pathways maintain a CD4 T cell population with memory-like properties during tuberculosis

PubMed Central

Moguche, Albanus O.; Shafiani, Shahin; Clemons, Corey; Larson, Ryan P.; Dinh, Crystal; Higdon, Lauren E.; Cambier, C.J.; Sissons, James R.; Gallegos, Alena M.; Fink, Pamela J.

2015-01-01

Immune control of persistent infection with Mycobacterium tuberculosis (Mtb) requires a sustained pathogen-specific CD4 T cell response; however, the molecular pathways governing the generation and maintenance of Mtb protective CD4 T cells are poorly understood. Using MHCII tetramers, we show that Mtb-specific CD4 T cells are subject to ongoing antigenic stimulation. Despite this chronic stimulation, a subset of PD-1+ cells is maintained within the lung parenchyma during tuberculosis (TB). When transferred into uninfected animals, these cells persist, mount a robust recall response, and provide superior protection to Mtb rechallenge when compared to terminally differentiated Th1 cells that reside preferentially in the lung-associated vasculature. The PD-1+ cells share features with memory CD4 T cells in that their generation and maintenance requires intrinsic Bcl6 and intrinsic ICOS expression. Thus, the molecular pathways required to maintain Mtb-specific CD4 T cells during ongoing infection are similar to those that maintain memory CD4 T cells in scenarios of antigen deprivation. These results suggest that vaccination strategies targeting the ICOS and Bcl6 pathways in CD4 T cells may provide new avenues to prevent TB. PMID:25918344

Preferential flow, connectivity and the principle of "minimum time to equilibrium": a new perspective on environmental water flow

NASA Astrophysics Data System (ADS)

Zehe, E.; Blume, T.; Bloeschl, G.

2008-12-01

Preferential/rapid flow and transport is known as one key process in soil hydrology for more than 20 years. It seems to be rather the rule, than the exception. It occurs in soils, in surface rills and river networks. If connective preferential are present at any scale, they crucially control water flow and solute transport. Why? Is there an underlying principle? If energy is conserved a system follows Fermat's principle of minimum action i.e. it follows the trajectory that minimise the integral of the total energy/ La Grangian over time. Hydrological systems are, however, non-conservative as surface and subsurface water flows dissipate energy. From thermodynamics it is well known that natural processes minimize the free energy of the system. For hydrological systems we suggest, therefore, that flow in a catchment arranges in such a way that time to a minimum of free energy becomes minimal for a given rainfall input (disturbance) and under given constraints. Free energy in a soil is determined by potential energy and capillary energy. The pore size distribution of the soil, soil structures, depth to groundwater and most important vegetation make up the constraints. The pore size distribution determines whether potential energy or capillarity dominates the free energy of the soil system. The first term is minimal when the pore space is completely de-saturated the latter becomes minimal at soil saturation. Hence, the soil determines a) the amount of excess (gravity) water that has to be exported from the soil to reach a minimum state of free energy and b) whether redistribution or groundwater recharge is more efficient to reach that equilibrium. On the other hand, the pore size distribution of the soil and the connectivity of preferential pathways (root channels, worm holes and cracks) determine flow velocities and the redistribution of water within the pore space. As water flow and ground water recharge are fast in sandy soils and capillary energy is of minor importance, connective preferential pathways do not mean any advantage for an efficient transition to an equilibrium in these systems. In fine grained soils Darcy velocities and therefore redistribution of water is 2-4 orders of magnitude slower. As capillary energy dominates in these soils an effective redistribution of water within the pore space is crucial for a fast transition of system to an equilibrium state. Connective preferential pathways ore even cracks allow a faster redistribution of water and seem therefore necessary for a fast transition into a state of minimum free energy. The suggested principle "of minimum time to equilibrium" may explain the "advantage" of preferential flow as a much more efficient dissipation of energy in fine grained soils and therefore why connective preferential pathways control environmental flow. From a fundamental, long term perspective the principle may help us to understand whether and why soil structures and even cracks evolve in different landscapes and climates and b) to link soil hydrology and (landscape) ecology. Along the lines the proposed study will present model results to test the stated hypothesis.

Pilocytic Astrocytoma of the Optic Pathway: A Tumour Deriving from Radial Glia Cells with a Specific Gene Signature

ERIC Educational Resources Information Center

Tchoghandjian, Aurelie; Fernandez, Carla; Colin, Carole; El Ayachi, Ikbale; Voutsinos-Porche, Brigitte; Fina, Frederic; Scavarda, Didier; Piercecchi-Marti, Marie-Dominique; Intagliata, Dominique; Ouafik, L'Houcine; Fraslon-Vanhulle, Caroline; Figarella-Branger, Dominique

2009-01-01

Pilocytic astrocytomas are WHO grade I gliomas that occur predominantly in childhood. They share features of both astroglial and oligodendroglial lineages. These tumours affect preferentially the cerebellum (benign clinical course) and the optic pathway, especially the hypothalamo-chiasmatic region (poor prognosis). Understanding the molecular…

ICOS and Bcl6-dependent pathways maintain a CD4 T cell population with memory-like properties during tuberculosis.

PubMed

Moguche, Albanus O; Shafiani, Shahin; Clemons, Corey; Larson, Ryan P; Dinh, Crystal; Higdon, Lauren E; Cambier, C J; Sissons, James R; Gallegos, Alena M; Fink, Pamela J; Urdahl, Kevin B

2015-05-04

Immune control of persistent infection with Mycobacterium tuberculosis (Mtb) requires a sustained pathogen-specific CD4 T cell response; however, the molecular pathways governing the generation and maintenance of Mtb protective CD4 T cells are poorly understood. Using MHCII tetramers, we show that Mtb-specific CD4 T cells are subject to ongoing antigenic stimulation. Despite this chronic stimulation, a subset of PD-1(+) cells is maintained within the lung parenchyma during tuberculosis (TB). When transferred into uninfected animals, these cells persist, mount a robust recall response, and provide superior protection to Mtb rechallenge when compared to terminally differentiated Th1 cells that reside preferentially in the lung-associated vasculature. The PD-1(+) cells share features with memory CD4 T cells in that their generation and maintenance requires intrinsic Bcl6 and intrinsic ICOS expression. Thus, the molecular pathways required to maintain Mtb-specific CD4 T cells during ongoing infection are similar to those that maintain memory CD4 T cells in scenarios of antigen deprivation. These results suggest that vaccination strategies targeting the ICOS and Bcl6 pathways in CD4 T cells may provide new avenues to prevent TB. © 2015 Moguche et al.

A feedback mechanism controlling SCRAMBLED receptor accumulation and cell-type pattern in Arabidopsis.

PubMed

Kwak, Su-Hwan; Schiefelbein, John

2008-12-23

Cellular pattern formation in the root epidermis of Arabidopsis occurs in a position-dependent manner, generating root-hair (H) cells contacting two underlying cortical cells and nonhair (N) cells contacting one cortical cell. SCRAMBLED (SCM), a leucine-rich repeat receptor-like kinase (LRR-RLK), mediates this process through its effect on a downstream transcription factor regulatory network. After perception of a positional cue, the SCM signaling pathway is proposed to preferentially repress WEREWOLF (WER) transcription factor expression in H cells and thereby bias the outcome of mutual lateral inhibition acting between H and N cells. However, the molecular mechanism responsible for this preferential SCM signaling is unknown. Here, we analyze the distribution of the SCM receptor and the biological effect of altering its accumulation pattern. We find that SCM expression and accumulation in the epidermal cell layer is necessary and sufficient to direct the cell-type pattern. Further, SCM preferentially accumulates in H cells, and this accumulation pattern is dependent on the downstream transcription factors. Thus, SCM participates in an autoregulatory feedback loop, enabling cells engaged in SCM signaling to maintain high levels of SCM receptor, which provides a simple mechanism for reinforcing a bias in receptor-mediated signaling to ensure robust pattern formation.

The Development of Novel Small Molecule Inhibitors of the Phosphoinositide-3-Kinase Pathway Through High-Throughput Cell-Based Screens

DTIC Science & Technology

2005-02-01

Akt in the P13K pathway. Given the emerging data for a positive feedback loop induced by mTOR inhibition, a bispecific 5 inhibitor might be attractive...cells relatively sensitive to rapamycin are also sensitive to thioridazine. PTEN null cells are known to be preferentially sensitized to mTOR ...a potent mTOR inhibitor, a downstream protein kinase in the Akt pathway. Rapamycin showed strong growth inhibitory effect in PTEN-null cells but 786

Motile hepatocellular carcinoma cells preferentially secret sugar metabolism regulatory proteins via exosomes.

PubMed

Zhang, Jing; Lu, Shaohua; Zhou, Ye; Meng, Kun; Chen, Zhipeng; Cui, Yizhi; Shi, Yunfeng; Wang, Tong; He, Qing-Yu

2017-07-01

Exosomes are deliverers of critically functional proteins, capable of transforming target cells in numerous cancers, including hepatocellular carcinoma (HCC). We hypothesize that the motility of HCC cells can be featured by comparative proteome of exosomes. Hence, we performed the super-SILAC-based MS analysis on the exosomes secreted by three human HCC cell lines, including the non-motile Hep3B cell, and the motile 97H and LM3 cells. More than 1400 exosomal proteins were confidently quantified in each MS analysis with highly biological reproducibility. We justified that 469 and 443 exosomal proteins represented differentially expressed proteins (DEPs) in the 97H/Hep3B and LM3/Hep3B comparisons, respectively. These DEPs focused on sugar metabolism-centric canonical pathways per ingenuity pathway analysis, which was consistent with the gene ontology analysis on biological process enrichment. These pathways included glycolysis I, gluconeogenesis I and pentose phosphate pathways; and the DEPs enriched in these pathways could form a tightly connected network. By analyzing the relative abundance of proteins and translating mRNAs, we found significantly positive correlation between exosomes and cells. The involved exosomal proteins were again focusing on sugar metabolism. In conclusion, motile HCC cells tend to preferentially export more sugar metabolism-associated proteins via exosomes that differentiate them from non-motile HCC cells. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Transcriptomic basis of functional difference and coordination between seeds and the silique wall of Brassica napus during the seed-filling stage.

PubMed

Liu, Han; Yang, Qingyong; Fan, Chuchuan; Zhao, Xiaoqin; Wang, Xuemin; Zhou, Yongming

2015-04-01

The silique of oilseed rape (Brassica napus) is a composite organ including seeds and the silique wall (SW) that possesses distinctly physiological, biochemical and functional differentiations. Yet, the molecular events controlling such differences between the SW and seeds, as well as their coordination during silique development at transcriptional level are largely unknown. Here, we identified large sets of differentially expressed genes in the SW and seeds of siliques at 21-22 days after flowering with a Brassica 95K EST microarray. At this particular stage, there were 3278 SW preferentially expressed genes and 2425 seed preferentially expressed genes. Using the MapMan visualization software, genes differentially regulated in various metabolic pathways and sub-pathways between the SW and seeds were revealed. Photosynthesis and transport-related genes were more actively transcripted in the SW, while those involved in lipid metabolism were more active in seeds during the seed filling stage. On the other hand, genes involved in secondary metabolisms were selectively regulated in the SW and seeds. Large numbers of transcription factors were identified to be differentially expressed between the SW and seeds, suggesting a complex pattern of transcriptional control in these two organs. Furthermore, most genes discussed in categories or pathways showed a similar expression pattern through 21 DAF to 42 DAF. Our results thus provide insights into the coordination of seeds and the SW in the developing silique at the transcriptional levels, which will facilitate the functional studies of important genes for improving B. napus seed productivity and quality. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

36 CFR 51.76 - May the Director include in a concession contract or otherwise grant a concessioner a...

Code of Federal Regulations, 2010 CFR

2010-07-01

... concession contract or otherwise grant a concessioner a preferential right to provide new or additional... include in a concession contract or otherwise grant a concessioner a preferential right to provide new or... grant a concessioner a preferential right to provide new or additional visitor services under the terms...

Microcirculation of the pancreas. A quantitative study of physiology and changes in pancreatitis.

PubMed

Klar, E; Endrich, B; Messmer, K

1990-02-01

A rabbit model was designed to study the microcirculation of the pancreas with special reference to changes occurring during acute pancreatitis. Intravital microscopy was used in conjunction with video techniques allowing for continuous observation and off-line evaluation of microvessel diameters and blood cell velocities. Based on the microvessel geometry a functional microvascular unit could be defined at the level of the pancreatic lobule consisting of intralobular arteries and veins and an arcade-like preferential pathway framing the capillary network. Experimental acute pancreatitis resulted in immediate leakage of the macromolecular plasma marker (FITC-Dextran 70) from the microvasculature suggesting increased permeability. In contrast to control conditions, pancreatic capillaries were excluded from the circulation during acute pancreatitis starting 30 min after induction with only single capillaries remaining perfused after 3 hours. At the same time, there was constant blood flow through the preferential pathways representing shunt perfusion.

Defining the Pathophysiological Role of Tau in Experimental TBI

DTIC Science & Technology

2016-10-01

in AD. This pathway is a major source for excitatory innervation of hippocampus , a structure vital for memory formation. Damage to the EC or...hippocampal input pathway that is both preferentially vulnerable in early-stage AD and critically important for long-term memory . The model confines...structure and function of the hippocampus after single or repetitive mild TBI, and whether mild TBI exacerbates ongoing tauopathy to promote a chronic

Estimation of Unsaturated Zone Traveltimes for Rainier Mesa and Shoshone Mountain, Nevada Test Site, Nevada, Using a Source-Responsive Preferential-Flow Model

USGS Publications Warehouse

Ebel, Brian A.; Nimmo, John R.

2009-01-01

Traveltimes for contaminant transport by water from a point in the unsaturated zone to the saturated zone are a concern at Rainier Mesa and Shoshone Mountain in the Nevada Test Site, Nevada. Where nuclear tests were conducted in the unsaturated zone, contaminants must traverse hundreds of meters of variably saturated rock before they enter the saturated zone in the carbonate rock, where the regional groundwater system has the potential to carry them substantial distances to a location of concern. The unsaturated-zone portion of the contaminant transport path may cause a significant delay, in addition to the time required to travel within the saturated zone, and thus may be important in the overall evaluation of the potential hazard from contamination. Downward contaminant transport through the unsaturated zone occurs through various processes and pathways; this can lead to a broad distribution of contaminant traveltimes, including exceedingly slow and unexpectedly fast extremes. Though the bulk of mobile contaminant arrives between the time-scale end members, the fastest contaminant transport speed, in other words the speed determined by the combination of possible processes and pathways that would bring a measureable quantity of contaminant to the aquifer in the shortest time, carries particular regulatory significance because of its relevance in formulating the most conservative hazard-prevention scenarios. Unsaturated-zone flow is usually modeled as a diffusive process responding to gravity and pressure gradients as mediated by the unsaturated hydraulic properties of the materials traversed. The mathematical formulation of the diffuse-flow concept is known as Richards' equation, which when coupled to a solute transport equation, such as the advection-dispersion equation, provides a framework to simulate contaminant migration in the unsaturated zone. In recent decades awareness has increased that much fluid flow and contaminant transport within the unsaturated zone takes place as preferential flow, faster than would be predicted by the coupled Richards' and advection-dispersion equations with hydraulic properties estimated by traditional means. At present the hydrologic community has not achieved consensus as to whether a modification of Richards' equation, or a fundamentally different formulation, would best quantify preferential flow. Where the fastest contaminant transport speed is what needs to be estimated, there is the possibility of simplification of the evaluation process. One way of doing so is by a two-step process in which the first step is to evaluate whether significant preferential flow and solute transport is possible for the media and conditions of concern. The second step is to carry out (a) a basic Richards' and advection-dispersion equation analysis if it is concluded that preferential flow is not possible or (b) an analysis that considers only the fastest possible preferential-flow processes, if preferential flow is possible. For the preferential-flow situation, a recently published model describable as a Source-Responsive Preferential-Flow (SRPF) model is an easily applied option. This report documents the application of this two-step process to flow through the thick unsaturated zones of Rainier Mesa and Shoshone Mountain in the Nevada Test Site. Application of the SRPF model involves distinguishing between continuous and intermittent water supply to preferential flow paths. At Rainier Mesa and Shoshone Mountain this issue is complicated by the fact that contaminant travel begins at a location deep in the subsurface, where there may be perched water that may or may not act like a continuous supply, depending on such features as the connectedness of fractures and the nature of impeding layers. We have treated this situation by hypothesizing both continuous and intermittent scenarios for contaminant transport to the carbonate aquifer and reporting estimation of the fastest speed for both of th

Estimation of unsaturated zone traveltimes for Rainier Mesa and Shoshone Mountain, Nevada Test Site, Nevada, using a source-responsive preferential-flow model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brian A. Ebel; John R. Nimmo

2009-09-11

Traveltimes for contaminant transport by water from a point in the unsaturated zone to the saturated zone are a concern at Rainier Mesa and Shoshone Mountain in the Nevada Test Site, Nevada. Where nuclear tests were conducted in the unsaturated zone, contaminants must traverse hundreds of meters of variably saturated rock before they enter the saturated zone in the carbonate rock, where the regional groundwater system has the potential to carry them substantial distances to a location of concern. The unsaturated-zone portion of the contaminant transport path may cause a significant delay, in addition to the time required to travelmore » within the saturated zone, and thus may be important in the overall evaluation of the potential hazard from contamination. Downward contaminant transport through the unsaturated zone occurs through various processes and pathways; this can lead to a broad distribution of contaminant traveltimes, including exceedingly slow and unexpectedly fast extremes. Though the bulk of mobile contaminant arrives between the time-scale end members, the fastest contaminant transport speed, in other words the speed determined by the combination of possible processes and pathways that would bring a measureable quantity of contaminant to the aquifer in the shortest time, carries particular regulatory significance because of its relevance in formulating the most conservative hazard-prevention scenarios. Unsaturated-zone flow is usually modeled as a diffusive process responding to gravity and pressure gradients as mediated by the unsaturated hydraulic properties of the materials traversed. The mathematical formulation of the diffuse-flow concept is known as Richards' equation, which when coupled to a solute transport equation, such as the advection-dispersion equation, provides a framework to simulate contaminant migration in the unsaturated zone. In recent decades awareness has increased that much fluid flow and contaminant transport within the unsaturated zone takes place as preferential flow, faster than would be predicted by the coupled Richards' and advection-dispersion equations with hydraulic properties estimated by traditional means. At present the hydrologic community has not achieved consensus as to whether a modification of Richards' equation, or a fundamentally different formulation, would best quantify preferential flow. Where the fastest contaminant transport speed is what needs to be estimated, there is the possibility of simplification of the evaluation process. One way of doing so is by a two-step process in which the first step is to evaluate whether significant preferential flow and solute transport is possible for the media and conditions of concern. The second step is to carry out (a) a basic Richards' and advection-dispersion equation analysis if it is concluded that preferential flow is not possible or (b) an analysis that considers only the fastest possible preferential-flow processes, if preferential flow is possible. For the preferential-flow situation, a recently published model describable as a Source-Responsive Preferential-Flow (SRPF) model is an easily applied option. This report documents the application of this two-step process to flow through the thick unsaturated zones of Rainier Mesa and Shoshone Mountain in the Nevada Test Site. Application of the SRPF model involves distinguishing between continuous and intermittent water supply to preferential flow paths. At Rainier Mesa and Shoshone Mountain this issue is complicated by the fact that contaminant travel begins at a location deep in the subsurface, where there may be perched water that may or may not act like a continuous supply, depending on such features as the connectedness of fractures and the nature of impeding layers. We have treated this situation by hypothesizing both continuous and intermittent scenarios for contaminant transport to the carbonate aquifer and reporting estimation of the fastest speed for both of these end members.« less

Endocytic Crosstalk: Cavins, Caveolins, and Caveolae Regulate Clathrin-Independent Endocytosis

PubMed Central

Chaudhary, Natasha; Gomez, Guillermo A.; Howes, Mark T.; Lo, Harriet P.; McMahon, Kerrie-Ann; Rae, James A.; Schieber, Nicole L.; Hill, Michelle M.; Gaus, Katharina; Yap, Alpha S.; Parton, Robert G.

2014-01-01

Several studies have suggested crosstalk between different clathrin-independent endocytic pathways. However, the molecular mechanisms and functional relevance of these interactions are unclear. Caveolins and cavins are crucial components of caveolae, specialized microdomains that also constitute an endocytic route. Here we show that specific caveolar proteins are independently acting negative regulators of clathrin-independent endocytosis. Cavin-1 and Cavin-3, but not Cavin-2 or Cavin-4, are potent inhibitors of the clathrin-independent carriers/GPI-AP enriched early endosomal compartment (CLIC/GEEC) endocytic pathway, in a process independent of caveola formation. Caveolin-1 (CAV1) and CAV3 also inhibit the CLIC/GEEC pathway upon over-expression. Expression of caveolar protein leads to reduction in formation of early CLIC/GEEC carriers, as detected by quantitative electron microscopy analysis. Furthermore, the CLIC/GEEC pathway is upregulated in cells lacking CAV1/Cavin-1 or with reduced expression of Cavin-1 and Cavin-3. Inhibition by caveolins can be mimicked by the isolated caveolin scaffolding domain and is associated with perturbed diffusion of lipid microdomain components, as revealed by fluorescence recovery after photobleaching (FRAP) studies. In the absence of cavins (and caveolae) CAV1 is itself endocytosed preferentially through the CLIC/GEEC pathway, but the pathway loses polarization and sorting attributes with consequences for membrane dynamics and endocytic polarization in migrating cells and adult muscle tissue. We also found that noncaveolar Cavin-1 can act as a modulator for the activity of the key regulator of the CLIC/GEEC pathway, Cdc42. This work provides new insights into the regulation of noncaveolar clathrin-independent endocytosis by specific caveolar proteins, illustrating multiple levels of crosstalk between these pathways. We show for the first time a role for specific cavins in regulating the CLIC/GEEC pathway, provide a new tool to study this pathway, identify caveola-independent functions of the cavins and propose a novel mechanism for inhibition of the CLIC/GEEC pathway by caveolin. PMID:24714042

Temporal evolution of water repellency and preferential flow in the post-fire

NASA Astrophysics Data System (ADS)

Alanís, Nancy; Jordán, Antonio; Zavala, Lorena M.

2015-04-01

Forest fires usually intensify erosive process due to the reduction of vegetation cover and degradation of aggregation in the topsoil. Another common effect of wildifres is the development of soil water repellency, which in turn favors the formation of runoff, inhibiting or delaying infiltration. Under these conditions, infiltration occurs only when ponded water or runoff flow finds macropores and cracks in the soil surface, producing preferential flow pathways. When water infiltrates through these paths, a significant portion of the soil remains dry, limiting the supply of nutrients to the roots, favoring the rapid leaching of nutrients and agrochemicals, and other impacts on flora and hydrological processes at hillslope- or basin-scale. The existence of irregular wetting fronts has been observed frequently in burned or unburned water repellent soils. Although some authors have suggested that preferential flow paths may be more or less permanent in the case of unburned soils, the temporal evolution of preferential flow has been rarely studied in burned soils during the post-fire, after water repellency decreases or disappears. This research focuses on the temporal evolution of water repellency and preferential flows in an area affected by fire.

Evaluation of diffuse and preferential flow pathways of infiltrated precipitation and irrigation using oxygen and hydrogen isotopes

NASA Astrophysics Data System (ADS)

Ma, Bin; Liang, Xing; Liu, Shaohua; Jin, Menggui; Nimmo, John R.; Li, Jing

2017-05-01

Subsurface-water flow pathways in three different land-use areas (non-irrigated grassland, poplar forest, and irrigated arable land) in the central North China Plain were investigated using oxygen (18O) and hydrogen (2H) isotopes in samples of precipitation, soils, and groundwater. Soil water in the top 10 cm was significantly affected by both evaporation and infiltration. Water at 10-40 cm depth in the grassland and arable land, and 10-60 cm in poplar forest, showed a relatively short residence time, as a substantial proportion of antecedent soil water was mixed with a 92-mm storm infiltration event, whereas below those depths (down to 150 cm), depleted δ18O spikes suggested that some storm water bypassed the shallow soil layers. Significant differences, in soil-water content and δ18O values, within a small area, suggested that the proportion of immobile soil water and water flowing in subsurface pathways varies depending on local vegetation cover, soil characteristics and irrigation applications. Soil-water δ18O values revealed that preferential flow and diffuse flow coexist. Preferential flow was active within the root zone, independent of antecedent soil-water content, in both poplar forest and arable land, whereas diffuse flow was observed in grassland. The depleted δ18O spikes at 20-50 cm depth in the arable land suggested the infiltration of irrigation water during the dry season. Temporal isotopic variations in precipitation were subdued in the shallow groundwater, suggesting more complete mixing of different input waters in the unsaturated zone before reaching the shallow groundwater.

Phosphorus exchangeability and leaching losses from two grassland soils.

PubMed

Sinaj, S; Stamm, C; Toor, G S; Condron, L M; Hendry, T; Di, H J; Cameron, K C; Frossard, E

2002-01-01

Although phosphate phosphorus (P) is strongly sorbed in many soils, it may be quickly transported through the soil by preferential flow. Under flood irrigation, preferential flow is especially pronounced and associated solute losses may be important. Phosphorus losses induced by flood irrigation were investigated in a lysimeter study. Detailed soil chemical analyses revealed that P was very mobile in the topsoil, but the higher P-fixing capacity of the subsoil appeared to restrict P mobility. Application of a dye tracer enabled preferential flow pathways to be identified. Soil sampling according to dye staining patterns revealed that exchangeable P was significantly greater in preferential flow areas as compared with the unstained soil matrix. This could be partly attributed to the accumulation of organic carbon and P, together with enhanced leaching of Al- and Fe-oxides in the preferential flow areas, which resulted in reduced P sorption. The irrigation water caused a rapid hydrologic response by displacement of resident water from the subsoil. Despite the occurrence of preferential flow, most of the outflowing water was resident soil water and very low in P. In these soils the occurrence of preferential flow per se is not sufficient to cause large P losses even if the topsoil is rich in P. It appears that the P was retained in lower parts of the soil profile characterized by a very high P-fixing capacity. This study demonstrates the risks associated with assessing potential P losses on the basis of P mobility in the topsoil alone.

Not all water becomes wine: Sulfur inputs as an opportune tracer of hydrochemical losses from vineyards

USGS Publications Warehouse

Hinckley, Eve-Lyn S.; Kendall, Carol; Loague, Keith

2009-01-01

California's widespread and economically important vineyards offer substantial opportunities to understand the interface between hydrology and biogeochemistry in agricultural soils. The common use of native sulfur (S) as a fumigant or soil additive provides a novel way to isotopically differentiate among sulfate (SO42−) pools, allowing the estimation of water and SO42− budgets. The objectives of this study were (1) to characterize the near‐surface hydrological flow paths in a vineyard during irrigation and storm events and (2) to determine how those flow paths affect the fate and transport of SO42− across seasons. Integrating hydrological theory with measurements of SO42−concentration and sulfate‐S isotopic ratios (expressed as [SO42−] and δ34S, respectively) in inputs, soil water, and leachate provided a means of determining flow paths. Low [SO42−] and δ34S in leachate during 4‐h irrigation events reflect minimal engagement of the soil matrix, indicating that preferential flow was the dominant path for water in the near surface. In contrast, high [SO42−] and δ34S values during 8‐h irrigation and storm events reflect near‐complete engagement of the soil matrix, indicating that lateral flow was the dominant pathway. Because hydrologic response and SO42− mobility are tightly coupled in these soils, the magnitude of water fluxes through the near surface controls S cycling both on and off site. These results indicate that preferential flow is an important loss pathway to consider in managing both water resources and water quality (reactive elements) in vineyard land use systems.

A Synthetic Interaction Screen Identifies Factors Selectively Required for Proliferation and TERT Transcription in p53-Deficient Human Cancer Cells

PubMed Central

Park, Sung Mi; Zhu, Lihua J.; Debily, Marie-anne; Kittler, Ellen L. W.; Zapp, Maria L.; Lapointe, David; Gobeil, Stephane; Virbasius, Ching-Man; Green, Michael R.

2012-01-01

Numerous genetic and epigenetic alterations render cancer cells selectively dependent on specific genes and regulatory pathways, and represent potential vulnerabilities that can be therapeutically exploited. Here we describe an RNA interference (RNAi)–based synthetic interaction screen to identify genes preferentially required for proliferation of p53-deficient (p53−) human cancer cells. We find that compared to p53-competent (p53+) human cancer cell lines, diverse p53− human cancer cell lines are preferentially sensitive to loss of the transcription factor ETV1 and the DNA damage kinase ATR. In p53− cells, RNAi–mediated knockdown of ETV1 or ATR results in decreased expression of the telomerase catalytic subunit TERT leading to growth arrest, which can be reversed by ectopic TERT expression. Chromatin immunoprecipitation analysis reveals that ETV1 binds to a region downstream of the TERT transcriptional start-site in p53− but not p53+ cells. We find that the role of ATR is to phosphorylate and thereby stabilize ETV1. Our collective results identify a regulatory pathway involving ETV1, ATR, and TERT that is preferentially important for proliferation of diverse p53− cancer cells. PMID:23284306

Evaluation of afferent pain pathways in adrenomyeloneuropathic patients.

PubMed

Yagüe, Sara; Veciana, Misericordia; Casasnovas, Carlos; Ruiz, Montserrat; Pedro, Jordi; Valls-Solé, Josep; Pujol, Aurora

2018-03-01

Patients with adrenomyeloneuropathy may have dysfunctions of visual, auditory, motor and somatosensory pathways. We thought on examining the nociceptive pathways by means of laser evoked potentials (LEPs), to obtain additional information on the pathophysiology of this condition. In 13 adrenomyeloneuropathic patients we examined LEPs to leg, arm and face stimulation. Normative data were obtained from 10 healthy subjects examined in the same experimental conditions. We also examined brainstem auditory evoked potentials (BAEPs), pattern reversal full-field visual evoked potentials (VEPs), motor evoked potentials (MEPs) and somatosensory evoked potentials (SEPs). Upper and lower limb MEPs and SEPs, as well as BAEPs, were abnormal in all patients, while VEPs were abnormal in 3 of them (23.1%). LEPs revealed abnormalities to stimulation of the face in 4 patients (30.7%), the forearm in 4 patients (30.7%) and the leg in 10 patients (76.9%). The pathologic process of adrenomyeloneuropathy is characterized by a preferential involvement of auditory, motor and somatosensory tracts and less severely of the visual and nociceptive pathways. This non-inflammatory distal axonopathy preferably damages large myelinated spinal tracts but there is also partial involvement of small myelinated fibres. LEPs studies can provide relevant information about afferent pain pathways involvement in adrenomyeloneuropathic patients. Copyright © 2017 International Federation of Clinical Neurophysiology. Published by Elsevier B.V. All rights reserved.

Bioclogging in Porous Media: Preferential Flow Paths and Anomalous Transport

NASA Astrophysics Data System (ADS)

Holzner, M.; Carrel, M.; Morales, V.; Derlon, N.; Beltran, M. A.; Morgenroth, E.; Kaufmann, R.

2016-12-01

Biofilms are sessile communities of microorganisms held together by an extracellular polymeric substance that enables surface colonization. In porous media (e.g. soils, trickling filters etc.) biofilm growth has been shown to affect the hydrodynamics in a complex fashion at the pore-scale by clogging individual pores and enhancing preferential flow pathways and anomalous transport. These phenomena are a direct consequence of microbial growth and metabolism, mass transfer processes and complex flow velocity fields possibly exhibiting pronounced three-dimensional features. Despite considerable past work, however, it is not fully understood how bioclogging interacts with flow and mass transport processes in porous media. In this work we use imaging techniques to determine the flow velocities and the distribution of biofilm in a porous medium. Three-dimensional millimodels are packed with a transparent porous medium and a glucose solution to match the optical refractive index. The models are inoculated with planktonic wildtype bacteria and biofilm cultivated for 60 h under a constant flow and nutrient conditions. The pore flow velocities in the increasingly bioclogged medium are measured using 3D particle tracking velocimetry (3D-PTV). The three-dimensional spatial distribution of the biofilm within the pore space is assessed by imaging the model with X-Ray microtomography. We find that biofilm growth increases the complexity of the pore space, leading to the formation of preferential flow pathways and "dead" pore zones. The probability of persistent high and low velocity regions (within preferential paths resp. stagnant flow regions) thus increases upon biofilm growth, leading to an enhancement of anomalous transport. The structural data seems to indicate that the largest pores are not getting clogged and carry the preferential flow, whereas intricated structures develop in the smallest pores, where the flow becomes almost stagnant. These findings may be relevant for applications such as bioremediation of contaminated aquifers, groundwater injection wells for geothermal or drinking water purposes, tertiary oil recovery.

Self-potential monitoring of a thermal pulse advecting through a preferential flow path

NASA Astrophysics Data System (ADS)

Ikard, S. J.; Revil, A.

2014-11-01

There is a need to develop new non-intrusive geophysical methods to detect preferential flow paths in heterogeneous porous media. A laboratory experiment is performed to non-invasively localize a preferential flow pathway in a sandbox using a heat pulse monitored by time-lapse self-potential measurements. Our goal is to investigate the amplitude of the intrinsic thermoelectric self-potential anomalies and the ability of this method to track preferential flow paths. A negative self-potential anomaly (-10 to -15 mV with respect to the background signals) is observed at the surface of the tank after hot water is injected in the upstream reservoir during steady state flow between the upstream and downstream reservoirs of the sandbox. Repeating the same experiment with the same volume of water injected upstream, but at the same temperature as the background pore water, produces a negligible self-potential anomaly. The negative self-potential anomaly is possibly associated with an intrinsic thermoelectric effect, with the temperature dependence of the streaming potential coupling coefficient, or with an apparent thermoelectric effect associated with the temperature dependence of the electrodes themselves. We model the experiment in 3D using a finite element code. Our results show that time-lapse self-potential signals can be used to track the position of traveling heat flow pulses in saturated porous materials, and therefore to find preferential flow pathways, especially in a very permeable environment and in real time. The numerical model and the data allows quantifying the intrinsic thermoelectric coupling coefficient, which is on the order of -0.3 to -1.8 mV per degree Celsius. The temperature dependence of the streaming potential during the experiment is negligible with respect to the intrinsic thermoelectric coupling. However, the temperature dependence of the potential of the electrodes needs to be accounted for and is far from being negligible if the electrodes experience temperature changes.

Rapid debromination of polybrominated diphenyl ethers (PBDEs) by zero valent metal and bimetals: Mechanisms and pathways assisted by density function theory calculation.

PubMed

Wang, Rui; Tang, Ting; Lu, Guining; Huang, Kaibo; Yin, Hua; Lin, Zhang; Wu, Fengchang; Dang, Zhi

2018-05-17

Polybrominated diphenyl ethers (PBDEs) undergo debromination when they were exposed in zerovalent metal or bimetallic systems. Yet their debromination pathways and mechanisms in these systems were not well understood. Here we reported the debromination pathways of three BDE congeners (BDE-21, 25 and 29) by nano-zerovalent iron (n-ZVI). All these BDE congeners have three bromine substituents that were located in ortho-, meta- and para-positions. Results demonstrated that BDE-21, 25 and 29 preferentially debrominate meta-, ortho- and para-bromines, respectively, suggesting that bromine substituent at each position (i.e. ortho-, meta- or para-) of PBDEs can be preferentially removed. Singly occupied molecular orbitals of BDE anions are well correlated with their actual debromination pathways, which successfully explain why these BDE congeners exhibit certain debromination pathways in n-ZVI system. In addition, microscale zerovalent zinc (m-ZVZ), iron-based bimetals (Fe/Ag and Fe/Pd) were also used to debrominate PBDEs, with BDE-21 as target pollutant. We found that the debromination pathways of BDE-21 in m-ZVZ and Fe/Ag systems are the same to those in n-ZVI system, but were partially different from those in Fe/Pd systems. The debromination of BDE-21 in Pd-H 2 system as well as the solvent kinetic isotope effect in single metal and bimetallic systems suggests that H atom transfer is the dominant mechanism in Fe/Pd system, while e-transfer is still the dominant mechanism in Fe/Ag system. Copyright © 2018 Elsevier Ltd. All rights reserved.

A semi-synthetic natural product blocks collagen induced arthritis by preferentially suppressing the production of IL-6.

PubMed

Kulkarni-Almeida, Asha; Shah, Meet; Jadhav, Mahesh; Hegde, Bindu; Trivedi, Jacqueline; Mishra, Prabhu D; Mahajan, Girish B; Dadarkar, Shruta; Gupte, Ravindra; Dagia, Nilesh

2016-04-01

Rheumatoid arthritis (RA), an autoimmune-inflammatory disease is characterized by dysregulation of signal transduction pathways, increased production of pro-inflammatory cytokines, enhanced leukocyte infiltration into synovial microvascular endothelium, extensive formation of hyper proliferative pannus, degradation of cartilage and bone erosion. Several compounds that abrogate cytokine production demonstrate a therapeutic effect in experimental models of arthritis. In this study, we report that a novel semi-synthetic natural product (Compound A) being a preferential IL-6 inhibitor, is efficacious in a murine model of arthritis. In vitro evaluations of pro-inflammatory cytokine production reveal that Compound A preferentially inhibits induced production of IL-6 and not TNF-α from THP-1 cells and isolated human monocytes. Furthermore, Compound A robustly inhibits the spontaneous production of IL-6 from pathologically relevant synovial tissue cells isolated from patients with active RA. In a physiologically relevant assay, Compound A selectively inhibits the activated T cell contact-mediated production of IL-6 from human monocytes. Compound A, at pharmacologically efficacious concentrations, does not significantly curtail the LPS-induced activation of p38 MAPKs. In the collagen-induced arthritis (CIA) mouse model (i) macroscopic observations demonstrate that Compound A, administered subcutaneously in a therapeutic regimen, significantly and dose-dependently inhibits disease associated increases in articular index and paw thickness; (ii) histological analyses of paw tissues reveal that Compound A prominently diminishes joint destruction, hyperproliferative pannus formation and infiltration of inflammatory cells. Collectively, these results provide direct evidence that Compound A, a novel preferential IL-6 inhibitor, suppresses collagen-induced arthritis, and may be a potential therapeutic for treating patients with active RA. Copyright © 2016. Published by Elsevier B.V.

Sensory Contributions to Impaired Emotion Processing in Schizophrenia

PubMed Central

Butler, Pamela D.; Abeles, Ilana Y.; Weiskopf, Nicole G.; Tambini, Arielle; Jalbrzikowski, Maria; Legatt, Michael E.; Zemon, Vance; Loughead, James; Gur, Ruben C.; Javitt, Daniel C.

2009-01-01

Both emotion and visual processing deficits are documented in schizophrenia, and preferential magnocellular visual pathway dysfunction has been reported in several studies. This study examined the contribution to emotion-processing deficits of magnocellular and parvocellular visual pathway function, based on stimulus properties and shape of contrast response functions. Experiment 1 examined the relationship between contrast sensitivity to magnocellular- and parvocellular-biased stimuli and emotion recognition using the Penn Emotion Recognition (ER-40) and Emotion Differentiation (EMODIFF) tests. Experiment 2 altered the contrast levels of the faces themselves to determine whether emotion detection curves would show a pattern characteristic of magnocellular neurons and whether patients would show a deficit in performance related to early sensory processing stages. Results for experiment 1 showed that patients had impaired emotion processing and a preferential magnocellular deficit on the contrast sensitivity task. Greater deficits in ER-40 and EMODIFF performance correlated with impaired contrast sensitivity to the magnocellular-biased condition, which remained significant for the EMODIFF task even when nonspecific correlations due to group were considered in a step-wise regression. Experiment 2 showed contrast response functions indicative of magnocellular processing for both groups, with patients showing impaired performance. Impaired emotion identification on this task was also correlated with magnocellular-biased visual sensory processing dysfunction. These results provide evidence for a contribution of impaired early-stage visual processing in emotion recognition deficits in schizophrenia and suggest that a bottom-up approach to remediation may be effective. PMID:19793797

Sensory contributions to impaired emotion processing in schizophrenia.

PubMed

Butler, Pamela D; Abeles, Ilana Y; Weiskopf, Nicole G; Tambini, Arielle; Jalbrzikowski, Maria; Legatt, Michael E; Zemon, Vance; Loughead, James; Gur, Ruben C; Javitt, Daniel C

2009-11-01

Both emotion and visual processing deficits are documented in schizophrenia, and preferential magnocellular visual pathway dysfunction has been reported in several studies. This study examined the contribution to emotion-processing deficits of magnocellular and parvocellular visual pathway function, based on stimulus properties and shape of contrast response functions. Experiment 1 examined the relationship between contrast sensitivity to magnocellular- and parvocellular-biased stimuli and emotion recognition using the Penn Emotion Recognition (ER-40) and Emotion Differentiation (EMODIFF) tests. Experiment 2 altered the contrast levels of the faces themselves to determine whether emotion detection curves would show a pattern characteristic of magnocellular neurons and whether patients would show a deficit in performance related to early sensory processing stages. Results for experiment 1 showed that patients had impaired emotion processing and a preferential magnocellular deficit on the contrast sensitivity task. Greater deficits in ER-40 and EMODIFF performance correlated with impaired contrast sensitivity to the magnocellular-biased condition, which remained significant for the EMODIFF task even when nonspecific correlations due to group were considered in a step-wise regression. Experiment 2 showed contrast response functions indicative of magnocellular processing for both groups, with patients showing impaired performance. Impaired emotion identification on this task was also correlated with magnocellular-biased visual sensory processing dysfunction. These results provide evidence for a contribution of impaired early-stage visual processing in emotion recognition deficits in schizophrenia and suggest that a bottom-up approach to remediation may be effective.

Nanotechnologies for efficient solar and wind energy harvesting and storage

NASA Astrophysics Data System (ADS)

Eldada, Louay A.

2010-08-01

We describe nanotechnologies used to improve the efficient harvest of energy from the Sun and the wind, and the efficient storage of energy in secondary batteries and ultracapacitors, for use in a variety of applications including smart grids, electric vehicles, and portable electronics. We demonstrate high-quality nanostructured copper indium gallium selenide (CIGS) thin films for photovoltaic (PV) applications. The self-assembly of nanoscale p-n junction networks creates n-type networks that act as preferential electron pathways, and p-type networks that act as preferential hole pathways, allowing positive and negative charges to travel to the contacts in physically separated paths, reducing charge recombination. We also describe PV nanotechnologies used to enhance light trapping, photon absorption, charge generation, charge transport, and current collection. Furthermore, we describe nanotechnologies used to improve the efficiency of power-generating wind turbines. These technologies include nanoparticle-containing lubricants that reduce the friction generated from the rotation of the turbines, nanocoatings for de-icing and self-cleaning technologies, and advanced nanocomposites that provide lighter and stronger wind blades. Finally, we describe nanotechnologies used in advanced secondary batteries and ultracapacitors. Nanostructured powder-based and carbon-nanotube-based cathodes and anodes with ultra-high surface areas boost the energy and power densities in secondary batteries, including lithium-ion and sodium-sulfur batteries. Nanostructured carbon materials are also controlled on a molecular level to offer large surface areas for the electrodes of ultracapacitors, allowing to store and supply large bursts of energy needed in some applications.

Aß Facilitates LTD at Schaffer Collateral Synapses Preferentially in the Left Hippocampus.

PubMed

O'Riordan, Kenneth J; Hu, Neng-Wei; Rowan, Michael J

2018-02-20

Promotion of long-term depression (LTD) mechanisms by synaptotoxic soluble oligomers of amyloid-β (Aß) has been proposed to underlie synaptic dysfunction in Alzheimer's disease (AD). Previously, LTD was induced by relatively non-specific electrical stimulation. Exploiting optogenetics, we studied LTD using a more physiologically diffuse spatial pattern of selective pathway activation in the rat hippocampus in vivo. This relatively sparse synaptic LTD requires both the ion channel function and GluN2B subunit of the NMDA receptor but, in contrast to electrically induced LTD, is not facilitated by boosting endogenous muscarinic acetylcholine or metabotropic glutamate 5 receptor activation. Although in the absence of Aß, there is no evidence of hippocampal LTD asymmetry, in the presence of Aß, the induction of LTD is preferentially enhanced in the left hippocampus in an mGluR5-dependent manner. This circuit-selective disruption of synaptic plasticity by Aß provides a route to understanding the development of aberrant brain lateralization in AD. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Action-derived molecular dynamics simulations for the migration and coalescence of vacancies in graphene and carbon nanotubes.

PubMed

Lee, Alex Taekyung; Ryu, Byungki; Lee, In-Ho; Chang, K J

2014-03-19

We report the results of action-derived molecular dynamics simulations for the migration and coalescence processes of monovacancies in graphene and carbon nanotubes with different chiralities. In carbon nanotubes, the migration pathways and barriers of a monovacancy depend on the tube chirality, while there is no preferential pathway in graphene due to the lattice symmetry and the absence of the curvature effect. The probable pathway changes from the axial to circumferential direction as the chirality varies from armchair to zigzag. The chirality dependence is attributed to the preferential orientation of the reconstructed bond formed around each vacancy site. It is energetically more favourable for two monovacancies to coalesce into a divacancy via alternative movements rather than simultaneous movements. The energy barriers for coalescence are generally determined by the migration barrier for the monovacancy, although there are some variations due to interactions between two diffusing vacancies. In graphene and armchair nanotubes, two monovacancies prefer to migrate along different zigzag atomic chains rather than a single atomic chain connecting these vacancies. On the other hand, in zigzag tubes, the energy barrier for coalescence increases significantly unless monovacancies lie on the same circumference.

The quality of our Nation's waters: factors affecting public-supply-well vulnerability to contamination: understanding observed water quality and anticipating future water quality

USGS Publications Warehouse

Eberts, Sandra M.; Thomas, Mary Ann; Jagucki, Martha L.

2013-01-01

As part of the U.S. Geological Survey National Water-Quality Assessment (NAWQA) Program, a study was conducted from 2001 to 2011 to shed light on factors that affect the vulnerability of water from public-supply wells to contamination (referred to hereafter as “public-supply-well vulnerability”). The study was designed as a follow-up to earlier NAWQA studies that found mixtures of contaminants at low concentrations in groundwater near the water table in urban areas across the Nation and, less frequently, in deeper groundwater typically used for public supply. Beside the factors affecting public-supply-well vulnerability to contamination, this circular describes measures that can be used to determine which factor (or factors) plays a dominant role at an individual public-supply well. Case-study examples are used throughout to show how such information can be used to improve water quality. In general, the vulnerability of the water from public-supply wells to contamination is a function of contaminant input within the area that contributes water to a well, the mobility and persistence of a contaminant once released to the groundwater, and the ease of groundwater and contaminant movement from the point of recharge to the open interval of a well. The following measures described in this circular are particularly useful for indicating which contaminants in an aquifer might reach an individual public-supply well and when, how, and at what concentration they might arrive: * Sources of recharge—Information on the sources of recharge for a well provides insight into contaminants that might enter the aquifer with the recharge water and potentially reach the well. * Geochemical conditions—Information on the geochemical conditions encountered by groundwater traveling to a well provides insight into contaminants that might persist in the water all the way to the well. * Groundwater-age mixtures—Information on the ages of the different waters that mix in a well provides insight into the time lag between contaminant input at the water table and contaminant arrival at the well. It also provides insight into the potential for in-well dilution of contaminated water by unaffected groundwater of a different age that simultaneously enters the well. Preferential flow pathways—pathways that provide little resistance to flow—can influence how all other factors affect public-supply-well vulnerability to contamination. For example, preferential flow pathways can influence whether a contaminant source is physically linked to a well, whether contaminant concentrations are substantially altered before contaminated groundwater reaches a well, and whether contaminated groundwater can arrive at a well within a timeframe of concern to the well owner. Methods for recognizing the influence of preferential flow pathways on the quality of water from a public-supply well are presented in this circular and can provide opportunities to prevent or mitigate the deterioration of a water supply. Knowing what water-quality variables to measure, what spatial and temporal scales on which to measure them, and how to interpret the resulting data makes it possible for samples from public-supply wells to provide a broad window into a well’s past and present water quality—and possibly future water quality. Such insight can enable resource managers to prioritize actions for sustaining a high-quality groundwater source of drinking water.

Nitrate foraging by Arabidopsis roots is mediated by the transcription factor TCP20 through the systemic signaling pathway

PubMed Central

Guan, Peizhu; Wang, Rongchen; Nacry, Philippe; Breton, Ghislain; Kay, Steve A.; Pruneda-Paz, Jose L.; Davani, Ariea; Crawford, Nigel M.

2014-01-01

To compete for nutrients in diverse soil microenvironments, plants proliferate lateral roots preferentially in nutrient-rich zones. For nitrate, root foraging involves local and systemic signaling; however, little is known about the genes that function in the systemic signaling pathway. By using nitrate enhancer DNA to screen a library of Arabidopsis transcription factors in the yeast one-hybrid system, the transcription factor gene TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR1-20 (TCP20) was identified. TCP20, which belongs to an ancient, plant-specific gene family that regulates shoot, flower, and embryo development, was implicated in nitrate signaling by its ability to bind DNA in more than 100 nitrate-regulated genes. Analysis of insertion mutants of TCP20 showed that they had normal primary and lateral root growth on homogenous nitrate media but were impaired in preferential lateral root growth (root foraging) on heterogeneous media in split-root plates. Inhibition of preferential lateral root growth was still evident in the mutants even when ammonium was uniformly present in the media, indicating that the TCP20 response was to nitrate. Comparison of tcp20 mutants with those of nlp7 mutants, which are defective in local control of root growth but not in the root-foraging response, indicated that TCP20 function is independent of and distinct from NLP7 function. Further analysis showed that tcp20 mutants lack systemic control of root growth regardless of the local nitrate concentrations. These results indicate that TCP20 plays a key role in the systemic signaling pathway that directs nitrate foraging by Arabidopsis roots. PMID:25288754

Evaluation of diffuse and preferential flow pathways of infiltratedprecipitation and irrigation using oxygen and hydrogen isotopes

USGS Publications Warehouse

Ma, Bin; Liang, Xing; Liu, Shaohua; Jin, Menggui; Nimmo, John R.; Li, Jingxin

2017-01-01

Subsurface-water flow pathways in three different land-use areas (non-irrigated grassland, poplar forest, and irrigated arable land) in the central North China Plain were investigated using oxygen (18O) and hydrogen (2H) isotopes in samples of precipitation, soils, and groundwater. Soil water in the top 10 cm was significantly affected by both evaporation and infiltration. Water at 10–40 cm depth in the grassland and arable land, and 10–60 cm in poplar forest, showed a relatively short residence time, as a substantial proportion of antecedent soil water was mixed with a 92-mm storm infiltration event, whereas below those depths (down to 150 cm), depleted δ18O spikes suggested that some storm water bypassed the shallow soil layers. Significant differences, in soil-water content and δ18O values, within a small area, suggested that the proportion of immobile soil water and water flowing in subsurface pathways varies depending on local vegetation cover, soil characteristics and irrigation applications. Soil-water δ18O values revealed that preferential flow and diffuse flow coexist. Preferential flow was active within the root zone, independent of antecedent soil-water content, in both poplar forest and arable land, whereas diffuse flow was observed in grassland. The depleted δ18O spikes at 20–50 cm depth in the arable land suggested the infiltration of irrigation water during the dry season. Temporal isotopic variations in precipitation were subdued in the shallow groundwater, suggesting more complete mixing of different input waters in the unsaturated zone before reaching the shallow groundwater.

Coupling Deep Transcriptome Analysis with Untargeted Metabolic Profiling in Ophiorrhiza pumila to Further the Understanding of the Biosynthesis of the Anti-Cancer Alkaloid Camptothecin and Anthraquinones

PubMed Central

Yamazaki, Mami; Mochida, Keiichi; Asano, Takashi; Nakabayashi, Ryo; Chiba, Motoaki; Udomson, Nirin; Yamazaki, Yasuyo; Goodenowe, Dayan B.; Sankawa, Ushio; Yoshida, Takuhiro; Toyoda, Atsushi; Totoki, Yasushi; Sakaki, Yoshiyuki; Góngora-Castillo, Elsa; Buell, C. Robin; Sakurai, Tetsuya; Saito, Kazuki

2013-01-01

The Rubiaceae species, Ophiorrhiza pumila, accumulates camptothecin, an anti-cancer alkaloid with a potent DNA topoisomerase I inhibitory activity, as well as anthraquinones that are derived from the combination of the isochorismate and hemiterpenoid pathways. The biosynthesis of these secondary products is active in O. pumila hairy roots yet very low in cell suspension culture. Deep transcriptome analysis was conducted in O. pumila hairy roots and cell suspension cultures using the Illumina platform, yielding a total of 2 Gb of sequence for each sample. We generated a hybrid transcriptome assembly of O. pumila using the Illumina-derived short read sequences and conventional Sanger-derived expressed sequence tag clones derived from a full-length cDNA library constructed using RNA from hairy roots. Among 35,608 non-redundant unigenes, 3,649 were preferentially expressed in hairy roots compared with cell suspension culture. Candidate genes involved in the biosynthetic pathway for the monoterpenoid indole alkaloid camptothecin were identified; specifically, genes involved in post-strictosamide biosynthetic events and genes involved in the biosynthesis of anthraquinones and chlorogenic acid. Untargeted metabolomic analysis by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) indicated that most of the proposed intermediates in the camptothecin biosynthetic pathway accumulated in hairy roots in a preferential manner compared with cell suspension culture. In addition, a number of anthraquinones and chlorogenic acid preferentially accumulated in hairy roots compared with cell suspension culture. These results suggest that deep transcriptome and metabolome data sets can facilitate the identification of genes and intermediates involved in the biosynthesis of secondary products including camptothecin in O. pumila. PMID:23503598

Colloid transport in dual-permeability media

USDA-ARS?s Scientific Manuscript database

It has been widely reported that colloids can travel faster and over longer distances in natural structured porous media than in uniform structureless media used in laboratory studies. The presence of preferential pathways for colloids in the subsurface environment is of concern because of the incre...

Aminophylline preferentially inhibits chloroethylclonidine-insensitive alpha-adrenoceptor-mediated contractions in rat aorta.

PubMed

Duarte, J; Pérez-Vizcaíno, F; Zarzuelo, A; Jiménez, J; Tamargo, J

1993-11-01

1. In rat thoracic aortae, contractions induced by methoxamine were inhibited by chloroethylclonidine, whereas oxymetazoline-induced contractions, which were more dependent on Ca(2+)-entry, were insensitive to chloroethylclonidine. 2. Aminophylline inhibited the contractions and 45Ca(2+)-uptake induced by both methoxamine and oxymetazoline. However, oxymetazoline-induced contractions were more sensitive to inhibition by aminophylline and D600. 3. Thus, the partial selectivity of aminophylline for the chloroethylclonidine-resistant, highly dependent on extracellular Ca2+, oxymetazoline-mediated responses may be explained by a preferential inhibition of agonist-induced Ca2+ entry as compared to inhibition of other transduction pathways.

Degradation of Glyphosate by Mn-Oxide May Bypass Sarcosine and Form Glycine Directly after C-N Bond Cleavage.

PubMed

Li, Hui; Wallace, Adam F; Sun, Mingjing; Reardon, Patrick; Jaisi, Deb P

2018-02-06

Glyphosate is the active ingredient of the common herbicide Roundup. The increasing presence of glyphosate and its byproducts has raised concerns about its potential impact on the environment and human health. In this research, we investigated abiotic pathways of glyphosate degradation as catalyzed by birnessite under aerobic and neutral pH conditions to determine whether certain pathways have the potential to generate less harmful intermediate products. Nuclear magnetic resonance (NMR) spectroscopy and high-performance liquid chromatography (HPLC) were utilized to identify and quantify reaction products, and density functional theory (DFT) calculations were used to investigate the bond critical point (BCP) properties of the C-N bond in glyphosate and Mn(IV)-complexed glyphosate. We found that sarcosine, the commonly recognized precursor to glycine, was not present at detectable levels in any of our experiments despite the fact that its half-life (∼13.6 h) was greater than our sampling intervals. Abiotic degradation of glyphosate largely followed the glycine pathway rather than the AMPA (aminomethylphosphonic acid) pathway. Preferential cleavage of the phosphonate adjacent C-N bond to form glycine directly was also supported by our BCP analysis, which revealed that this C-N bond was disproportionately affected by the interaction of glyphosate with Mn(IV). Overall, these results provide useful insights into the potential pathways through which glyphosate may degrade via relatively benign intermediates.

A ruthenium anticancer compound interacts with histones and impacts differently on epigenetic and death pathways compared to cisplatin

PubMed Central

Capuozzo, Antonelle; Ali, Moussa; Santamaria, Rita; Armant, Olivier; Delalande, Francois; Dorsselaer, Alain Van; Cianferani, Sarah; Spencer, John; Pfeffer, Michel; Mellitzer, Georg; Gaiddon, Christian

2017-01-01

Ruthenium complexes are considered as potential replacements for platinum compounds in oncotherapy. Their clinical development is handicapped by a lack of consensus on their mode of action. In this study, we identify three histones (H3.1, H2A, H2B) as possible targets for an anticancer redox organoruthenium compound (RDC11). Using purified histones, we confirmed an interaction between the ruthenium complex and histones that impacted on histone complex formation. A comparative study of the ruthenium complex versus cisplatin showed differential epigenetic modifications on histone H3 that correlated with differential expression of histone deacetylase (HDAC) genes. We then characterized the impact of these epigenetic modifications on signaling pathways employing a transcriptomic approach. Clustering analyses showed gene expression signatures specific for cisplatin (42%) and for the ruthenium complex (30%). Signaling pathway analyses pointed to specificities distinguishing the ruthenium complex from cisplatin. For instance, cisplatin triggered preferentially p53 and folate biosynthesis while the ruthenium complex induced endoplasmic reticulum stress and trans-sulfuration pathways. To further understand the role of HDACs in these regulations, we used suberanilohydroxamic acid (SAHA) and showed that it synergized with cisplatin cytotoxicity while antagonizing the ruthenium complex activity. This study provides critical information for the characterization of signaling pathways differentiating both compounds, in particular, by the identification of a non-DNA direct target for an organoruthenium complex. PMID:27935863

Epistatic role of base excision repair and mismatch repair pathways in mediating cisplatin cytotoxicity

PubMed Central

Kothandapani, Anbarasi; Sawant, Akshada; Dangeti, Venkata Srinivas Mohan Nimai; Sobol, Robert W.; Patrick, Steve M.

2013-01-01

Base excision repair (BER) and mismatch repair (MMR) pathways play an important role in modulating cis-Diamminedichloroplatinum (II) (cisplatin) cytotoxicity. In this article, we identified a novel mechanistic role of both BER and MMR pathways in mediating cellular responses to cisplatin treatment. Cells defective in BER or MMR display a cisplatin-resistant phenotype. Targeting both BER and MMR pathways resulted in no additional resistance to cisplatin, suggesting that BER and MMR play epistatic roles in mediating cisplatin cytotoxicity. Using a DNA Polymerase β (Polβ) variant deficient in polymerase activity (D256A), we demonstrate that MMR acts downstream of BER and is dependent on the polymerase activity of Polβ in mediating cisplatin cytotoxicity. MSH2 preferentially binds a cisplatin interstrand cross-link (ICL) DNA substrate containing a mismatch compared with a cisplatin ICL substrate without a mismatch, suggesting a novel mutagenic role of Polβ in activating MMR in response to cisplatin. Collectively, these results provide the first mechanistic model for BER and MMR functioning within the same pathway to mediate cisplatin sensitivity via non-productive ICL processing. In this model, MMR participation in non-productive cisplatin ICL processing is downstream of BER processing and dependent on Polβ misincorporation at cisplatin ICL sites, which results in persistent cisplatin ICLs and sensitivity to cisplatin. PMID:23761438

Preferential flow occurs in unsaturated conditions

USGS Publications Warehouse

Nimmo, John R.

2012-01-01

Because it commonly generates high-speed, high-volume flow with minimal exposure to solid earth materials, preferential flow in the unsaturated zone is a dominant influence in many problems of infiltration, recharge, contaminant transport, and ecohydrology. By definition, preferential flow occurs in a portion of a medium – that is, a preferred part, whether a pathway, pore, or macroscopic subvolume. There are many possible classification schemes, but usual consideration of preferential flow includes macropore or fracture flow, funneled flow determined by macroscale heterogeneities, and fingered flow determined by hydraulic instability rather than intrinsic heterogeneity. That preferential flow is spatially concentrated associates it with other characteristics that are typical, although not defining: it tends to be unusually fast, to transport high fluxes, and to occur with hydraulic disequilibrium within the medium. It also has a tendency to occur in association with large conduits and high water content, although these are less universal than is commonly assumed. Predictive unsaturated-zone flow models in common use employ several different criteria for when and where preferential flow occurs, almost always requiring a nearly saturated medium. A threshold to be exceeded may be specified in terms of the following (i) water content; (ii) matric potential, typically a value high enough to cause capillary filling in a macropore of minimum size; (iii) infiltration capacity or other indication of incipient surface ponding; or (iv) other conditions related to total filling of certain pores. Yet preferential flow does occur without meeting these criteria. My purpose in this commentary is to point out important exceptions and implications of ignoring them. Some of these pertain mainly to macropore flow, others to fingered or funneled flow, and others to combined or undifferentiated flow modes.

Dysregulated cellular functions and cell stress pathways provide critical cues for activating and targeting natural killer cells to transformed and infected cells.

PubMed

Raulet, David H; Marcus, Assaf; Coscoy, Laurent

2017-11-01

Natural killer (NK) cells recognize and kill cancer cells and infected cells by engaging cell surface ligands that are induced preferentially or exclusively on these cells. These ligands are recognized by activating receptors on NK cells, such as NKG2D. In addition to activation by cell surface ligands, the acquisition of optimal effector activity by NK cells is driven in vivo by cytokines and other signals. This review addresses a developing theme in NK cell biology: that NK-activating ligands on cells, and the provision of cytokines and other signals that drive high effector function in NK cells, are driven by abnormalities that arise from transformation or the infected state. The pathways include genomic damage, which causes self DNA to be exposed in the cytosol of affected cells, where it activates the DNA sensor cGAS. The resulting signaling induces NKG2D ligands and also mobilizes NK cell activation. Other key pathways that regulate NKG2D ligands include PI-3 kinase activation, histone acetylation, and the integrated stress response. This review summarizes the roles of these pathways and their relevance in both viral infections and cancer. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Molecular spinning by a chiral train of short laser pulses

NASA Astrophysics Data System (ADS)

Floß, Johannes; Averbukh, Ilya Sh.

2012-12-01

We provide a detailed theoretical analysis of molecular rotational excitation by a chiral pulse train, a sequence of linearly polarized pulses with the polarization direction rotating from pulse to pulse by a controllable angle. Molecular rotation with a preferential rotational sense (clockwise or counterclockwise) can be excited by this scheme. We show that the directionality of the rotation is caused by quantum interference of different excitation pathways. The chiral pulse train is capable of selective excitation of molecular isotopologs and nuclear spin isomers in a mixture. We demonstrate this using 14N2 and 15N2 as examples for isotopologs and para- and ortho-nitrogen as examples for nuclear-spin isomers.

Application of a Transient Storage Zone Model o Soil Pipeflow Tracer Injection Experiments

USDA-ARS?s Scientific Manuscript database

Soil pipes, defined here as discrete preferential flow paths generally parallel to the slope, are important subsurface flow pathways that play a role in many soil erosion phenomena. However, limited research has been performed on quantifying and characterizing their flow and transport characteristic...

Soil pipe flow tracer experiments: 2. Application of a transient storage zone model

USDA-ARS?s Scientific Manuscript database

Soil pipes, defined here as discrete preferential flow paths generally parallel to the slope, are important subsurface flow pathways that play a role in many soil erosion phenomena. However, limited research has been performed on quantifying and characterizing their flow and transport characteristic...

CCK receptors-related signaling involved in nitric oxide production caused by gastrin 17 in porcine coronary endothelial cells.

PubMed

Grossini, Elena; Caimmi, Philippe; Molinari, Claudio; Uberti, Francesca; Mary, David; Vacca, Giovanni

2012-03-05

In anesthetized pigs gastrin-17 increased coronary blood flow through CCK1/CCK2 receptors and β(2)-adrenoceptors-related nitric oxide (NO) release. Since the intracellular pathway has not been investigated the purpose of this study was to examine in coronary endothelial cells the CCK1/CCK2 receptors-related signaling involved in the effects of gastrin-17 on NO release. Gastrin-17 caused a concentration-dependent increase of NO production (17.3-62.6%; p<0.05), which was augmented by CCK1/CCK2 receptors agonists (p<0.05). The effect of gastrin-17 was amplified by the adenylyl-cyclase activator and β(2)-adrenoceptors agonist (p<0.05), abolished by cAMP/PKA and β(2)-adrenoceptors and CCK1/CCK2 receptors blockers, and reduced by PLC/PKC inhibitor. Finally, Western-blot revealed the preferential involvement of PKA vs. PKC as downstream effectors of CCK1/CCK2 receptors activation leading to Akt, ERK, p38 and endothelial NOS (eNOS) phosphorylation. In conclusion, in coronary endothelial cells, gastrin-17 induced eNOS-dependent NO production through CCK1/CCK2 receptors- and β(2)-adrenoceptors-related pathway. The intracellular signaling involved a preferential PKA pathway over PKC. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Anaerobic Dehalogenation of Chloroanilines by Dehalococcoides mccartyi Strain CBDB1 and Dehalobacter Strain 14DCB1 via Different Pathways as Related to Molecular Electronic Structure.

PubMed

Zhang, Shangwei; Wondrousch, Dominik; Cooper, Myriel; Zinder, Stephen H; Schüürmann, Gerrit; Adrian, Lorenz

2017-04-04

Dehalococcoides mccartyi strain CBDB1 and Dehalobacter strain 14DCB1 are organohalide-respiring microbes of the phyla Chloroflexi and Firmicutes, respectively. Here, we report the transformation of chloroanilines by these two bacterial strains via dissimilar dehalogenation pathways and discuss the underlying mechanism with quantum chemically calculated net atomic charges of the substrate Cl, H, and C atoms. Strain CBDB1 preferentially removed Cl doubly flanked by two Cl or by one Cl and NH 2 , whereas strain 14DCB1 preferentially dechlorinated Cl that has an ortho H. For the CBDB1-mediated dechlorination, comparative analysis with Hirshfeld charges shows that the least-negative Cl discriminates active from nonactive substrates in 14 out of 15 cases and may represent the preferred site of primary attack through cob(I)alamin. For the latter trend, three of seven active substrates provide strong evidence, with partial support from three of the remaining four substrates. Regarding strain 14DCB1, the most positive carbon-attached H atom discriminates active from nonactive chloroanilines in again 14 out of 15 cases. Here, regioselectivity is governed for 10 of the 11 active substrates by the most positive H attached to the highest-charge (most positive or least negative) aromatic C carrying the Cl to be removed. These findings suggest the aromatic ring H as primary site of attack through the supernucleophile Co(I), converting an initial H bond to a full electron transfer as start of the reductive dehalogenation. For both mechanisms, one- and two-electron transfer to Cl (strain CBDB1) or H (strain 14DCB1) are compatible with the presently available data. Computational chemistry research into reaction intermediates and pathways may further aid in understanding the bacterial reductive dehalogenation at the molecular level.

The Cortical Connectivity of the Prefrontal Cortex in the Monkey Brain

PubMed Central

Yeterian, Edward H.; Pandya, Deepak N.; Tomaiuolo, Francesco; Petrides, Michael

2011-01-01

One dimension of understanding the functions of the prefrontal cortex is knowledge of cortical connectivity. We have surveyed three aspects of prefrontal cortical connections: local projections (within the frontal lobe), the termination patterns of long association (post-Rolandic) projections, and the trajectories of major fiber pathways. The local connections appear to be organized in relation to dorsal (hippocampal origin) and ventral (paleocortical origin) architectonic trends. According to the proposal of a dual origin of the cerebral cortex, cortical areas can be traced as originating from archicortex (hippocampus) on the one hand, and paleocortex, on the other hand, in a stepwise manner (e.g., Sanides, 1969; Pandya and Yeterian, 1985). Prefrontal areas within each trend are connected with less architectonically differentiated areas, and, on the other hand, with more differentiated areas. Such organization may allow for the systematic exchange of information within each architectonic trend. The long connections of the prefrontal cortex with post-Rolandic regions seem to be organized preferentially in relation to dorsal and ventral prefrontal architectonic trends. Prefrontal areas are connected with post-Rolandic auditory, visual and somatosensory association areas, and with multimodal and paralimbic regions. This long connectivity likely works in conjunction with local connections to serve prefrontal cortical functions. The afferent and efferent connections of the prefrontal cortex with post-Rolandic regions are conveyed by specific long association pathways. These pathways as well appear to be organized in relation to dorsal and ventral prefrontal architectonic trends. Finally, although prefrontal areas have preferential connections in relation to dual architectonic trends, it is clear that there are interconnections between and among areas in each trend, which may provide a substrate for the overall integrative function of the prefrontal cortex. Prefrontal corticocortical connectivity may help to elucidate both region-specific and integrative perspectives on the functions of the prefrontal cortex. PMID:21481342

An intracellular signaling hierarchy determines direction of migration in opposing chemotactic gradients.

PubMed

Heit, Bryan; Tavener, Samantha; Raharjo, Eko; Kubes, Paul

2002-10-14

Neutrophils must follow both endogenous and bacterial chemoattractant signals out of the vasculature and through the interstitium to arrive at a site of infection. By necessity, in the setting of multiple chemoattractants, the neutrophils must prioritize, favoring end target chemoattractants (e.g., fMLP and C5a) emanating from the site of infection over intermediary endogenous chemoattractants (e.g., IL-8 and LTB4) encountered en route to sites of infection. In this study, we propose a hierarchical model of two signaling pathways mediating the decision-making process of the neutrophils, which allows end target molecules to dominate over intermediary chemoattractants. In an under agarose assay, neutrophils predominantly migrated toward end target chemoattractants via p38 MAPK, whereas intermediary chemoattractant-induced migration was phosphoinositide 3-kinase (PI3K)/Akt dependent. When faced with competing gradients of end target and intermediary chemoattractants, Akt activation was significantly reduced within neutrophils, and the cells migrated preferentially toward end target chemoattractants even at 1/1,000th that of intermediary chemoattractants. End target molecules did not require chemotactic properties, since the p38 MAPK activator, LPS, also inhibited Akt and prevented migration to intermediary chemoattractants. p38 MAPK inhibitors not only reversed this hierarchy, such that neutrophils migrated preferentially toward intermediary chemoattractants, but also allowed neutrophils to be drawn out of a local end target chemoattractant environment and toward intermediary chemoattractants unexpectedly in an exaggerated (two- to fivefold) fashion. This was entirely related to significantly increased magnitude and duration of Akt activation. Finally, end target chemoattractant responses were predominantly Mac-1 dependent, whereas nondominant chemoattractants used primarily LFA-1. These data provide support for a two pathway signaling model wherein the end target chemoattractants activate p38 MAPK, which inhibits intermediary chemoattractant-induced PI3K/Akt pathway, establishing an intracellular signaling hierarchy.

PCDD/F and dioxin-like PCB bioaccumulation by Manila clam from polluted areas of Venice lagoon (Italy).

PubMed

Sfriso, Adriano; Facca, Chiara; Raccanelli, Stefano

2014-01-01

POP bioaccumulation pathways in the clam Tapes philippinarum were examined for two years from juveniles to adult size. Two polluted sites, one with sandy sediment, the other muddy were compared with a reference site characterized by low contamination levels. Juvenile clams coming from a hatchery were reared both on the sediment and in nets suspended at 30 cm from the bottom. POP changes in clam tissue were related to the concentrations recorded in sediments and in the particulate matter during the entire fattening period. Results provided interesting data on the relationships between environmental contamination and bioaccumulation. Contrary to studies on the decontamination times of the clams collected in polluted areas, this work investigates the preferential clam bioaccumulation pathways during growth under different environmental conditions. In general POP bioaccumulation resulted to be correlated to concentrations in SPM rather than in sediments and was higher in S-clams rather than in B-clams. Copyright © 2013 Elsevier Ltd. All rights reserved.

Hop (Humulus lupulus L.) Extract and 6-Prenylnaringenin Induce P450 1A1 Catalyzed Estrogen 2-Hydroxylation

PubMed Central

2016-01-01

Humulus lupulus L. (hops) is a popular botanical dietary supplement used by women as a sleep aid and for postmenopausal symptom relief. In addition to its efficacy for menopausal symptoms, hops can also modulate the chemical estrogen carcinogenesis pathway and potentially protect women from breast cancer. In the present study, an enriched hop extract and the key bioactive compounds [6-prenylnarigenin (6-PN), 8-prenylnarigenin (8-PN), isoxanthohumol (IX), and xanthohumol (XH)] were tested for their effects on estrogen metabolism in breast cells (MCF-10A and MCF-7). The methoxyestrones (2-/4-MeOE1) were analyzed as biomarkers for the nontoxic P450 1A1 catalyzed 2-hydroxylation and the genotoxic P450 1B1 catalyzed 4-hydroxylation pathways, respectively. The results indicated that the hop extract and 6-PN preferentially induced the 2-hydroxylation pathway in both cell lines. 8-PN only showed slight up-regulation of metabolism in MCF-7 cells, whereas IX and XH did not have significant effects in either cell line. To further explore the influence of hops and its bioactive marker compounds on P450 1A1/1B1, mRNA expression and ethoxyresorufin O-dealkylase (EROD) activity were measured. The results correlated with the metabolism data and showed that hop extract and 6-PN preferentially enhanced P450 1A1 mRNA expression and increased P450 1A1/1B1 activity. The aryl hydrocarbon receptor (AhR) activation by the isolated compounds was tested using xenobiotic response element (XRE) luciferase construct transfected cells. 6-PN was found to be an AhR agonist that significantly induced XRE activation and inhibited 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) induced XRE activity. 6-PN mediated induction of EROD activity was also inhibited by the AhR antagonist CH223191. These data show that the hop extract and 6-PN preferentially enhance the nontoxic estrogen 2-hydroxylation pathway through AhR mediated up-regulation of P450 1A1, which further emphasizes the importance of standardization of botanical extracts to multiple chemical markers for both safety and desired bioactivity. PMID:27269377

AMP and adenosine are both ligands for adenosine 2B receptor signaling.

PubMed

Holien, Jessica K; Seibt, Benjamin; Roberts, Veena; Salvaris, Evelyn; Parker, Michael W; Cowan, Peter J; Dwyer, Karen M

2018-01-15

Adenosine is considered the canonical ligand for the adenosine 2B receptor (A 2B R). A 2B R is upregulated following kidney ischemia augmenting post ischemic blood flow and limiting tubular injury. In this context the beneficial effect of A 2B R signaling has been attributed to an increase in the pericellular concentration of adenosine. However, following renal ischemia both kidney adenosine monophosphate (AMP) and adenosine levels are substantially increased. Using computational modeling and calcium mobilization assays, we investigated whether AMP could also be a ligand for A 2B R. The computational modeling suggested that AMP interacts with more favorable energy to A 2B R compared with adenosine. Furthermore, AMPαS, a non-hydrolyzable form of AMP, increased calcium uptake by Chinese hamster ovary (CHO) cells expressing the human A 2B R, indicating preferential signaling via the G q pathway. Therefore, a putative AMP-A 2B R interaction is supported by the computational modeling data and the biological results suggest this interaction involves preferential G q activation. These data provide further insights into the role of purinergic signaling in the pathophysiology of renal IRI. Copyright © 2017 Elsevier Ltd. All rights reserved.

Tissue-Specific Profiling Reveals Transcriptome Alterations in Arabidopsis Mutants Lacking Morphological Phenotypes[C][W

PubMed Central

Simon, Marissa; Bruex, Angela; Kainkaryam, Raghunandan M.; Zheng, Xiaohua; Huang, Ling; Woolf, Peter J.; Schiefelbein, John

2013-01-01

Traditional genetic analysis relies on mutants with observable phenotypes. Mutants lacking visible abnormalities may nevertheless exhibit molecular differences useful for defining gene function. To examine this, we analyzed tissue-specific transcript profiles from Arabidopsis thaliana transcription factor gene mutants with known roles in root epidermis development, but lacking a single-gene mutant phenotype due to genetic redundancy. We discovered substantial transcriptional changes in each mutant, preferentially affecting root epidermal genes in a manner consistent with the known double mutant effects. Furthermore, comparing transcript profiles of single and double mutants, we observed remarkable variation in the sensitivity of target genes to the loss of one or both paralogous genes, including preferential effects on specific branches of the epidermal gene network, likely reflecting the pathways of paralog subfunctionalization during evolution. In addition, we analyzed the root epidermal transcriptome of the transparent testa glabra2 mutant to clarify its role in the network. These findings provide insight into the molecular basis of genetic redundancy and duplicate gene diversification at the level of a specific gene regulatory network, and they demonstrate the usefulness of tissue-specific transcript profiling to define gene function in mutants lacking informative visible changes in phenotype. PMID:24014549

Induction and repair of DNA double strand breaks: the increasing spectrum of non-homologous end joining pathways.

PubMed

Mladenov, Emil; Iliakis, George

2011-06-03

A defining characteristic of damage induced in the DNA by ionizing radiation (IR) is its clustered character that leads to the formation of complex lesions challenging the cellular repair mechanisms. The most widely investigated such complex lesion is the DNA double strand break (DSB). DSBs undermine chromatin stability and challenge the repair machinery because an intact template strand is lacking to assist restoration of integrity and sequence in the DNA molecule. Therefore, cells have evolved a sophisticated machinery to detect DSBs and coordinate a response on the basis of inputs from various sources. A central function of cellular responses to DSBs is the coordination of DSB repair. Two conceptually different mechanisms can in principle remove DSBs from the genome of cells of higher eukaryotes. Homologous recombination repair (HRR) uses as template a homologous DNA molecule and is therefore error-free; it functions preferentially in the S and G2 phases. Non-homologous end joining (NHEJ), on the other hand, simply restores DNA integrity by joining the two ends, is error prone as sequence is only fortuitously preserved and active throughout the cell cycle. The basis of DSB repair pathway choice remains unknown, but cells of higher eukaryotes appear programmed to utilize preferentially NHEJ. Recent work suggests that when the canonical DNA-PK dependent pathway of NHEJ (D-NHEJ), becomes compromised an alternative NHEJ pathway and not HRR substitutes in a quasi-backup function (B-NHEJ). Here, we outline aspects of DSB induction by IR and review the mechanisms of their processing in cells of higher eukaryotes. We place particular emphasis on backup pathways of NHEJ and summarize their increasing significance in various cellular processes, as well as their potential contribution to carcinogenesis. 2011 Elsevier B.V. All rights reserved.

Arachidonic acid metabolites follow the preferential course of cyclooxygenase pathway for the basal tone in the internal anal sphincter.

PubMed

de Godoy, Márcio A F; Rattan, Neeru; Rattan, Satish

2009-04-01

Present studies determined the roles of the cyclooxygenase (COX) versus the lipoxygenase (LO) pathways in the metabolic pathway of arachidonic acid (AA) in the internal anal sphincter (IAS) tone. Studies were performed in the rat IAS versus the nontonic rectal smooth muscle (RSM). Indomethacin, the dual COX inhibitor, but not nordihydroguaiaretic acid (NDGA), the LO inhibitor, produced a precipitous decrease in the IAS tone. However, when added in the background of indomethacin, NDGA caused significant reversal of the IAS tone. These inhibitors had no significant effect on the RSM. To follow the significance of COX versus LO pathways, we examined the effects of AA and its metabolites. In the IAS, AA caused an increase in the IAS tone (Emax=38.8+/-3.0% and pEC50=3.4+/-0.1). In the RSM, AA was significantly less efficacious and potent (Emax=11.3+/-3.5% and pEC50=2.2+/-0.3). The AA metabolites (via COXs) PGF2alpha and U-46619 (a stable analog of thromboxane A2) produced increases in the IAS tone and force in the RSM. Conversely, AA metabolites (via 5-LO) lipoxin A4, 5-HETE, and leukotriene C4 decreased the IAS tone. Finally, the contractile effects of AA in the IAS were selectively attenuated by the COX-1 but not the COX-2 inhibitor. Collectively, the specific effects of AA and the COX inhibitor, the Western blot and RT-PCR analyses showing specifically higher levels of COX-1, suggest a preferential role of the COX (specifically COX-1) pathway versus the LO in the regulation of the IAS tone.

p21WAF1 and tumourigenesis: 20 years after.

PubMed

Warfel, Noel A; El-Deiry, Wafik S

2013-01-01

This review provides an overview of the structure, regulation and physiological functions of p21, the product of the cyclin-dependent kinase inhibitor 1A (CDKN1A) gene, with a focus on its dual role in promoting and repressing biological processes that are hallmarks of tumourigenesis. Recent work has provided a better understanding of the molecular mechanisms of how oncogenic signalling pathways influence p21 expression. In response to cellular stimuli, p21 expression is tightly regulated at transcriptional and post-translational levels through mechanisms involving RNA stabilization, phosphorylation and ubiquitination. As a result, growing evidence reveals that several important tumour suppressor and oncogenic signalling pathways alter p21 expression to elicit their effects on cell cycle progression and survival. Thus, p21 expression can both promote and inhibit tumourigenic processes, depending on the cellular context. Since its discovery, it has become increasingly clear that p21 can function as both a classical tumour suppressor and an oncogene. In order to effectively utilize p21 as a therapeutic target, it will be necessary to design therapeutic strategies that preferentially block the ability of p21 to promote senescence, stem cell renewal and cyclin/CDK activation, while leaving its tumour suppressive functions intact.

Experimental evidence of site specific preferential processing of either ice algae or phytoplankton by benthic macroinfauna in Lancaster Sound and North Water Polynyas, Canada

NASA Astrophysics Data System (ADS)

Mäkelä, Anni; Witte, Ursula; Archambault, Philippe

2016-04-01

Rapid warming is dramatically reducing the extent and thickness of summer sea ice of the Arctic Ocean, changing both the quantity and type of marine primary production as the longer open water period favours phytoplankton growth and reduces ice algal production. The benthic ecosystem is dependent on this sinking organic matter for source of energy, and ice algae is thought to be a superior quality food source due to higher essential fatty acid content. The resilience of the benthos to changing quality and quantity of food was investigated through sediment incubation experiments in the summer 2013 in two highly productive Arctic polynyas in the North Water and Lancaster Sound, Canada. The pathways of organic matter processing and contribution of different organisms to these processes was assessed through 13C and 15N isotope assimilation into macroinfaunal tissues. In North Water Polynya, the total and biomass specific uptake of ice algal derived C and N was higher than the uptake of phytoplankton, whereas an opposite trend was observed in Lancaster Sound. Polychaetes, especially individuals of families Sabellidae and Spionidae, unselectively ingested both algal types and were significant in the overall organic matter processing at both sites. Feeding preference was observed in crustaceans, which preferentially fed on ice algae at Lancaster Sound, but preferred phytoplankton in North Water Polynya. Bivalves also had a significant role in the organic matter processing overall, but only showed preferential feeding on phytoplankton at Lancaster Sound polynya. Overall the filter feeders and surface deposit feeders occupying lowest trophic levels were responsible for majority of the processing of both algal types. The results provide direct evidence of preferential resource utilisation by benthic macrofauna and highlight spatial differences in the processes. This helps to predict future patterns of nutrient cycling in Arctic sediments, with implications to benthic-pelagic coupling and overall marine productivity.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Paterson, Carolyn P.; Ayalew, Lisanework E.; Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK S7N 5E3 S7N 5B4 Canada

The L1 region of bovine adenovirus (BAdV)-3 encodes a non-structural protein designated 52K. Anti-52K serum detected a protein of 40 kDa, which localized to the nucleus but not to the nucleolus in BAdV-3-infected or transfected cells. Analysis of mutant 52K proteins suggested that three basic residues ({sup 105}RKR{sup 107}) of the identified domain (amino acids {sup 102}GMPRKRVLT{sup 110}) are essential for nuclear localization of 52K. The nuclear import of a GST-52K fusion protein utilizes the classical importin {alpha}/{beta}-dependent nuclear transport pathway. The 52K protein is preferentially bound to the cellular nuclear import receptor importin {alpha}3. Although deletion of amino acidmore » 102-110 is sufficient to abrogate the nuclear localization of 52K, amino acid 90-133 are required for interaction with importin-{alpha}3 and localizing a cytoplasmic protein to the nucleus. These results suggest that 52K contains a bipartite NLS, which preferentially utilize an importin {alpha}3 nuclear import receptor-mediated pathway to transport 52K to the nucleus.« less

Identification of Preferential Groundwater Flow Pathways from Local Tracer Breakthrough Curves

NASA Astrophysics Data System (ADS)

Kokkinaki, A.; Sleep, B. E.; Dearden, R.; Wealthall, G.

2009-12-01

Characterizing preferential groundwater flow paths in the subsurface is a key factor in the design of in situ remediation technologies. When applying reaction-based remediation methods, such as enhanced bioremediation, preferential flow paths result in fast solute migration and potentially ineffective delivery of reactants, thereby adversely affecting treatment efficiency. The presence of such subsurface conduits was observed at the SABRe (Source Area Bioremediation) research site. Non-uniform migration of contaminants and electron donor during the field trials of enhanced bioremediation supported this observation. To better determine the spatial flow field of the heterogeneous aquifer, a conservative tracer test was conducted. Breakthrough curves were obtained at a reference plane perpendicular to the principal groundwater flow direction. The resulting dataset was analyzed using three different methods: peak arrival times, analytical solution fitting and moment analysis. Interpretation using the peak arrival time method indicated areas of fast plume migration. However, some of the high velocities are supported by single data points, thus adding considerable uncertainty to the estimated velocity distribution. Observation of complete breakthrough curves indicated different types of solute breakthrough, corresponding to different transport mechanisms. Sharp peaks corresponded to high conductivity preferential flow pathways, whereas more dispersed breakthrough curves with long tails were characteristic of significant dispersive mixing and dilution. While analytical solutions adequately quantified flow characteristics for the first type of curves, they failed to do so for the second type, in which case they gave unrealistic results. Therefore, a temporal moment analysis was performed to obtain complete spatial distributions of mass recovery, velocity and dispersivity. Though the results of moment analysis qualitatively agreed with the results of previous methods, more realistic estimates of velocities were obtained and the presence of one major preferential flow pathway was confirmed. However, low mass recovery and deviations from the 10% scaling rule for dispersivities indicate that insufficient spatial and temporal monitoring, as well as interpolation and truncation errors introduced uncertainty in the flow and transport parameters estimated by the method of moments. The results of the three analyses are valuable for enhancing the understanding of mass transport and remediation performance. Comparing the different interpretation methods, increasing the amount of concentration data considered in the analysis, the derived velocity fields were smoother and the estimated local velocities and dispersivities became more realistic. In conclusion, moment analysis is a method that represents a smoothed average of the velocity across the entire breakthrough curve, whereas the peak arrival time, which may be a less well constrained estimate, represents the physical peak arrival and typically yields a higher velocity than the moment analysis. This is an important distinction when applying the results of the tracer test to field sites.

ABI3, a component of the WAVE2 complex, is potentially regulated by PI3K/AKT pathway

PubMed Central

Moraes, Lais; Zanchin, Nilson I.T.; Cerutti, Janete M.

2017-01-01

We previously reported that ABI3 expression is lost in follicular thyroid carcinomas and its restoration significantly inhibited cell growth, invasiveness, migration, and reduced tumor growth in vivo. The mechanistic basis by which ABI3 exerts its tumor suppressive effects is not fully understood. In this study, we show that ABI3 is a phosphoprotein. Using proteomic array analysis, we showed that ABI3 modulated distinct cancer-related pathways in thyroid cancer cells. The KEA analysis found that PI3K substrates were enriched and forced expression of ABI3 markedly decreased the phosphorylation of AKT and the downstream-targeted protein pGSK3β. We next used immunoprecipitation combined with mass spectrometry to identify ABI3-interacting proteins that may be involved in modulating/integrating signaling pathways. We identified 37 ABI3 partners, including several components of the canonical WAVE regulatory complex (WRC) such as WAVE2/CYF1P1/NAP1, suggesting that ABI3 function might be regulated through WRC. Both, pharmacological inhibition of the PI3K/AKT pathway and mutation at residue S342 of ABI3, which is predicted to be phosphorylated by AKT, provided evidences that the non-phosphorylated form of ABI3 is preferentially present in the WRC protein complex. Collectively, our findings suggest that ABI3 might be a downstream mediator of the PI3K/AKT pathway that might disrupt WRC via ABI3 phosphorylation. PMID:28978070

ABI3, a component of the WAVE2 complex, is potentially regulated by PI3K/AKT pathway.

PubMed

Moraes, Lais; Zanchin, Nilson I T; Cerutti, Janete M

2017-09-15

We previously reported that ABI3 expression is lost in follicular thyroid carcinomas and its restoration significantly inhibited cell growth, invasiveness, migration, and reduced tumor growth in vivo . The mechanistic basis by which ABI3 exerts its tumor suppressive effects is not fully understood. In this study, we show that ABI3 is a phosphoprotein. Using proteomic array analysis, we showed that ABI3 modulated distinct cancer-related pathways in thyroid cancer cells. The KEA analysis found that PI3K substrates were enriched and forced expression of ABI3 markedly decreased the phosphorylation of AKT and the downstream-targeted protein pGSK3β. We next used immunoprecipitation combined with mass spectrometry to identify ABI3-interacting proteins that may be involved in modulating/integrating signaling pathways. We identified 37 ABI3 partners, including several components of the canonical WAVE regulatory complex (WRC) such as WAVE2/CYF1P1/NAP1, suggesting that ABI3 function might be regulated through WRC. Both, pharmacological inhibition of the PI3K/AKT pathway and mutation at residue S342 of ABI3, which is predicted to be phosphorylated by AKT, provided evidences that the non-phosphorylated form of ABI3 is preferentially present in the WRC protein complex. Collectively, our findings suggest that ABI3 might be a downstream mediator of the PI3K/AKT pathway that might disrupt WRC via ABI3 phosphorylation.

Transcriptome analysis reveals enrichment of genes associated with auditory system in swimbladder of channel catfish.

PubMed

Yang, Yujia; Wang, Xiaozhu; Liu, Yang; Fu, Qiang; Tian, Changxu; Wu, Chenglong; Shi, Huitong; Yuan, Zihao; Tan, Suxu; Liu, Shikai; Gao, Dongya; Dunham, Rex; Liu, Zhanjiang

2018-04-30

In aquatic organisms, hearing is an important sense for acoustic communications and detection of sound-emitting predators and prey. Channel catfish is a dominant aquaculture species in the United States. As channel catfish can hear sounds of relatively high frequency, it serves as a good model for study auditory mechanisms. In catfishes, Weberian ossicles connect the swimbladder to the inner ear to transfer the forced vibrations and improve hearing ability. In this study, we examined the transcriptional profiles of channel catfish swimbladder and other four tissues (gill, liver, skin, and intestine). We identified a total of 1777 genes that exhibited preferential expression pattern in swimbladder of channel catfish. Based on Gene Ontology enrichment analysis, many of swimbladder-enriched genes were categorized into sensory perception of sound, auditory behavior, response to auditory stimulus, or detection of mechanical stimulus involved in sensory perception of sound, such as coch, kcnq4, sptbn1, sptbn4, dnm1, ush2a, and col11a1. Six signaling pathways associated with hearing (Glutamatergic synapse, GABAergic synapse pathways, Axon guidance, cAMP signaling pathway, Ionotropic glutamate receptor pathway, and Metabotropic glutamate receptor group III pathway) were over-represented in KEGG and PANTHER databases. Protein interaction prediction revealed an interactive relationship among the swimbladder-enriched genes and genes involved in sensory perception of sound. This study identified a set of genes and signaling pathways associated with auditory system in the swimbladder of channel catfish and provide resources for further study on the biological and physiological roles in catfish swimbladder. Copyright © 2018 Elsevier Inc. All rights reserved.

Title VII and Preferential Treatment: Response to EEOC Affirmative Action Guidelines.

ERIC Educational Resources Information Center

Schaffrau, Andrew J.

1979-01-01

Argues that Title VII prohibits preferential treatment of any group unless ordered by a court pursuant to a judicial finding of unlawful discrimination and unless the preferential treatment is limited to providing relief to judicially identified victims of that discrimination. Available from Georgetown Law Journal, 600 New Jersey Avenue,…

Estimating Preferential Flow in Karstic Aquifers Using Statistical Mixed Models

PubMed Central

Anaya, Angel A.; Padilla, Ingrid; Macchiavelli, Raul; Vesper, Dorothy J.; Meeker, John D.; Alshawabkeh, Akram N.

2013-01-01

Karst aquifers are highly productive groundwater systems often associated with conduit flow. These systems can be highly vulnerable to contamination, resulting in a high potential for contaminant exposure to humans and ecosystems. This work develops statistical models to spatially characterize flow and transport patterns in karstified limestone and determines the effect of aquifer flow rates on these patterns. A laboratory-scale Geo-HydroBed model is used to simulate flow and transport processes in a karstic limestone unit. The model consists of stainless-steel tanks containing a karstified limestone block collected from a karst aquifer formation in northern Puerto Rico. Experimental work involves making a series of flow and tracer injections, while monitoring hydraulic and tracer response spatially and temporally. Statistical mixed models are applied to hydraulic data to determine likely pathways of preferential flow in the limestone units. The models indicate a highly heterogeneous system with dominant, flow-dependent preferential flow regions. Results indicate that regions of preferential flow tend to expand at higher groundwater flow rates, suggesting a greater volume of the system being flushed by flowing water at higher rates. Spatial and temporal distribution of tracer concentrations indicates the presence of conduit-like and diffuse flow transport in the system, supporting the notion of both combined transport mechanisms in the limestone unit. The temporal response of tracer concentrations at different locations in the model coincide with, and confirms the preferential flow distribution generated with the statistical mixed models used in the study. PMID:23802921

Estimating preferential flow in karstic aquifers using statistical mixed models.

PubMed

Anaya, Angel A; Padilla, Ingrid; Macchiavelli, Raul; Vesper, Dorothy J; Meeker, John D; Alshawabkeh, Akram N

2014-01-01

Karst aquifers are highly productive groundwater systems often associated with conduit flow. These systems can be highly vulnerable to contamination, resulting in a high potential for contaminant exposure to humans and ecosystems. This work develops statistical models to spatially characterize flow and transport patterns in karstified limestone and determines the effect of aquifer flow rates on these patterns. A laboratory-scale Geo-HydroBed model is used to simulate flow and transport processes in a karstic limestone unit. The model consists of stainless steel tanks containing a karstified limestone block collected from a karst aquifer formation in northern Puerto Rico. Experimental work involves making a series of flow and tracer injections, while monitoring hydraulic and tracer response spatially and temporally. Statistical mixed models (SMMs) are applied to hydraulic data to determine likely pathways of preferential flow in the limestone units. The models indicate a highly heterogeneous system with dominant, flow-dependent preferential flow regions. Results indicate that regions of preferential flow tend to expand at higher groundwater flow rates, suggesting a greater volume of the system being flushed by flowing water at higher rates. Spatial and temporal distribution of tracer concentrations indicates the presence of conduit-like and diffuse flow transport in the system, supporting the notion of both combined transport mechanisms in the limestone unit. The temporal response of tracer concentrations at different locations in the model coincide with, and confirms the preferential flow distribution generated with the SMMs used in the study. © 2013, National Ground Water Association.

Addition of nitromethane to a disilene and a digermene: comparison to surface reactivity and the facile formation of 1,3,2-dioxazolidines.

PubMed

Tashkandi, Nada Y; Parsons, Frederick; Guo, Jiacheng; Baines, Kim M

2015-01-26

The addition of nitromethane to tetramesityldisilene and tetramesityldigermene leads to the formation of the novel 1,3,2,4,5-dioxazadisil- and digermolidine ring systems, respectively. The 1,3,2,4,5-dioxazadisilolidine isomerizes to the 1,4,2,3,5-dioxazadisilolidine ring system, whereas the 1,3,2,4,5-dioxazadigermolidine undergoes ring opening to the isomeric oxime. The preferential formation of the 1,3,2,4,5-dioxazadisilolidine, and its rearrangement to a 1,4,2,3,5-dioxazadisilolidine, provides support for the suggested reaction pathway between nitromethane and the Si(100) 2×1 reconstructed surface. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Surface geophysics and porewater evaluation at the Lower Darby Creek Area Superfund Site, Philadelphia, Pennsylvania, 2013

USGS Publications Warehouse

Walker, Charles W.; Degnan, James R.; Brayton, Michael J.; Cruz, Roberto M.; Lorah, Michelle M.

2015-01-01

In cooperation with the U.S. Environmental Protection Agency (EPA), Region 3, the U.S. Geological Survey (USGS) is participating in an ongoing study to aid in the identification of subsurface heterogeneities that may act as preferential pathways for contaminant transport in and around the Lower Darby Creek Area (LDCA) Superfund Site, Philadelphia Pa. Lower Darby Creek, which flows into the Delaware River, borders the western part of the former landfill site. In 2013, the USGS conducted surface geophysics measurements and stream porewater sampling to provide additional data for EPA’s site characterization. This report contains data collected from field measurements of direct current (DC) resistivity, frequency-domain electromagnetic (FDEM) surveys, and stream porewater specific conductance (SC).

A Novel Role for Banana MaASR in the Regulation of Flowering Time in Transgenic Arabidopsis

PubMed Central

Yu, Xiaomeng; Jia, Caihong; Liu, Juhua; Zhang, Jianbin; Wang, Jingyi; Wang, Zhuo; Wang, Anbang; Xu, Biyu; Jin, Zhiqiang

2016-01-01

The abscisic acid (ABA)-, stress-, and ripening-induced (ASR) protein is a plant-specific hydrophilic transcriptional factor involved in fruit ripening and the abiotic stress response. To date, there have been no studies on the role of ASR genes in delayed flowering time. Here, we found that the ASR from banana, designated as MaASR, was preferentially expressed in the banana female flowers from the eighth, fourth, and first cluster of the inflorescence. MaASR transgenic lines (L14 and L38) had a clear delayed-flowering phenotype. The number of rosette leaves, sepals, and pedicel trichomes in L14 and L38 was greater than in the wild type (WT) under long day (LD) conditions. The period of buds, mid-flowers, and full bloom of L14 and L38 appeared later than the WT. cDNA microarray and quantitative real-time PCR (qRT-PCR) analyses revealed that overexpression of MaASR delays flowering through reduced expression of several genes, including photoperiod pathway genes, vernalization pathway genes, gibberellic acid pathway genes, and floral integrator genes, under short days (SD) for 28 d (from vegetative to reproductive transition stage); however, the expression of the autonomous pathway genes was not affected. This study provides the first evidence of a role for ASR genes in delayed flowering time in plants. PMID:27486844

A Novel Role for Banana MaASR in the Regulation of Flowering Time in Transgenic Arabidopsis.

PubMed

Sun, Peiguang; Miao, Hongxia; Yu, Xiaomeng; Jia, Caihong; Liu, Juhua; Zhang, Jianbin; Wang, Jingyi; Wang, Zhuo; Wang, Anbang; Xu, Biyu; Jin, Zhiqiang

2016-01-01

The abscisic acid (ABA)-, stress-, and ripening-induced (ASR) protein is a plant-specific hydrophilic transcriptional factor involved in fruit ripening and the abiotic stress response. To date, there have been no studies on the role of ASR genes in delayed flowering time. Here, we found that the ASR from banana, designated as MaASR, was preferentially expressed in the banana female flowers from the eighth, fourth, and first cluster of the inflorescence. MaASR transgenic lines (L14 and L38) had a clear delayed-flowering phenotype. The number of rosette leaves, sepals, and pedicel trichomes in L14 and L38 was greater than in the wild type (WT) under long day (LD) conditions. The period of buds, mid-flowers, and full bloom of L14 and L38 appeared later than the WT. cDNA microarray and quantitative real-time PCR (qRT-PCR) analyses revealed that overexpression of MaASR delays flowering through reduced expression of several genes, including photoperiod pathway genes, vernalization pathway genes, gibberellic acid pathway genes, and floral integrator genes, under short days (SD) for 28 d (from vegetative to reproductive transition stage); however, the expression of the autonomous pathway genes was not affected. This study provides the first evidence of a role for ASR genes in delayed flowering time in plants.

Striatopallidal dysfunction underlies repetitive behavior in Shank3-deficient model of autism

PubMed Central

Wang, Wenting; Li, Chenchen; Chen, Qian; Hawrot, James; Yao, Annie Y.; Gao, Xian; Lu, Congyi; Zang, Ying; Lyman, Katherine; Wang, Dongqing; Guo, Baolin; Wu, Shengxi; Gerfen, Charles R.; Fu, Zhanyan

2017-01-01

The postsynaptic scaffolding protein SH3 and multiple ankyrin repeat domains 3 (SHANK3) is critical for the development and function of glutamatergic synapses. Disruption of the SHANK3-encoding gene has been strongly implicated as a monogenic cause of autism, and Shank3 mutant mice show repetitive grooming and social interaction deficits. Although basal ganglia dysfunction has been proposed to underlie repetitive behaviors, few studies have provided direct evidence to support this notion and the exact cellular mechanisms remain largely unknown. Here, we utilized the Shank3B mutant mouse model of autism to investigate how Shank3 mutation may differentially affect striatonigral (direct pathway) and striatopallidal (indirect pathway) medium spiny neurons (MSNs) and its relevance to repetitive grooming behavior in Shank3B mutant mice. We found that Shank3 deletion preferentially affects synapses onto striatopallidal MSNs. Striatopallidal MSNs showed profound defects, including alterations in synaptic transmission, synaptic plasticity, and spine density. Importantly, the repetitive grooming behavior was rescued by selectively enhancing the striatopallidal MSN activity via a Gq-coupled human M3 muscarinic receptor (hM3Dq), a type of designer receptors exclusively activated by designer drugs (DREADD). Our findings directly demonstrate the existence of distinct changes between 2 striatal pathways in a mouse model of autism and indicate that the indirect striatal pathway disruption might play a causative role in repetitive behavior of Shank3B mutant mice. PMID:28414301

NRASG12V oncogene facilitates self-renewal in a murine model of acute myelogenous leukemia

PubMed Central

LaRue, Rebecca S.; Nguyen, Hanh T.; Sachs, Karen; Noble, Klara E.; Mohd Hassan, Nurul Azyan; Diaz-Flores, Ernesto; Rathe, Susan K.; Sarver, Aaron L.; Bendall, Sean C.; Ha, Ngoc A.; Diers, Miechaleen D.; Nolan, Garry P.; Shannon, Kevin M.; Largaespada, David A.

2014-01-01

Mutant RAS oncoproteins activate signaling molecules that drive oncogenesis in multiple human tumors including acute myelogenous leukemia (AML). However, the specific functions of these pathways in AML are unclear, thwarting the rational application of targeted therapeutics. To elucidate the downstream functions of activated NRAS in AML, we used a murine model that harbors Mll-AF9 and a tetracycline-repressible, activated NRAS (NRASG12V). Using computational approaches to explore our gene-expression data sets, we found that NRASG12V enforced the leukemia self-renewal gene-expression signature and was required to maintain an MLL-AF9– and Myb-dependent leukemia self-renewal gene-expression program. NRASG12V was required for leukemia self-renewal independent of its effects on growth and survival. Analysis of the gene-expression patterns of leukemic subpopulations revealed that the NRASG12V-mediated leukemia self-renewal signature is preferentially expressed in the leukemia stem cell–enriched subpopulation. In a multiplexed analysis of RAS-dependent signaling, Mac-1Low cells, which harbor leukemia stem cells, were preferentially sensitive to NRASG12V withdrawal. NRASG12V maintained leukemia self-renewal through mTOR and MEK pathway activation, implicating these pathways as potential targets for cancer stem cell–specific therapies. Together, these experimental results define a RAS oncogene–driven function that is critical for leukemia maintenance and represents a novel mechanism of oncogene addiction. PMID:25316678

Divergent Human Cortical Regions for Processing Distinct Acoustic-Semantic Categories of Natural Sounds: Animal Action Sounds vs. Vocalizations

PubMed Central

Webster, Paula J.; Skipper-Kallal, Laura M.; Frum, Chris A.; Still, Hayley N.; Ward, B. Douglas; Lewis, James W.

2017-01-01

A major gap in our understanding of natural sound processing is knowledge of where or how in a cortical hierarchy differential processing leads to categorical perception at a semantic level. Here, using functional magnetic resonance imaging (fMRI) we sought to determine if and where cortical pathways in humans might diverge for processing action sounds vs. vocalizations as distinct acoustic-semantic categories of real-world sound when matched for duration and intensity. This was tested by using relatively less semantically complex natural sounds produced by non-conspecific animals rather than humans. Our results revealed a striking double-dissociation of activated networks bilaterally. This included a previously well described pathway preferential for processing vocalization signals directed laterally from functionally defined primary auditory cortices to the anterior superior temporal gyri, and a less well-described pathway preferential for processing animal action sounds directed medially to the posterior insulae. We additionally found that some of these regions and associated cortical networks showed parametric sensitivity to high-order quantifiable acoustic signal attributes and/or to perceptual features of the natural stimuli, such as the degree of perceived recognition or intentional understanding. Overall, these results supported a neurobiological theoretical framework for how the mammalian brain may be fundamentally organized to process acoustically and acoustic-semantically distinct categories of ethologically valid, real-world sounds. PMID:28111538

Differential Expression Patterns of occ1-Related Genes in Adult Monkey Visual Cortex

PubMed Central

Takahata, Toru; Komatsu, Yusuke; Watakabe, Akiya; Hashikawa, Tsutomu; Tochitani, Shiro

2009-01-01

We have previously revealed that occ1 is preferentially expressed in the primary visual area (V1) of the monkey neocortex. In our attempt to identify more area-selective genes in the macaque neocortex, we found that testican-1, an occ1-related gene, and its family members also exhibit characteristic expression patterns along the visual pathway. The expression levels of testican-1 and testican-2 mRNAs as well as that of occ1 mRNA start of high in V1, progressively decrease along the ventral visual pathway, and end of low in the temporal areas. Complementary to them, the neuronal expression of SPARC mRNA is abundant in the association areas and scarce in V1. Whereas occ1, testican-1, and testican-2 mRNAs are preferentially distributed in thalamorecipient layers including “blobs,” SPARC mRNA expression avoids these layers. Neither SC1 nor testican-3 mRNA expression is selective to particular areas, but SC1 mRNA is abundantly observed in blobs. The expressions of occ1, testican-1, testican-2, and SC1 mRNA were downregulated after monocular tetrodotoxin injection. These results resonate with previous works on chemical and functional gradients along the primate occipitotemporal visual pathway and raise the possibility that these gradients and functional architecture may be related to the visual activity–dependent expression of these extracellular matrix glycoproteins. PMID:19073625

Hydraulic and geochemical framework of the Idaho National Engineering and Environmental Laboratory vadose zone

USGS Publications Warehouse

Nimmo, John R.; Rousseau, Joseph P.; Perkins, Kim S.; Stollenwerk, Kenneth G.; Glynn, Pierre D.; Bartholomay, Roy C.; Knobel, LeRoy L.

2004-01-01

Questions of major importance for subsurface contaminant transport at the Idaho National Engineering and Environmental Laboratory (INEEL) include (i) travel times to the aquifer, both average or typical values and the range of values to be expected, and (ii) modes of contaminant transport, especially sorption processes. The hydraulic and geochemical framework within which these questions are addressed is dominated by extreme heterogeneity in a vadose zone and aquifer consisting of interbedded basalts and sediments. Hydraulically, major issues include diverse possible types of flow pathways, extreme anisotropy, preferential flow, combined vertical and horizontal flow, and temporary saturation or perching. Geochemically, major issues include contaminant mobility as influenced by redox conditions, the concentration of organic and inorganic complexing solutes and other local variables, the interaction with infiltrating waters and with the contaminant source environment, and the aqueous speciation of contaminants such as actinides. Another major issue is the possibility of colloid transport, which inverts some of the traditional concepts of mobility, as sorbed contaminants on mobile colloids may be transported with ease compared with contaminants that are not sorbed. With respect to the goal of minimizing aquifer concentrations of contaminants, some characteristics of the vadose zone are essentially completely favorable. Examples include the great thickness (200 m) of the vadose zone, and the presence of substantial quantities of fine sediments that can retard contaminant transport both hydraulically and chemically. Most characteristics, however, have both favorable and unfavorable aspects. For example, preferential flow, as promoted by several notable features of the vadose zone at the INEEL, can provide fast, minimally sorbing pathways for contaminants to reach the aquifer easily, but it also leads to a wide dispersal of contaminants in a large volume of subsurface material, thus increasing the opportunity for dilution and sorption.

Identification of pathway-biased and deleterious melatonin receptor mutants in autism spectrum disorders and in the general population.

PubMed

Chaste, Pauline; Clement, Nathalie; Mercati, Oriane; Guillaume, Jean-Luc; Delorme, Richard; Botros, Hany Goubran; Pagan, Cécile; Périvier, Samuel; Scheid, Isabelle; Nygren, Gudrun; Anckarsäter, Henrik; Rastam, Maria; Ståhlberg, Ola; Gillberg, Carina; Serrano, Emilie; Lemière, Nathalie; Launay, Jean Marie; Mouren-Simeoni, Marie Christine; Leboyer, Marion; Gillberg, Christopher; Jockers, Ralf; Bourgeron, Thomas

2010-07-15

Melatonin is a powerful antioxidant and a synchronizer of many physiological processes. Alteration of the melatonin pathway has been reported in circadian disorders, diabetes and autism spectrum disorders (ASD). However, very little is known about the genetic variability of melatonin receptors in humans. Here, we sequenced the melatonin receptor MTNR1A and MTNR1B, genes coding for MT1 and MT2 receptors, respectively, in a large panel of 941 individuals including 295 patients with ASD, 362 controls and 284 individuals from different ethnic backgrounds. We also sequenced GPR50, coding for the orphan melatonin-related receptor GPR50 in patients and controls. We identified six non-synonymous mutations for MTNR1A and ten for MTNR1B. The majority of these variations altered receptor function. Particularly interesting mutants are MT1-I49N, which is devoid of any melatonin binding and cell surface expression, and MT1-G166E and MT1-I212T, which showed severely impaired cell surface expression. Of note, several mutants possessed pathway-selective signaling properties, some preferentially inhibiting the adenylyl cyclase pathway, others preferentially activating the MAPK pathway. The prevalence of these deleterious mutations in cases and controls indicates that they do not represent major risk factor for ASD (MTNR1A case 3.6% vs controls 4.4%; MTNR1B case 4.7% vs 3% controls). Concerning GPR50, we detected a significant association between ASD and two variations, Delta502-505 and T532A, in affected males, but it did not hold up after Bonferonni correction for multiple testing. Our results represent the first functional ascertainment of melatonin receptors in humans and constitute a basis for future structure-function studies and for interpreting genetic data on the melatonin pathway in patients.

Chemoprevention with Cyclooxygenase and Epidermal Growth Factor Receptor Inhibitors in Familial Adenomatous Polyposis Patients: mRNA Signatures of Duodenal Neoplasia.

PubMed

Delker, Don A; Wood, Austin C; Snow, Angela K; Samadder, N Jewel; Samowitz, Wade S; Affolter, Kajsa E; Boucher, Kenneth M; Pappas, Lisa M; Stijleman, Inge J; Kanth, Priyanka; Byrne, Kathryn R; Burt, Randall W; Bernard, Philip S; Neklason, Deborah W

2018-01-01

To identify gene expression biomarkers and pathways targeted by sulindac and erlotinib given in a chemoprevention trial with a significant decrease in duodenal polyp burden at 6 months ( P < 0.001) in familial adenomatous polyposis (FAP) patients, we biopsied normal and polyp duodenal tissues from patients on drug versus placebo and analyzed the RNA expression. RNA sequencing was performed on biopsies from the duodenum of FAP patients obtained at baseline and 6-month endpoint endoscopy. Ten FAP patients on placebo and 10 on sulindac and erlotinib were selected for analysis. Purity of biopsied polyp tissue was calculated from RNA expression data. RNAs differentially expressed between endpoint polyp and paired baseline normal were determined for each group and mapped to biological pathways. Key genes in candidate pathways were further validated by quantitative RT-PCR. RNA expression analyses of endpoint polyp compared with paired baseline normal for patients on placebo and drug show that pathways activated in polyp growth and proliferation are blocked by this drug combination. Directly comparing polyp gene expression between patients on drug and placebo also identified innate immune response genes (IL12 and IFNγ) preferentially expressed in patients on drug. Gene expression analyses from tissue obtained at endpoint of the trial demonstrated inhibition of the cancer pathways COX2/PGE2, EGFR, and WNT. These findings provide molecular evidence that the drug combination of sulindac and erlotinib reached the intended tissue and was on target for the predicted pathways. Furthermore, activation of innate immune pathways from patients on drug may have contributed to polyp regression. Cancer Prev Res; 11(1); 4-15. ©2017 AACR See related editorial by Shureiqi, p. 1 . ©2017 American Association for Cancer Research.

Soil, Water, Plants and Preferred Flow in All Directions: A Biosphere-2 Experiment

NASA Astrophysics Data System (ADS)

McDonnell, J.; Evaristo, J. A.; Kim, M.; Van Haren, J. L. M.; Pangle, L. A.; Harman, C. J.; Troch, P. A. A.

2016-12-01

Measuring, understanding and predicting preferential flow in the critical zone is impossibly difficult, but we must try. While past work has focused on specific features of preferential flow pathways and model parameterizations, the resultant effect of preferential flow is often difficult to detect because we do not know the boundary conditions of our flow domain. Here we take a holistic view of preferential flow at the ecosystem level. We present new results from the tropical rainforest biome at Biosphere 2. We test the null hypothesis that the ecohydrological system is well mixed and that water forming groundwater recharge and plant transpiration is from a common pool. Our specific research question is what is the nature of preferential flow and partitioning of groundwater recharge, soil water recharge, and transpiration water after rainfall events? We performed a 10-week drought experiment and then added 66 mm of labelled rainfall with 152‰ deuterium (D), distributed over four events (mean 16.5 mm per event). This was followed by a total of 87 mm of rainfall (-60‰ D) distributed over 13 events that were spaced every 2-3 days. Our results show that flow in all ecohydrological domains (soil water, groundwater recharge and plant transpiration) was preferential. With known boundary conditions, we found that groundwater recharge was 3-8 times younger ( 8 days) than transpired water (range 24-64 days). The "age" of transpired water showed strong dependence on species and was intimately linked to driving force (difference between soil matric potential and midday leaf water potential). These results suggest that preferential flow in the critical zone is one whereby transpiration is strongly species-dependent, and groundwater recharge is controlled by inherent subsurface heterogeneity. The marked difference in the ages associated with these two fluxes supports the concept of ecohydrological separation—in this case, in a `time-based' context.

Characterization of preferential flow pathways in a siliciclastic aquifer system using human enteric viruses and groundwater geochemistry

USDA-ARS?s Scientific Manuscript database

Human enteric viruses have been recognized as an emerging groundwater contaminant and are found only in human waste. In urban environments the most likely source of human waste is from sanitary sewers. Determining the travel time for near-surface contaminants to reach deep public supply wells is i...

A Synthetic Recursive “+1” Pathway for Carbon Chain Elongation

PubMed Central

Marcheschi, Ryan J.; Li, Han; Zhang, Kechun; Noey, Elizabeth L.; Kim, Seonah; Chaubey, Asha; Houk, K. N.; Liao, James C.

2013-01-01

Nature uses four methods of carbon chain elongation for the production of 2-ketoacids, fatty acids, polyketides, and isoprenoids. Using a combination of quantum mechanical (QM) modeling, protein–substrate modeling, and protein and metabolic engineering, we have engineered the enzymes involved in leucine biosynthesis for use as a synthetic “+1” recursive metabolic pathway to extend the carbon chain of 2-ketoacids. This modified pathway preferentially selects longer-chain substrates for catalysis, as compared to the non-recursive natural pathway, and can recursively catalyze five elongation cycles to synthesize bulk chemicals, such as 1-heptanol, 1-octanol, and phenylpropanol directly from glucose. The “+1” chemistry is a valuable metabolic tool in addition to the “+5” chemistry and “+2” chemistry for the biosynthesis of isoprenoids, fatty acids, or polyketides. PMID:22242720

Towards a Validation of the Three Pathways Model of Pathological Gambling.

PubMed

Valleur, Marc; Codina, Irène; Vénisse, Jean-Luc; Romo, Lucia; Magalon, David; Fatséas, Mélina; Chéreau-Boudet, Isabelle; Gorsane, Mohamed-Ali; Guilleux, Alice; Grall-Bronnec, Marie; Challet-Bouju, Gaëlle

2016-06-01

With the aim of validating the three pathways hypothesis of pathological gambling (Blaszczynski and Nower in Addiction 97:487-499, 2002) 372 pathological gamblers meeting DSM IV (2000) criteria were assessed via a structured clinical interview as well as being subjected to personality tests and evaluation of their gambling practices. Our results show that it is possible to identify three subgroups corresponding to the three pathways: behaviourally conditioned problem gamblers, emotionally vulnerable problem gamblers and antisocial impulsivist problem gamblers. Our results particularly demonstrate that impulsivist gamblers preferentially choose semi-skilful gambling (horse racing and sports gambling) whereas emotionally vulnerable gamblers are significantly more attracted to games of chance (one-armed bandits, scratch cards, etc.) This led us to propose a functional presentation of the three pathways model which differs somewhat from the Blaszczynski and Nower presentation.

Zebrafish sex: a complicated affair

PubMed Central

Liew, Woei Chang

2014-01-01

In this review, we provide a detailed overview of studies on the elusive sex determination (SD) and gonad differentiation mechanisms of zebrafish (Danio rerio). We show that the data obtained from most studies are compatible with polygenic sex determination (PSD), where the decision is made by the allelic combinations of several loci. These loci are typically dispersed throughout the genome, but in some teleost species a few of them might be located on a preferential pair of (sex) chromosomes. The PSD system has a much higher level of variation of SD genotypes both at the level of gametes and the sexual genotype of individuals, than that of the chromosomal sex determination systems. The early sexual development of zebrafish males is a complicated process, as they first develop a ‘juvenile ovary’, that later undergoes a transformation to give way to a testis. To date, three major developmental pathways were shown to be involved with gonad differentiation through the modulation of programmed cell death. In our opinion, there are more pathways participating in the regulation of zebrafish gonad differentiation/transformation. Introduction of additional powerful large-scale genomic approaches into the analysis of zebrafish reproduction will result in further deepening of our knowledge as well as identification of additional pathways and genes associated with these processes in the near future. PMID:24148942

PINK1/Parkin-Dependent Mitochondrial Surveillance: From Pleiotropy to Parkinson's Disease

PubMed Central

Mouton-Liger, Francois; Jacoupy, Maxime; Corvol, Jean-Christophe; Corti, Olga

2017-01-01

Parkinson's disease (PD) is one of the most frequent neurodegenerative disease caused by the preferential, progressive degeneration of the dopaminergic (DA) neurons of the substantia nigra (SN) pars compacta. PD is characterized by a multifaceted pathological process involving protein misfolding, mitochondrial dysfunction, neuroinflammation and metabolism deregulation. The molecular mechanisms governing the complex interplay between the different facets of this process are still unknown. PARK2/Parkin and PARK6/PINK1, two genes responsible for familial forms of PD, act as a ubiquitous core signaling pathway, coupling mitochondrial stress to mitochondrial surveillance, by regulating mitochondrial dynamics, the removal of damaged mitochondrial components by mitochondria-derived vesicles, mitophagy, and mitochondrial biogenesis. Over the last decade, PINK1/Parkin-dependent mitochondrial quality control emerged as a pleiotropic regulatory pathway. Loss of its function impinges on a number of physiological processes suspected to contribute to PD pathogenesis. Its role in the regulation of innate immunity and inflammatory processes stands out, providing compelling support to the contribution of non-cell-autonomous immune mechanisms in PD. In this review, we illustrate the central role of this multifunctional pathway at the crossroads between mitochondrial stress, neuroinflammation and metabolism. We discuss how its dysfunction may contribute to PD pathogenesis and pinpoint major unresolved questions in the field. PMID:28507507

Metabolome analysis-based design and engineering of a metabolic pathway in Corynebacterium glutamicum to match rates of simultaneous utilization of D-glucose and L-arabinose.

PubMed

Kawaguchi, Hideo; Yoshihara, Kumiko; Hara, Kiyotaka Y; Hasunuma, Tomohisa; Ogino, Chiaki; Kondo, Akihiko

2018-05-17

L-Arabinose is the second most abundant component of hemicellulose in lignocellulosic biomass, next to D-xylose. However, few microorganisms are capable of utilizing pentoses, and catabolic genes and operons enabling bacterial utilization of pentoses are typically subject to carbon catabolite repression by more-preferred carbon sources, such as D-glucose, leading to a preferential utilization of D-glucose over pentoses. In order to simultaneously utilize both D-glucose and L-arabinose at the same rate, a modified metabolic pathway was rationally designed based on metabolome analysis. Corynebacterium glutamicum ATCC 31831 utilized D-glucose and L-arabinose simultaneously at a low concentration (3.6 g/L each) but preferentially utilized D-glucose over L-arabinose at a high concentration (15 g/L each), although L-arabinose and D-glucose were consumed at comparable rates in the absence of the second carbon source. Metabolome analysis revealed that phosphofructokinase and pyruvate kinase were major bottlenecks for D-glucose and L-arabinose metabolism, respectively. Based on the results of metabolome analysis, a metabolic pathway was engineered by overexpressing pyruvate kinase in combination with deletion of araR, which encodes a repressor of L-arabinose uptake and catabolism. The recombinant strain utilized high concentrations of D-glucose and L-arabinose (15 g/L each) at the same consumption rate. During simultaneous utilization of both carbon sources at high concentrations, intracellular levels of phosphoenolpyruvate declined and acetyl-CoA levels increased significantly as compared with the wild-type strain that preferentially utilized D-glucose. These results suggest that overexpression of pyruvate kinase in the araR deletion strain increased the specific consumption rate of L-arabinose and that citrate synthase activity becomes a new bottleneck in the engineered pathway during the simultaneous utilization of D-glucose and L-arabinose. Metabolome analysis identified potential bottlenecks in D-glucose and L-arabinose metabolism and was then applied to the following rational metabolic engineering. Manipulation of only two genes enabled simultaneous utilization of D-glucose and L-arabinose at the same rate in metabolically engineered C. glutamicum. This is the first report of rational metabolic design and engineering for simultaneous hexose and pentose utilization without inactivating the phosphotransferase system.

Preferential dealkylation reactions of s-triazine herbicides in the unsaturated zone

USGS Publications Warehouse

Mills, M.S.; Michael, Thurman E.

1994-01-01

The preferential dealkylation pathways of the s-triazine herbicides, atrazine (2-chloro-4-ethylamino-6-isopropylamino-s-triazine), propazine [2-chloro-4,6-bis(isopropylamino)-s-triazine], and simazine [2-chloro-4,6-bis(ethylamino)-s-triazine], and two monodealkylated triazine metabolites, deisopropylatrazine (DIA: 2-amino-4-chloro-6-ethylamino-s-triazine) and deethylatrazine (DEA: 2-amino-4-chloro-6-isopropylamino-s-triazine) were investigated on two adjacent Eudora silt-loam plots growing corn (Zea mays L.). Results from the shallow unsaturated zone and surface-water runoff showed preferential removal of an ethyl side chain from atrazine, simazine, and DIA relative to an isopropyl side chain from atrazine, propazine, and DEA. It is hypothesized that deethylation reactions may proceed at 2-3 times the rate of deisopropylation reactions. It is concluded that small concentrations of DIA reportedly associated with the degradation of atrazine may be due to a rapid turnover rate of the metabolite in the unsaturated zone, not to small production levels. Because of continued dealkylation of both monodealkylated metabolites, a strong argument is advanced for the presence of a didealkylated metabolite in the unsaturated zone.

Nuclear organization of nucleotide excision repair is mediated by RING1B dependent H2A-ubiquitylation

PubMed Central

Chitale, Shalaka; Richly, Holger

2017-01-01

One of the major cellular DNA repair pathways is nucleotide excision repair (NER). It is the primary pathway for repair of various DNA lesions caused by exposure to ultraviolet (UV) light, such as cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts. Although lesion-containing DNA associates with the nuclear matrix after UV irradiation it is still not understood how nuclear organization affects NER. Analyzing unscheduled DNA synthesis (UDS) indicates that NER preferentially occurs in specific nuclear areas, viz the nucleolus. Upon inducing localized damage, we observe migration of damaged DNA towards the nucleolus. Employing a LacR-based tethering system we demonstrate that H2A-ubiquitylation via the UV-RING1B complex localizes chromatin close to the nucleolus. We further show that the H2A-ubiquitin binding protein ZRF1 resides in the nucleolus, and that it anchors ubiquitylated chromatin along with XPC. Our data thus provide insight into the sub-nuclear organization of NER and reveal a novel role for histone H2A-ubiquitylation. PMID:28416769

Mixed matrix membranes with fast and selective transport pathways for efficient CO2 separation

NASA Astrophysics Data System (ADS)

Hou, Jinpeng; Li, Xueqin; Guo, Ruili; Zhang, Jianshu; Wang, Zhongming

2018-03-01

To improve CO2 separation performance, porous carbon nanosheets (PCNs) were used as a filler into a Pebax MH 1657 (Pebax) matrix, fabricating mixed matrix membranes (MMMs). The PCNs exhibited a preferential horizontal orientation within the Pebax matrix because of the extremely large 2D plane and nanoscale thickness of the matrix. Therefore, the micropores of the PCNs provided fast CO2 transport pathways, which led to increased CO2 permeability. The reduced pore size of the PCNs was a consequence of the overlapping of PCNs and the polymer chains penetrating into the pores of the PCNs. The reduction in the pore size of the PCNs improved the CO2/gas selectivity. As a result, the CO2 permeability and CO2/CH4 selectivity of the Pebax membrane with 10 wt% PCNs-loading (Pebax-PCNs-10) were 520 barrer and 51, respectively, for CO2/CH4 mixed-gas. The CO2 permeability and CO2/N2 selectivity of the Pebax-PCNs-10 membrane were 614 barrer and 61, respectively, for CO2/N2 mixed-gas.

Classical non-homologous end-joining pathway utilizes nascent RNA for error-free double-strand break repair of transcribed genes

PubMed Central

Chakraborty, Anirban; Tapryal, Nisha; Venkova, Tatiana; Horikoshi, Nobuo; Pandita, Raj K.; Sarker, Altaf H.; Sarkar, Partha S.; Pandita, Tej K.; Hazra, Tapas K.

2016-01-01

DNA double-strand breaks (DSBs) leading to loss of nucleotides in the transcribed region can be lethal. Classical non-homologous end-joining (C-NHEJ) is the dominant pathway for DSB repair (DSBR) in adult mammalian cells. Here we report that during such DSBR, mammalian C-NHEJ proteins form a multiprotein complex with RNA polymerase II and preferentially associate with the transcribed genes after DSB induction. Depletion of C-NHEJ factors significantly abrogates DSBR in transcribed but not in non-transcribed genes. We hypothesized that nascent RNA can serve as a template for restoring the missing sequences, thus allowing error-free DSBR. We indeed found pre-mRNA in the C-NHEJ complex. Finally, when a DSB-containing plasmid with several nucleotides deleted within the E. coli lacZ gene was allowed time to repair in lacZ-expressing mammalian cells, a functional lacZ plasmid could be recovered from control but not C-NHEJ factor-depleted cells, providing important mechanistic insights into C-NHEJ-mediated error-free DSBR of the transcribed genome. PMID:27703167

Subunit- and pathway-specific localization of NMDA receptors and scaffolding proteins at ganglion cell synapses in rat retina

PubMed Central

Zhang, Jun; Diamond, Jeffrey S.

2014-01-01

Retinal ganglion cells (RGCs) receive excitatory glutamatergic input from ON and OFF bipolar cells in distinct sublaminae of the inner plexiform layer (IPL). AMPA and NMDA receptors (AMPARs and NMDARs) mediate excitatory inputs in both synaptic layers, but specific roles for NMDARs at RGC synapses remain unclear. NMDARs comprise NR1 and NR2 subunits and are anchored by membrane associated guanylate kinases (MAGUKs), but it is unknown whether particular NR2 subunits associate preferentially with particular NR1 splice variants and MAGUKs. Here, we used postembedding immunogold electron microscopy (EM) techniques to examine the subsynaptic localization of NMDAR subunits and MAGUKs at ON and OFF synapses onto rat RGCs. We found that the NR2A subunit, the NR1C2‘ splice variant and MAGUKs PSD-95 and PSD-93 are localized to the postsynaptic density (PSD), preferentially at OFF synapses, whereas the NR2B subunit, the NR1C2 splice variant and the MAGUK SAP102 are localized perisynaptically, with NR2B exhibiting a preference for ON synapses. Consistent with these anatomical data, spontaneous EPSCs (sEPSCs) recorded from OFF cells exhibited an NMDAR component that was insensitive to the NR2B antagonist Ro 25-6981. In ON cells, sEPSCs expressed an NMDAR component, partially sensitive to Ro 25-6981, only when glutamate transport was inhibited, indicating perisynaptic expression of NR2B NMDARs. These results provide the first evidence for preferential association of particular NR1 splice variants, NR2 subunits and MAGUKs at central synapses and suggest that different NMDAR subtypes may play specific roles at functionally distinct synapses in the retinal circuitry. PMID:19339621

Pre-ordering of interfacial water in the pathway of heterogeneous ice nucleation does not lead to a two-step crystallization mechanism.

PubMed

Lupi, Laura; Peters, Baron; Molinero, Valeria

2016-12-07

According to Classical Nucleation Theory (CNT), the transition from liquid to crystal occurs in a single activated step with a transition state controlled by the size of the crystal embryo. This picture has been challenged in the last two decades by several reports of two-step crystallization processes in which the liquid first produces pre-ordered or dense domains, within which the crystal nucleates in a second step. Pre-ordering preceding crystal nucleation has been recently reported in simulations of ice crystallization, raising the question of whether the mechanism of ice nucleation involves two steps. In this paper, we investigate the heterogeneous nucleation of ice on carbon surfaces. We use molecular simulations with efficient coarse-grained models combined with rare event sampling methods and free energy calculations to elucidate the role of pre-ordering of liquid water at the carbon surface in the reaction coordinate for heterogeneous nucleation. We find that ice nucleation proceeds through a classical mechanism, with a single barrier between liquid and crystal. The reaction coordinate that determines the crossing of the nucleation barrier is the size of the crystal nucleus, as predicted by CNT. Wetting of the critical ice nuclei within pre-ordered domains decreases the nucleation barrier, increasing the nucleation rates. The preferential pathway for crystallization involves the early creation of pre-ordered domains that are the birthplace of the ice crystallites but do not represent a minimum in the free energy pathway from liquid to ice. We conclude that a preferential pathway through an intermediate-order precursor does not necessarily result in a two-step mechanism.

Identification of candidate genes affecting Δ9-tetrahydrocannabinol biosynthesis in Cannabis sativa

PubMed Central

Marks, M. David; Tian, Li; Wenger, Jonathan P.; Omburo, Stephanie N.; Soto-Fuentes, Wilfredo; He, Ji; Gang, David R.; Weiblen, George D.; Dixon, Richard A.

2009-01-01

RNA isolated from the glands of a Δ9-tetrahydrocannabinolic acid (THCA)-producing strain of Cannabis sativa was used to generate a cDNA library containing over 100 000 expressed sequence tags (ESTs). Sequencing of over 2000 clones from the library resulted in the identification of over 1000 unigenes. Candidate genes for almost every step in the biochemical pathways leading from primary metabolites to THCA were identified. Quantitative PCR analysis suggested that many of the pathway genes are preferentially expressed in the glands. Hexanoyl-CoA, one of the metabolites required for THCA synthesis, could be made via either de novo fatty acids synthesis or via the breakdown of existing lipids. qPCR analysis supported the de novo pathway. Many of the ESTs encode transcription factors and two putative MYB genes were identified that were preferentially expressed in glands. Given the similarity of the Cannabis MYB genes to those in other species with known functions, these Cannabis MYBs may play roles in regulating gland development and THCA synthesis. Three candidates for the polyketide synthase (PKS) gene responsible for the first committed step in the pathway to THCA were characterized in more detail. One of these was identical to a previously reported chalcone synthase (CHS) and was found to have CHS activity. All three could use malonyl-CoA and hexanoyl-CoA as substrates, including the CHS, but reaction conditions were not identified that allowed for the production of olivetolic acid (the proposed product of the PKS activity needed for THCA synthesis). One of the PKS candidates was highly and specifically expressed in glands (relative to whole leaves) and, on the basis of these expression data, it is proposed to be the most likely PKS responsible for olivetolic acid synthesis in Cannabis glands. PMID:19581347

Preferential flow in connected soil structures and the principle of "maximum energy dissipation": A thermodynamic perspective

NASA Astrophysics Data System (ADS)

Zehe, E.; Blume, T.; Bloeschl, G.

2009-04-01

"There is preferential flow at all scales"? This was a key message in a talk on ?Idle thoughts on a unifying theory of catchment hydrology? given by Bloeschl (2006). In this context ?preferential flow? was used to address rapid water flow along spatially connected flow paths of minimum flow resistance. Preferential flow seems in fact rather the rule than the exception. It occurs locally in non capillary macropores, at the hillslope scale in surface rills or through subsurface pipes. Rapid flow in connected biopores or sometimes shrinkage cracks is today accepted to play a key role for transport of agrochemicals in cohesive soils. The spatial distribution of worm burrows in the landscape may, furthermore, exert crucial control on rainfall runoff response and sediment yields at the hillslope and catchment scales. However, even if the population of connected biopores/macropores is known in soil we struggle in predicting onset, timing and strength of preferential flow events. Preferential flow is an intermittent, threshold phenomenon. Onset and intensity seems to be determined by the strength of the rainfall forcing and the wetness state of the soil. Furthermore, burrows of deep digging aenecic earthworms can ? even when being abandoned ? persist over decades as suggested by accumulation of clay particles or even radio nuclides. Thus, these structures ?survive? severe rainfall and subsurface flow events and still remain functional in the hydrological system. Why is it sometimes ?favourable? to take flow paths of minimum flow resistance and sometimes not? Why do these flow paths/ structures persist such a long time? Following Kleidon and Schimansky (2008) we suggest that a thermodynamic perspective ? looking at soil water flow as dissipative process in an open, non equilibrium thermodynamic system ? may help unrevealing these questions. However, we suggest a complementary perspective on soil water flow focusing rather on entropy production but on dissipation of Helmholtz free energy. Thermodynamic equilibrium is a state of minimum free energy. The latter is determined by potential energy and capillary energy in soil, which in turn strongly depends on soil moisture, pore size distribution and depth to groundwater. The objective of this study is threefold. First, we will introduce the necessary theoretical background. Second we suggest ? based on simulations with a physically based hydrological model ? that water flow in connected preferential pathways assures a faster relaxation towards thermodynamic equilibrium through a faster drainage of ?excess water? and a faster redistribution of ?capillary water? within the soil. The latter process is of prime importance in case of cohesive soils where the pore size distribution is dominated by medium and small pores. Third, an application of a physically based hydrological model to predict water flow and runoff response from a pristine catchment in the Chilenean Andes underpins this hypothesis. Behavioral model structures that allow a good match of the observed hydrographs turned out to be most efficient in dissipating free energy by means of preferential flow. It seems that a population of connected preferential pathways is favourable both for resilience and stability of these soils during extreme events and to retain water resources for the ecosystem at the same time. We suggest that this principle of ?maximum energy dissipation? may on the long term help us to better understand why soil structures remain stable, threshold nature of preferential as well as offer a means to further reduce model structural uncertainty. Bloeschl, G. 2006. Idle thoughts on a unifying theory of catchment Hydrology. Geophysical Research Abstracts, Vol. 8, 10677, 2006 SRef-ID: 1607-7962/gra/EGU06-A-10677 European Geosciences Union 2006 Kleidon, A., and S. Schymanski (2008), Thermodynamics and optimality of the water budget on land: A review, Geophys. Res. Lett., 35, L20404, doi:10.1029/ 2008GL035393.

Can we model solute transfer in heterogeneous soils with MIM model?

NASA Astrophysics Data System (ADS)

Ben Slimene, Erij; Lassabatere, Laurent; Winiarski, Thierry; Gourdon, Remy

2017-04-01

The fate of pollutants in the vadose zone must be understood, in particular, underneath infiltration basins for an optimum management of these plants. Stormwaters carry pollutants (heavy metals, organics, emerging pollutant like nanoparticles, etc.) and thus constitute a risk for groundwater and soil quality. Most infiltration basins are settled over highly permeable soils that exhibit a strong lithological heterogeneity. The impact of such lithological heterogeneity on flow and solute transfer has already been questioned. Previous studies have already proved that lithological heterogeneity was prone to the establishment of preferential flows. In more details, the concomitance of several materials with contrasting hydraulic properties induces funneled flow at the interfaces between less permeable and more permeable lithofacies. Solutes are then carried by water fluxes quickly along preferential flow pathways and have restricted access to zones far from these pathways. It can clearly be imagined that such pattern could be modeled by a MIM model postulating water fraction into two fractions, one mobile and the other immobile, with solute transport by convection and dispersion in mobile water fraction and solute diffusion at the interface between mobile and immobile water fractions. The application of MIM approach to the case of solute transport in strongly heterogeneous soils may be quite advantageous: simplification of the problem, fewer parameters, ease of modeling, numerical computation, gain in computation time, etc. However, such consistency has never been investigated in details. In this paper, we focus on the possibility to model solute transport in a strongly heterogeneous deposit using MIM model. The deposit has been the subject of intensive campaigns of characterization of its lithology and the hydraulic and hydrodispersive properties of its lithofacies. Numerical computations were performed for a section of deposit 13.5 m wide and 2.5 m deep. Numerical results clearly showed the establishment of preferential flows with funneling mostly under unsaturated conditions. Solute elution at 2.5 m depth was characterized and discussed as a function of solute reactivity. Solutes breakthrough curves show clear evidence of MIM like pattern. In this paper, we clearly demonstrate that MIM model accurately reproduces solute elution at 2.5m depths but also at different depths. MIM approach accuracy is ensured provided that related parameters are optimized as a function of depth, hydric and hydraulic conditions and the contrast in hydraulic parameters of the lithofacies that constitute the deposit.

Formate production through biocatalysis

PubMed Central

Alissandratos, Apostolos; Kim, Hye-Kyung; Easton, Christopher J

2013-01-01

The generation of formate from CO2 provides a method for sequestration of this greenhouse gas as well as the production of a valuable commodity chemical and stabilized form of hydrogen fuel. Formate dehydrogenases are enzymes with the potential to catalyze this reaction; however they generally favor the reverse process, i.e., formate oxidation. By contrast, the formate dehydrogenase of the acetogen Clostridium carboxidivorans has been found to preferentially catalyze the reduction of CO2. This is in accord with its natural role to introduce CO2 as a carbon source in the Wood-Ljungdahl pathway. The direction of catalysis derives from the enzyme’s low affinity for formate. This enzyme is therefore an excellent candidate for biotechnological applications aimed at producing formic acid and derivative chemicals from CO2. PMID:23841981

The cyclolignan PPP induces activation loop-specific inhibition of tyrosine phosphorylation of the insulin-like growth factor-1 receptor. Link to the phosphatidyl inositol-3 kinase/Akt apoptotic pathway.

PubMed

Vasilcanu, Daiana; Girnita, Ada; Girnita, Leonard; Vasilcanu, Radu; Axelson, Magnus; Larsson, Olle

2004-10-14

The insulin-like growth factor-1 receptor (IGF-1R) is crucial for many functions in neoplastic cells, for example, antiapoptosis. Recently, we demonstrated that the cyclolignan PPP efficiently inhibited phosphorylation of IGF-1R without interfering with insulin receptor activity. PPP preferentially reduced phosphorylated Akt, as compared to phosphorylated Erk1/2, and caused apoptosis. Now, we aimed to investigate how PPP inhibits the IGF-1R tyrosine kinase (IGF-1RTK) and the PI3K/Akt apoptotic pathway. Using a baculovirus driven IGF-1RTK we found that PPP interfered with tyrosine phosphorylation in the activation loop of the kinase domain. Specifically, it blocked phosphorylation of tyrosine (Y) 1136, while sparing the two others (Y1131 and Y1135). To explore the impact of inhibition of Y1136 on Akt phosphorylation we transfected P6 cells (overexpressing IGF-1R) and malignant melanoma cells with different IGF-1R mutants, including Y1136F (tyrosine replaced by phenylalanine). Y1136F was found to strongly decrease IGF-1 stimulated phosphorylation of Akt. Conversely, Akt phosphorylation was weakly affected in the Y1131F transfectant. Taken together, our data suggest that the preferential inhibition of phosphorylated Akt, after PPP treatment, may be due to specific inhibition of Y1136. PPP was proven not to interfere directly with Akt or any of its downstream molecules in the apoptotic pathway.

Trail Marking by Caterpillars of the Silverspot Butterfly Dione Juno Huascuma

PubMed Central

Pescador-Rubio, Alfonso; Stanford-Camargo, Sergio G.; Páez-Gerardo, Luis E; Ramírez-Reyes, Alberto J.; Ibarra-Jiménez, René A.; Fitzgerald, Terrence D.

2011-01-01

A pheromone is implicated in the trail marking behavior of caterpillars of the nymphalid silverspot butterfly, Dione juno huascuma (Reakirt) (Lepidoptera: Heliconiinae) that feed gregariously on Passiflora (Malpighiales: Passifloraceae) vines in Mexico. Although they mark pathways leading from one feeding site to another with silk, this study shows that the silk was neither adequate nor necessary to elicit trail following behavior. Caterpillars marked trails with a long-lived pheromone that was deposited when they brushed the ventral surfaces of the tips of their abdomens along branch pathways. The caterpillars distinguished between pathways deposited by different numbers of siblings and between trails of different ages. Caterpillars also preferentially followed the trails of conspecifics over those of another nymphalid, Nymphalis antiopa L., the mourning cloak butterfly. PMID:21861659

Common mycorrhizal networks amplify competition by preferential mineral nutrient allocation to large host plants.

PubMed

Weremijewicz, Joanna; Sternberg, Leonel da Silveira Lobo O'Reilly; Janos, David P

2016-10-01

Arbuscular mycorrhizal (AM) fungi interconnect plants in common mycorrhizal networks (CMNs) which can amplify competition among neighbors. Amplified competition might result from the fungi supplying mineral nutrients preferentially to hosts that abundantly provide fixed carbon, as suggested by research with organ-cultured roots. We examined whether CMNs supplied (15) N preferentially to large, nonshaded, whole plants. We conducted an intraspecific target-neighbor pot experiment with Andropogon gerardii and several AM fungi in intact, severed or prevented CMNs. Neighbors were supplied (15) N, and half of the target plants were shaded. Intact CMNs increased target dry weight (DW), intensified competition and increased size inequality. Shading decreased target weight, but shaded plants in intact CMNs had mycorrhizal colonization similar to that of sunlit plants. AM fungi in intact CMNs acquired (15) N from the substrate of neighbors and preferentially allocated it to sunlit, large, target plants. Sunlit, intact CMN, target plants acquired as much as 27% of their nitrogen from the vicinity of their neighbors, but shaded targets did not. These results suggest that AM fungi in CMNs preferentially provide mineral nutrients to those conspecific host individuals best able to provide them with fixed carbon or representing the strongest sinks, thereby potentially amplifying asymmetric competition below ground. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Cancer metabolism and the Warburg effect: the role of HIF-1 and PI3K.

PubMed

Courtnay, Rupert; Ngo, Darleen C; Malik, Neha; Ververis, Katherine; Tortorella, Stephanie M; Karagiannis, Tom C

2015-04-01

Cancer cells have been shown to have altered metabolism when compared to normal non-malignant cells. The Warburg effect describes a phenomenon in which cancer cells preferentially metabolize glucose by glycolysis, producing lactate as an end product, despite being the presence of oxygen. The phenomenon was first described by Otto Warburg in the 1920s, and has resurfaced as a controversial theory, with both supportive and opposing arguments. The biochemical aspects of the Warburg effect outline a strong explanation for the cause of cancer cell proliferation, by providing the biological requirements for a cell to grow. Studies have shown that pathways such as phosphoinositide 3-kinase/protein kinase B/mammalian target of rapamycin (PI3K/Akt/mTOR) as well as hypoxia inducible factor-1 (HIF-1) are central regulators of glycolysis, cancer metabolism and cancer cell proliferation. Studies have shown that PI3K signaling pathways have a role in many cellular processes such as metabolism, inflammation, cell survival, motility and cancer progression. Herein, the cellular aspects of the PI3K pathway are described, as well as the influence HIF has on cancer cell metabolism. HIF-1 activation has been related to angiogenesis, erythropoiesis and modulation of key enzymes involved in aerobic glycolysis, thereby modulating key processes required for the Warburg effect. In this review we discuss the molecular aspects of the Warburg effect with a particular emphasis on the role of the HIF-1 and the PI3K pathway.

Using Smoke Injection in Drains to Identify Potential Preferential Pathways in a Drained Arable Field

NASA Astrophysics Data System (ADS)

Nielsen, M. H.; Petersen, C. T.; Hansen, S.

2014-12-01

Macropores forming a continuous pathway between the soil surface and subsurface drains favour the transport of many contaminants from agricultural fields to surface waters. The smoke injection method presented by Shipitalo and Gibbs (2000) used for demonstrating and quantifying such pathways has been further developed and used on a drained Danish sandy loam. In order to identify the preferential pathways to drains, smoke was injected in three 1.15 m deep tile drains (total drain length 93 m), and smoke emitting macropores (SEMP) at the soil surface were counted and characterized as producing either strong or weak plumes compared to reference plumes from 3 and 6 mm wide tubes. In the two situations investigated in the present study - an early spring and an autumn situation, smoke only penetrated the soil surface layer via earthworm burrows located in a 1.0 m wide belt directly above the drain lines. However, it is known from previous studies that desiccation fractures in a dry summer situation also can contribute to the smoke pattern. The distance between SEMP measured along the drain lines was on average 0.46 m whereas the average spacing between SEMP with strong plumes was 2.3 m. Ponded water was applied in 6 cm wide rings placed above 52 burrows including 17 reference burrows which did not emit smoke. Thirteen pathways in the soil were examined using dye tracer and profile excavation. SEMP with strong plumes marked the entrance of highly efficient transport pathways conducting surface applied water and dye tracer into the drain. However, no single burrow was traced all the way from the surface into the drain, the dye patterns branched off in a network of other macropores. Water infiltration rates were significantly higher (P < 0.05) in SEMP with strong plumes (average rate: 247 mL min-1 n = 19) compared to SEMP with weak plumes (average rate: 87 mL min-1 n = 16) and no plumes (average rate: 56 mL min-1 n = 17). The results suggest that the smoke injection method is useful for identification of potentially efficient pathways for surface applied contaminants to drains and surface waters, pathways being associated primarily with unevenly distributed SEMP producing strong smoke plumes.

Vadose zone process that control landslide initiation and debris flow propagation

NASA Astrophysics Data System (ADS)

Sidle, Roy C.

2015-04-01

Advances in the areas of geotechnical engineering, hydrology, mineralogy, geomorphology, geology, and biology have individually advanced our understanding of factors affecting slope stability; however, the interactions among these processes and attributes as they affect the initiation and propagation of landslides and debris flows are not well understood. Here the importance of interactive vadose zone processes is emphasized related to the mechanisms, initiation, mode, and timing of rainfall-initiated landslides that are triggered by positive pore water accretion, loss of soil suction and increase in overburden weight, and long-term cumulative rain water infiltration. Both large- and small-scale preferential flow pathways can both contribute to and mitigate instability, by respectively concentrating and dispersing subsurface flow. These mechanisms are influenced by soil structure, lithology, landforms, and biota. Conditions conducive to landslide initiation by infiltration versus exfiltration are discussed relative to bedrock structure and joints. The effects of rhizosphere processes on slope stability are examined, including root reinforcement of soil mantles, evapotranspiration, and how root structures affect preferential flow paths. At a larger scale, the nexus between hillslope landslides and in-channel debris flows is examined with emphasis on understanding the timing of debris flows relative to chronic and episodic infilling processes, as well as the episodic nature of large rainfall and related stormflow generation in headwater streams. The hydrogeomorphic processes and conditions that determine whether or not landslides immediately mobilize into debris flows is important for predicting the timing and extent of devastating debris flow runout in steep terrain. Given the spatial footprint of individual landslides, it is necessary to assess vadose zone processes at appropriate scales to ascertain impacts on mass wasting phenomena. Articulating the appropriate level of detail of small-scale vadose zone processes into landslide models is a particular challenge. As such, understanding flow pathways in regoliths susceptible to mass movement is critical, including distinguishing between conditions conducive to vertical recharge of water through relatively homogeneous soil mantles and conditions where preferential flow dominates - either by rapid infiltration and lateral flow through interconnected preferential flow networks or via exfiltration through bedrock fractures. These different hydrologic scenarios have major implications for the occurrence, timing, and mode of slope failures.

Controlled CO preferential oxidation

DOEpatents

Meltser, M.A.; Hoch, M.M.

1997-06-10

Method is described for controlling the supply of air to a PROX (PReferential OXidation for CO cleanup) reactor for the preferential oxidation in the presence of hydrogen wherein the concentration of the hydrogen entering and exiting the PROX reactor is monitored, the difference there between correlated to the amount of air needed to minimize such difference, and based thereon the air supply to the PROX reactor adjusted to provide such amount and minimize such difference. 2 figs.

Development of macromolecular prodrug for rheumatoid arthritis☆

PubMed Central

Yuan, Fang; Quan, Ling-dong; Cui, Liao; Goldring, Steven R.; Wang, Dong

2012-01-01

Rheumatoid arthritis (RA) is a chronic autoimmune disease that is considered to be one of the major public health problems worldwide. The development of therapies that target tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6) and co-stimulatory pathways that regulate the immune system have revolutionized the care of patients with RA. Despite these advances, many patients continue to experience symptomatic and functional impairment. To address this issue, more recent therapies that have been developed are designed to target intracellular signaling pathways involved in immunoregulation. Though this approach has been encouraging, there have been major challenges with respect to off-target organ side effects and systemic toxicities related to the widespread distribution of these signaling pathways in multiple cell types and tissues. These limitations have led to an increasing interest in the development of strategies for the macromolecularization of anti-rheumatic drugs, which could target them to the inflamed joints. This approach enhances the efficacy of the therapeutic agent with respect to synovial inflammation, while markedly reducing non-target organ adverse side effects. In this manuscript, we provide a comprehensive overview of the rational design and optimization of macromolecular prodrugs for treatment of RA. The superior and the sustained efficacy of the prodrug may be partially attributed to their Extravasation through Leaky Vasculature and subsequent Inflammatory cell-mediated Sequestration (ELVIS) in the arthritic joints. This biologic process provides a plausible mechanism, by which macromolecular prodrugs preferentially target arthritic joints and illustrates the potential benefits of applying this therapeutic strategy to the treatment of other inflammatory diseases. PMID:22433784

Effect of volcanic dykes on coastal groundwater flow and saltwater intrusion: A field-scale multiphysics approach and parameter evaluation

NASA Astrophysics Data System (ADS)

Comte, J.-C.; Wilson, C.; Ofterdinger, U.; González-Quirós, A.

2017-03-01

Volcanic dykes are common discrete heterogeneities in aquifers; however, there is a lack of field examples of, and methodologies for, comprehensive in situ characterization of their properties with respect to groundwater flow and solute transport. We have applied an integrated multiphysics approach to quantify the effect of dolerite dykes on saltwater intrusion in a coastal sandstone aquifer. The approach involved ground geophysical imaging (passive magnetics and electrical resistivity tomography), well hydraulic testing, and tidal propagation analysis, which provided constraints on the geometry of the dyke network, the subsurface saltwater distribution, and the sandstone hydrodynamic properties and connectivity. A three-dimensional variable-density groundwater model coupled with a resistivity model was further calibrated using groundwater and geophysical observations. A good agreement of model simulations with tide-induced head fluctuations, geophysically derived pore water salinities, and measured apparent resistivities was obtained when dykes' hydraulic conductivity, storativity, and effective porosity are respectively about 3, 1, and 1 orders of magnitude lower than the host aquifer. The presence of the dykes results in barrier-like alterations of groundwater flow and saltwater intrusion. Preferential flow paths occur parallel to observed dyke orientations. Freshwater inflows from upland recharge areas concentrate on the land-facing side of the dykes and saltwater penetration is higher on their sea-facing side. This has major implications for managing groundwater resources in dyke-intruded aquifers, including in coastal and island regions and provides wider insights on preferential pathways of groundwater flow and transport in highly heterogeneous aquifer systems.

Minimum Disclosure Counting for the Alternative Vote

NASA Astrophysics Data System (ADS)

Wen, Roland; Buckland, Richard

Although there is a substantial body of work on preventing bribery and coercion of voters in cryptographic election schemes for plurality electoral systems, there are few attempts to construct such schemes for preferential electoral systems. The problem is preferential systems are prone to bribery and coercion via subtle signature attacks during the counting. We introduce a minimum disclosure counting scheme for the alternative vote preferential system. Minimum disclosure provides protection from signature attacks by revealing only the winning candidate.

Introduction to the Special Issue: Precarious Solidarity-Preferential Access in Canadian Health Care.

PubMed

Reid, Lynette

2017-06-01

Systems of universal health coverage may aspire to provide care based on need and not ability to pay; the complexities of this aspiration (conceptual, practical, and ethical) call for normative analysis. This special issue arises in the wake of a judicial inquiry into preferential access in the Canadian province of Alberta, the Vertes Commission. I describe this inquiry and set out a taxonomy of forms of differential and preferential access. Papers in this special issue focus on the conceptual specification of health system boundaries (the concept of medical need) and on the normative questions raised by complex models of funding and delivery of care, where patients, providers, and services cross system boundaries.

Dissolution-Driven Permeability Reduction of a Fractured Carbonate Caprock

PubMed Central

Ellis, Brian R.; Fitts, Jeffrey P.; Bromhal, Grant S.; McIntyre, Dustin L.; Tappero, Ryan; Peters, Catherine A.

2013-01-01

Abstract Geochemical reactions may alter the permeability of leakage pathways in caprocks, which serve a critical role in confining CO2 in geologic carbon sequestration. A caprock specimen from a carbonate formation in the Michigan sedimentary Basin was fractured and studied in a high-pressure core flow experiment. Inflowing brine was saturated with CO2 at 40°C and 10 MPa, resulting in an initial pH of 4.6, and had a calcite saturation index of −0.8. Fracture permeability decreased during the experiment, but subsequent analyses did not reveal calcite precipitation. Instead, experimental observations indicate that calcite dissolution along the fracture pathway led to mobilization of less soluble mineral particles that clogged the flow path. Analyses of core sections via electron microscopy, synchrotron-based X-ray diffraction imaging, and the first application of microbeam Ca K-edge X-ray absorption near edge structure, provided evidence that these occlusions were fragments from the host rock rather than secondary precipitates. X-ray computed tomography showed a significant loss of rock mass within preferential flow paths, suggesting that dissolution also removed critical asperities and caused mechanical closure of the fracture. The decrease in fracture permeability despite a net removal of material along the fracture pathway demonstrates a nonintuitive, inverse relationship between dissolution and permeability evolution in a fractured carbonate caprock. PMID:23633894

Accessible triple-phase boundary length: A performance metric to account for transport pathways in heterogeneous electrochemical materials

NASA Astrophysics Data System (ADS)

Nakajo, A.; Cocco, A. P.; DeGostin, M. B.; Peracchio, A. A.; Cassenti, B. N.; Cantoni, M.; Van herle, J.; Chiu, W. K. S.

2016-09-01

The performance of materials for electrochemical energy conversion and storage depends upon the number of electrocatalytic sites available for reaction and their accessibility by the transport of reactants and products. For solid oxide fuel/electrolysis cell materials, standard 3-D measurements such as connected triple-phase boundary (TPB) length and effective transport properties partially inform on how local geometry and network topology causes variability in TPB accessibility. A new measurement, the accessible TPB, is proposed to quantify these effects in detail and characterize material performance. The approach probes the reticulated pathways to each TPB using an analytical electrochemical fin model applied to a 3-D discrete representation of the heterogeneous structure provided by skeleton-based partitioning. The method is tested on artificial and real structures imaged by 3-D x-ray and electron microscopy. The accessible TPB is not uniform and the pattern varies depending upon the structure. Connected TPBs can be even passivated. The sensitivity to manipulations of the local 3-D geometry and topology that standard measurements cannot capture is demonstrated. The clear presence of preferential pathways showcases a non-uniform utilization of the 3-D structure that potentially affects the performance and the resilience to alterations due to degradation phenomena. The concepts presented also apply to electrochemical energy storage and conversion devices such as other types of fuel cells, electrolyzers, batteries and capacitors.

Effects of Peptone Supplementation in Different Culture Media on Growth, Metabolic Pathway and Productivity of CHO DG44 Cells; a New Insight into Amino Acid Profiles.

PubMed

Davami, Fatemeh; Eghbalpour, Farnaz; Nematollahi, Leila; Barkhordari, Farzaneh; Mahboudi, Fereidoun

2015-01-01

The optimization of bioprocess conditions towards improved growth profile and productivity yield is considered of great importance in biopharmaceutical manufacturing. Peptones as efficient sources of nutrients have been studied for their effect on media development; however, their role on metabolic pathway is not well understood. In the present study, the effect of different concentration of peptones on a recombinant Chinese hamster ovary (CHO) cell line grown in three serum-free suspension cultures was determined. Six peptones of different origins and available amino acid profiles were investigated regarding their impact on cell growth, productivity, and metabolic pathways changes. In optimized feeding strategies, increases of 136% and 159% in volumetric productivity (for a low-nutrient culture media) and 55% (for a high-nutrient culture media) were achieved. Furthermore, particular sources of peptones with specific amino acid profile developed preferential results for each different culture medium. Two peptones, SoyA2SC and SoyE-110, were the only hydrolysates that showed production improvement in all three media. Casein Peptone plus Tryptone N1 and SoyA3SC showed different improved results based on their implemented concentration for each individual basal medium. The amino acid profile of peptones may provide clues to identify the most effective feeding strategies for recombinant CHO cells.

Nrf2 target genes are induced under marginal selenium-deficiency

PubMed Central

Müller, Mike; Banning, Antje; Brigelius-Flohé, Regina

2010-01-01

A suboptimal selenium supply appears to prevail in Europe. The current study, therefore, was focused on the changes in gene expression under a suboptimal selenium intake. Previous microarray analyses in the colon of mice fed either a selenium-adequate or a moderately deficient diet revealed a change in genes of several pathways. Severe selenium-deficiency has been found previously to influence Nrf2-regulated genes of the adaptive response. Since the previous pathway analyses were done with a program not searching for Nrf2 target genes, respective genes were manually selected and confirmed by qPCR. qPCR revealed an induction of phase II (Nqo1, Gsts, Sult1b1 and Ugt1a6) and antioxidant enzymes (Hmox1, Mt2, Prdx1, Srxn1, Sod1 and Gclc) under the selenium-poor diet, which is considered to compensate for the loss of selenoproteins. The strongest effects were observed in the duodenum where preferentially genes for antioxidant enzymes were up-regulated. These also include the mRNA of the selenoproteins TrxR1 and GPx2 that would enable their immediate translation upon selenium refeeding. The down-regulation of Gsk3β in moderate selenium-deficiency observed in the previous paper provides a possible explanation for the activation of the Nrf2 pathway, because inhibition of GSK3β results in the nuclear accumulation of Nrf2. PMID:21189866

Effects of Peptone Supplementation in Different Culture Media on Growth, Metabolic Pathway and Productivity of CHO DG44 Cells; a New Insight into Amino Acid Profiles

PubMed Central

Davami, Fatemeh; Eghbalpour, Farnaz; Nematollahi, Leila; Barkhordari, Farzaneh; Mahboudi, Fereidoun

2015-01-01

Background: The optimization of bioprocess conditions towards improved growth profile and productivity yield is considered of great importance in biopharmaceutical manufacturing. Peptones as efficient sources of nutrients have been studied for their effect on media development; however, their role on metabolic pathway is not well understood. Methods: In the present study, the effect of different concentration of peptones on a recombinant Chinese hamster ovary (CHO) cell line grown in three serum-free suspension cultures was determined. Six peptones of different origins and available amino acid profiles were investigated regarding their impact on cell growth, productivity, and metabolic pathways changes. Results: In optimized feeding strategies, increases of 136% and 159% in volumetric productivity (for a low-nutrient culture media) and 55% (for a high-nutrient culture media) were achieved. Furthermore, particular sources of peptones with specific amino acid profile developed preferential results for each different culture medium. Two peptones, SoyA2SC and SoyE-110, were the only hydrolysates that showed production improvement in all three media. Casein Peptone plus Tryptone N1 and SoyA3SC showed different improved results based on their implemented concentration for each individual basal medium. Conclusion: The amino acid profile of peptones may provide clues to identify the most effective feeding strategies for recombinant CHO cells. PMID:26232332

Genetic landscape and deregulated pathways in B-cell lymphoid malignancies.

PubMed

Rosenquist, R; Beà, S; Du, M-Q; Nadel, B; Pan-Hammarström, Q

2017-11-01

With the introduction of next-generation sequencing, the genetic landscape of the complex group of B-cell lymphoid malignancies has rapidly been unravelled in recent years. This has provided important information about recurrent genetic events and identified key pathways deregulated in each lymphoma subtype. In parallel, there has been intense search and development of novel types of targeted therapy that 'hit' central mechanisms in lymphoma pathobiology, such as BTK, PI3K or BCL2 inhibitors. In this review, we will outline the current view of the genetic landscape of selected entities: follicular lymphoma, diffuse large B-cell lymphoma, mantle cell lymphoma, chronic lymphocytic leukaemia and marginal zone lymphoma. We will detail recurrent alterations affecting important signalling pathways, that is the B-cell receptor/NF-κB pathway, NOTCH signalling, JAK-STAT signalling, p53/DNA damage response, apoptosis and cell cycle regulation, as well as other perhaps unexpected cellular processes, such as immune regulation, cell migration, epigenetic regulation and RNA processing. Whilst many of these pathways/processes are commonly altered in different lymphoid tumors, albeit at varying frequencies, others are preferentially targeted in selected B-cell malignancies. Some of these genetic lesions are either involved in disease ontogeny or linked to the evolution of each disease and/or specific clinicobiological features, and some of them have been demonstrated to have prognostic and even predictive impact. Future work is especially needed to understand the therapy-resistant disease, particularly in patients treated with targeted therapy, and to identify novel targets and therapeutic strategies in order to realize true precision medicine in this clinically heterogeneous patient group. © 2017 The Association for the Publication of the Journal of Internal Medicine.

Review: Metabolic Control of Immune System Activation in Rheumatic Diseases.

PubMed

Perl, Andras

2017-12-01

Metabolic pathways mediate lineage specification within the immune system through the regulation of glucose utilization, a process that generates energy in the form of ATP and synthesis of amino acids, nucleotides, and lipids to enable cell growth, proliferation, and survival. CD4+ T cells, a proinflammatory cell subset, preferentially produce ATP through glycolysis, whereas cells with an antiinflammatory lineage, such as memory and regulatory T cells, favor mitochondrial ATP generation. In conditions of metabolic stress or a shortage of nutrients, cells rely on autophagy to secure amino acids and other substrates, while survival depends on the sparing of mitochondria and maintenance of a reducing environment. The pentose phosphate pathway acts as a key gatekeeper of inflammation by supplying ribose-5-phosphate for cell proliferation and NADPH for antioxidant defenses. Increased lysosomal catabolism, accumulation of branched amino acids, glutamine, kynurenine, and histidine, and depletion of glutathione and cysteine activate the mechanistic target of rapamycin (mTOR), an arbiter of lineage development within the innate and adaptive immune systems. Mapping the impact of susceptibility genes to metabolic pathways allows for better understanding and therapeutic targeting of disease-specific expansion of proinflammatory cells. Therapeutic approaches aimed at glutathione depletion and mTOR pathway activation appear to be safe and effective for treating lupus, while an opposing intervention may be of benefit in rheumatoid arthritis. Environmental sources of origin for metabolites within immune cells may include microbiota and plants. Thus, a better understanding of the pathways of immunometabolism could provide new insights into the pathogenesis and treatment of the rheumatic diseases. © 2017 The Authors. Arthritis & Rheumatology published by Wiley Periodicals, Inc. on behalf of American College of Rheumatology.

A stapled p53 helix overcomes HDMX-mediated suppression of p53.

PubMed

Bernal, Federico; Wade, Mark; Godes, Marina; Davis, Tina N; Whitehead, David G; Kung, Andrew L; Wahl, Geoffrey M; Walensky, Loren D

2010-11-16

Cancer cells neutralize p53 by deletion, mutation, proteasomal degradation, or sequestration to achieve a pathologic survival advantage. Targeting the E3 ubiquitin ligase HDM2 can lead to a therapeutic surge in p53 levels. However, the efficacy of HDM2 inhibition can be compromised by overexpression of HDMX, an HDM2 homolog that binds and sequesters p53. Here, we report that a stapled p53 helix preferentially targets HDMX, blocks the formation of inhibitory p53-HDMX complexes, induces p53-dependent transcriptional upregulation, and thereby overcomes HDMX-mediated cancer resistance in vitro and in vivo. Importantly, our analysis of p53 interaction dynamics provides a blueprint for reactivating the p53 pathway in cancer by matching HDM2, HDMX, or dual inhibitors to the appropriate cellular context. Copyright © 2010 Elsevier Inc. All rights reserved.

Paravascular channels, cisterns, and the subarachnoid space in the rat brain: A single compartment with preferential pathways

PubMed Central

Bedussi, Beatrice; van der Wel, Nicole N; de Vos, Judith; van Veen, Henk; Siebes, Maria; VanBavel, Ed

2016-01-01

Recent evidence suggests an extensive exchange of fluid and solutes between the subarachnoid space and the brain interstitium, involving preferential pathways along blood vessels. We studied the anatomical relations between brain vasculature, cerebrospinal fluid compartments, and paravascular spaces in male Wistar rats. A fluorescent tracer was infused into the cisterna magna, without affecting intracranial pressure. Tracer distribution was analyzed using a 3D imaging cryomicrotome, confocal microscopy, and correlative light and electron microscopy. We found a strong 3D colocalization of tracer with major arteries and veins in the subarachnoid space and large cisterns, attributed to relatively large subarachnoid space volumes around the vessels. Confocal imaging confirmed this colocalization and also revealed novel cisternal connections between the subarachnoid space and ventricles. Unlike the vessels in the subarachnoid space, penetrating arteries but not veins were surrounded by tracer. Correlative light and electron microscopy images indicated that this paravascular space was located outside of the endothelial layer in capillaries and just outside of the smooth muscle cells in arteries. In conclusion, the cerebrospinal fluid compartment, consisting of the subarachnoid space, cisterns, ventricles, and para-arteriolar spaces, forms a continuous and extensive network that surrounds and penetrates the rat brain, in which mixing may facilitate exchange between interstitial fluid and cerebrospinal fluid. PMID:27306753

Paravascular channels, cisterns, and the subarachnoid space in the rat brain: A single compartment with preferential pathways.

PubMed

Bedussi, Beatrice; van der Wel, Nicole N; de Vos, Judith; van Veen, Henk; Siebes, Maria; VanBavel, Ed; Bakker, Erik Ntp

2017-04-01

Recent evidence suggests an extensive exchange of fluid and solutes between the subarachnoid space and the brain interstitium, involving preferential pathways along blood vessels. We studied the anatomical relations between brain vasculature, cerebrospinal fluid compartments, and paravascular spaces in male Wistar rats. A fluorescent tracer was infused into the cisterna magna, without affecting intracranial pressure. Tracer distribution was analyzed using a 3D imaging cryomicrotome, confocal microscopy, and correlative light and electron microscopy. We found a strong 3D colocalization of tracer with major arteries and veins in the subarachnoid space and large cisterns, attributed to relatively large subarachnoid space volumes around the vessels. Confocal imaging confirmed this colocalization and also revealed novel cisternal connections between the subarachnoid space and ventricles. Unlike the vessels in the subarachnoid space, penetrating arteries but not veins were surrounded by tracer. Correlative light and electron microscopy images indicated that this paravascular space was located outside of the endothelial layer in capillaries and just outside of the smooth muscle cells in arteries. In conclusion, the cerebrospinal fluid compartment, consisting of the subarachnoid space, cisterns, ventricles, and para-arteriolar spaces, forms a continuous and extensive network that surrounds and penetrates the rat brain, in which mixing may facilitate exchange between interstitial fluid and cerebrospinal fluid.

Monitoring radionuclide contamination in the unsaturated zone - Lessons learned at the Amargosa Desert Research Site, Nye County, Nevada

USGS Publications Warehouse

Stonestrom, David A.; Abraham, Jared D.; Andraski, Brian J.; Baker, Ronald J.; Mayers, C. Justin; Michel, Robert L.; Prudic, David E.; Striegl, Robert G.; Walvoord, Michelle Ann

2004-01-01

Contaminant-transport processes are being investigated at the U.S. Geological Survey’s Amargosa Desert Research Site (A DRS), adjacent to the Nation’s first commercial disposal facility for low-level radioactive waste. Gases containing tritium and radiocarbon are migrating through a 110-m thick unsaturated zone from unlined trenches that received waste from 1962 to 1992. Results relevant to long- term monitoring of radionuclides are summarized as follows. Contaminant plumes have unexpected histories and spatial configurations due to uncertainties in the: (1) geologic framework, (2) biochemical reactions involving waste components, (3) interactions between plume components and unsaturated-zone materials, (4) disposal practices, and (5) physical transport processes. Information on plume dynamics depends on ex-situ wet-chemical techniques because in-situ sensors for the radionuclides of interest do not exist. As at other radioactive-waste disposal facilities, radionuclides at the ADRS are mixed with varying amounts of volatile organic compounds (VOCs). Carbon-dioxide and VOC anomalies provide proxies for radioactive contamination. Contaminants in the unsaturated zone migrate along preferential pathways. Effective monitoring thus requires accurate geologic characterization. Direct- current electrical-resistivity imaging successfully mapped geologic units controlling preferential transport at the ADRS. Direct sampling of water from the unsaturated zone is complex and time consuming. Sampling plant water is an efficient alternative for mapping shallow tritium contamination.

Differential ubiquitination of Smad1 mediated by CHIP: implications in the regulation of the bone morphogenetic protein signaling pathway.

PubMed

Li, Ren-Feng; Shang, Yu; Liu, Di; Ren, Ze-Song; Chang, Zhijie; Sui, Sen-Fang

2007-11-30

Smad1, a downstream regulator of the bone morphogenetic protein (BMP) receptors, is tightly regulated by the ubiquitin-proteasomal degradation system. To dissect the mechanisms that underlie the regulation of Smad1, it is important to investigate the specific ubiquitination site(s) in Smad1. Here we report that the alpha-NH(2) group of the N terminus and the epsilon-NH(2) groups of internal lysine residues 116, 118 and 269 (K116, K118 and K269) of Smad1 are ubiquitin acceptor sites mediated by the carboxyl terminus of Hsc70-interacting protein (CHIP). The in vitro degradation assay indicates that ubiquitination at the N terminus partially contributes to the degradation of Smad1. Furthermore, we demonstrate that the ubiquitination level of pseudo-phosphorylated Smad1 by CHIP is stronger than that of wild-type Smad1 and can be strongly inhibited by a phosphorylated tail of Smad1, PIS(pS)V(pS). Third, our results indicate that Hsp70 facilitates CHIP-mediated poly-ubiquitination of Smad1 whereas it attenuates CHIP-meditated mono-ubiquitination of Smad1. Finally, consistent with the in vitro observation, we show that CHIP preferentially mediates the degradation of phospho-Smad1/5 in vivo. Taken together, these results provide us a hint that CHIP might preferentially regulate phosphorylated Smad1 and thus the BMP signaling.

The type III inositol 1,4,5-trisphosphate receptor preferentially transmits apoptotic Ca2+ signals into mitochondria.

PubMed

Mendes, Carolina C P; Gomes, Dawidson A; Thompson, Mayerson; Souto, Natalia C; Goes, Tercio S; Goes, Alfredo M; Rodrigues, Michele A; Gomez, Marcus V; Nathanson, Michael H; Leite, M Fatima

2005-12-09

There are three isoforms of the inositol 1,4,5- trisphosphate receptor (InsP(3)R), each of which has a distinct effect on Ca(2+) signaling. However, it is not known whether each isoform similarly plays a distinct role in the activation of Ca(2+)-mediated events. To investigate this question, we examined the effects of each InsP(3)R isoform on transmission of Ca(2+) signals to mitochondria and induction of apoptosis. Each isoform was selectively silenced using isoform-specific small interfering RNA in Chinese hamster ovary cells, which express all three InsP(3)R isoforms. ATP-induced cytosolic Ca(2+) signaling patterns were altered, regardless of which isoform was silenced, but in a different fashion depending on the isoform. ATP also induced Ca(2+) signals in mitochondria, which were inhibited more effectively by silencing the type III InsP(3)R than by silencing either the type I or type II isoform. The type III isoform also co-localized most strongly with mitochondria. When apoptosis was induced by activation of either the extrinsic or intrinsic apoptotic pathway, induction was reduced most effectively by silencing the type III InsP(3)R. These findings provide evidence that the type III isoform of the InsP(3)R plays a special role in induction of apoptosis by preferentially transmitting Ca(2+) signals into mitochondria.

Interaction of TIF-90 and filamin A in the regulation of rRNA synthesis in leukemic cells.

PubMed

Nguyen, Le Xuan Truong; Chan, Steven M; Ngo, Tri Duc; Raval, Aparna; Kim, Kyeong Kyu; Majeti, Ravindra; Mitchell, Beverly S

2014-07-24

The transcription initiation factor I (TIF-IA) is an important regulator of the synthesis of ribosomal RNA (rRNA) through its facilitation of the recruitment of RNA polymerase I (Pol I) to the ribosomal DNA promoter. Activation of the phosphoinositide 3-kinase (PI3K)/protein kinase B (Akt) pathway, which occurs commonly in acute myelogenous leukemia, enhances rRNA synthesis through TIF-IA stabilization and phosphorylation. We have discovered that TIF-IA coexists with a splicing isoform, TIF-90, which is expressed preferentially in the nucleolus and at higher levels in proliferating and transformed hematopoietic cells. TIF-90 interacts directly with Pol I to increase rRNA synthesis as a consequence of Akt activation. Furthermore, TIF-90 binds preferentially to a 90-kDa cleavage product of the actin binding protein filamin A (FLNA) that inhibits rRNA synthesis. Increased expression of TIF-90 overcomes the inhibitory effect of this cleavage product and stimulates rRNA synthesis. Because activated Akt also reduces FLNA cleavage, these results indicate that activated Akt and TIF-90 function in parallel to increase rRNA synthesis and, as a consequence, cell proliferation in leukemic cells. These results provide evidence that the direct targeting of Akt would be an effective therapy in acute leukemias in which Akt is activated. © 2014 by The American Society of Hematology.

Haptoglobin preferentially binds β but not α subunits cross-linked hemoglobin tetramers with minimal effects on ligand and redox reactions.

PubMed

Jia, Yiping; Wood, Francine; Buehler, Paul W; Alayash, Abdu I

2013-01-01

Human hemoglobin (Hb) and haptoglobin (Hp) exhibit an extremely high affinity for each other, and the dissociation of Hb tetramers into dimers is generally believed to be a prerequisite for complex formation. We have investigated Hp interactions with native Hb, αα, and ββ cross-linked Hb (ααXLHb and ββXLHb, respectively), and rapid kinetics of Hb ligand binding as well as the redox reactivity in the presence of and absence of Hp. The quaternary conformation of ββ subunit cross-linking results in a higher binding affinity than that of αα subunit cross-linked Hb. However, ββ cross-linked Hb exhibits a four fold slower association rate constant than the reaction rate of unmodified Hb with Hp. The Hp contact regions in the Hb dimer interfaces appear to be more readily exposed in ββXLHb than ααXLHb. In addition, apart from the functional changes caused by chemical modifications, Hp binding does not induce appreciable effects on the ligand binding and redox reactions of ββXLHb. Our findings may therefore be relevant to the design of safer Hb-based oxygen therapeutics by utilizing this preferential binding of ββXLHb to Hp. This may ultimately provide a safe oxidative inactivation and clearance pathway for chemically modified Hbs in circulation.

An attempt to understand glioma stem cell biology through centrality analysis of a protein interaction network.

PubMed

Mallik, Mrinmay Kumar

2018-02-07

Biological networks can be analyzed using "Centrality Analysis" to identify the more influential nodes and interactions in the network. This study was undertaken to create and visualize a biological network comprising of protein-protein interactions (PPIs) amongst proteins which are preferentially over-expressed in glioma cancer stem cell component (GCSC) of glioblastomas as compared to the glioma non-stem cancer cell (GNSC) component and then to analyze this network through centrality analyses (CA) in order to identify the essential proteins in this network and their interactions. In addition, this study proposes a new centrality analysis method pertaining exclusively to transcription factors (TFs) and interactions amongst them. Moreover the relevant molecular functions, biological processes and biochemical pathways amongst these proteins were sought through enrichment analysis. A protein interaction network was created using a list of proteins which have been shown to be preferentially expressed or over-expressed in GCSCs isolated from glioblastomas as compared to the GNSCs. This list comprising of 38 proteins, created using manual literature mining, was submitted to the Reactome FIViz tool, a web based application integrated into Cytoscape, an open source software platform for visualizing and analyzing molecular interaction networks and biological pathways to produce the network. This network was subjected to centrality analyses utilizing ranked lists of six centrality measures using the FIViz application and (for the first time) a dedicated centrality analysis plug-in ; CytoNCA. The interactions exclusively amongst the transcription factors were nalyzed through a newly proposed centrality analysis method called "Gene Expression Associated Degree Centrality Analysis (GEADCA)". Enrichment analysis was performed using the "network function analysis" tool on Reactome. The CA was able to identify a small set of proteins with consistently high centrality ranks that is indicative of their strong influence in the protein protein interaction network. Similarly the newly proposed GEADCA helped identify the transcription factors with high centrality values indicative of their key roles in transcriptional regulation. The enrichment studies provided a list of molecular functions, biological processes and biochemical pathways associated with the constructed network. The study shows how pathway based databases may be used to create and analyze a relevant protein interaction network in glioma cancer stem cells and identify the essential elements within it to gather insights into the molecular interactions that regulate the properties of glioma stem cells. How these insights may be utilized to help the development of future research towards formulation of new management strategies have been discussed from a theoretical standpoint. Copyright © 2017 Elsevier Ltd. All rights reserved.

The TGFβ pathway is a key player for the endothelial-to-hematopoietic transition in the embryonic aorta.

PubMed

Lempereur, A; Canto, P Y; Richard, C; Martin, S; Thalgott, J; Raymond, K; Lebrin, F; Drevon, C; Jaffredo, T

2018-02-15

The embryonic aorta produces hematopoietic stem and progenitor cells from a hemogenic endothelium localized in the aortic floor through an endothelial to hematopoietic transition. It has been long proposed that the Bone Morphogenetic Protein (BMP)/Transforming Growth Factor ß (TGFß) signaling pathway was implicated in aortic hematopoiesis but the very nature of the signal was unknown. Here, using thorough expression analysis of the BMP/TGFß signaling pathway members in the endothelial and hematopoietic compartments of the aorta at pre-hematopoietic and hematopoietic stages, we show that the TGFß pathway is preferentially balanced with a prominent role of Alk1/TgfßR2/Smad1 and 5 on both chicken and mouse species. Functional analysis using embryonic stem cells mutated for Acvrl1 revealed an enhanced propensity to produce hematopoietic cells. Collectively, we reveal that TGFß through the Alk1/TgfßR2 receptor axis is acting on endothelial cells to produce hematopoiesis. Copyright © 2017 Elsevier Inc. All rights reserved.

Local anesthetic and antiepileptic drug access and binding to a bacterial voltage-gated sodium channel

PubMed Central

Boiteux, Céline; Vorobyov, Igor; French, Robert J.; French, Christopher; Yarov-Yarovoy, Vladimir; Allen, Toby W.

2014-01-01

Voltage-gated sodium (Nav) channels are important targets in the treatment of a range of pathologies. Bacterial channels, for which crystal structures have been solved, exhibit modulation by local anesthetic and anti-epileptic agents, allowing molecular-level investigations into sodium channel-drug interactions. These structures reveal no basis for the “hinged lid”-based fast inactivation, seen in eukaryotic Nav channels. Thus, they enable examination of potential mechanisms of use- or state-dependent drug action based on activation gating, or slower pore-based inactivation processes. Multimicrosecond simulations of NavAb reveal high-affinity binding of benzocaine to F203 that is a surrogate for FS6, conserved in helix S6 of Domain IV of mammalian sodium channels, as well as low-affinity sites suggested to stabilize different states of the channel. Phenytoin exhibits a different binding distribution owing to preferential interactions at the membrane and water–protein interfaces. Two drug-access pathways into the pore are observed: via lateral fenestrations connecting to the membrane lipid phase, as well as via an aqueous pathway through the intracellular activation gate, despite being closed. These observations provide insight into drug modulation that will guide further developments of Nav inhibitors. PMID:25136136

CO2 migration in the vadose zone: experimental and numerical modelling of controlled gas injection

NASA Astrophysics Data System (ADS)

gasparini, andrea; credoz, anthony; grandia, fidel; garcia, david angel; bruno, jordi

2014-05-01

The mobility of CO2 in the vadose zone and its subsequent transfer to the atmosphere is a matter of concern in the risk assessment of the geological storage of CO2. In this study the experimental and modelling results of controlled CO2 injection are reported to better understanding of the physical processes affecting CO2 and transport in the vadose zone. CO2 was injected through 16 micro-injectors during 49 days of experiments in a 35 m3 experimental unit filled with sandy material, in the PISCO2 facilities at the ES.CO2 centre in Ponferrada (North Spain). Surface CO2 flux were monitored and mapped periodically to assess the evolution of CO2 migration through the soil and to the atmosphere. Numerical simulations were run to reproduce the experimental results, using TOUGH2 code with EOS7CA research module considering two phases (gas and liquid) and three components (H2O, CO2, air). Five numerical models were developed following step by step the injection procedure done at PISCO2. The reference case (Model A) simulates the injection into a homogeneous soil(homogeneous distribution of permeability and porosity in the near-surface area, 0.8 to 0.3 m deep from the atmosphere). In another model (Model B), four additional soil layers with four specific permeabilities and porosities were included to predict the effect of differential compaction on soil. To account for the effect of higher soil temperature, an isothermal simulation called Model C was also performed. Finally, the assessment of the rainfall effects (soil water saturation) on CO2 emission on surface was performed in models called Model D and E. The combined experimental and modelling approach shows that CO2 leakage in the vadose zone quickly comes out through preferential migration pathways and spots with the ranges of fluxes in the ground/surface interface from 2.5 to 600 g·m-2·day-1. This gas channelling is mainly related to soil compaction and climatic perturbation. This has significant implications to design adapted detection and monitoring strategies of early leakage in commercial CO2 storage. The presence of soils with different compactions at surface influences the CO2 dispersion. The inclusion of soils with different permeability, porosity and liquid saturation results in preferential pathways. The formation of preferential pathways in the soil and hot spots on the surface has commonly been observed in natural systems where deep CO2 fluxes interact with shallow aquifers. Increase of ambient temperature increases CO2 fluxes intensity whereas rainfall decreases CO2 emission in gas phase and trap it as aqueous species in the porous media of the soil. A good accuracy has been obtained for surface CO2 fluxes location and intensity between experimental and modelling results taking into account the selected equation of state, the soil characteristics and the operational conditions. Phenomena of compaction and preferential pathways located only in the first centimetres of the soil can explain the heterogeneity of CO2 fluxes in the 16 m2 surface area of PISCO2 experimental platform.

Differential expression of jasmonate biosynthesis genes in cacao genotypes contrasting for resistance against Moniliophthora perniciosa.

PubMed

Litholdo, Celso G; Leal, Gildemberg A; Albuquerque, Paulo S B; Figueira, Antonio

2015-10-01

The resistance mechanism of cacao against M. perniciosa is likely to be mediated by JA/ET-signaling pathways due to the preferential TcAOS and TcSAM induction in a resistant genotype. The basidiomycete Moniliophthora perniciosa causes a serious disease in cacao (Theobroma cacao L.), and the use of resistant varieties is the only sustainable long-term solution. Cacao resistance against M. perniciosa is characterized by pathogen growth inhibition with reduced colonization and an attenuation of disease symptoms, suggesting a regulation by jasmonate (JA)/ethylene (ET) signaling pathways. The hypothesis that genes involved in JA biosynthesis would be active in the interaction of T. cacao and M. perniciosa was tested here. The cacao JA-related genes were evaluated for their relative quantitative expression in susceptible and resistant genotypes upon the exogenous application of ET, methyl-jasmonate (MJ), and salicylic acid (SA), or after M. perniciosa inoculation. MJ treatment triggered changes in the expression of genes involved in JA biosynthesis, indicating that the mechanism of positive regulation by exogenous MJ application occurs in cacao. However, a higher induction of these genes was observed in the susceptible genotype. Further, a contrast in JA-related transcriptional expression was detected between susceptible and resistant plants under M. perniciosa infection, with the induction of the allene oxide synthase gene (TcAOS), which encodes a key enzyme in the JA biosynthesis pathway in the resistant genotype. Altogether, this work provides additional evidences that the JA-dependent signaling pathway is modulating the defense response against M. perniciosa in a cacao-resistant genotype.

Analysis of Hydra PIWI proteins and piRNAs uncover early evolutionary origins of the piRNA pathway.

PubMed

Lim, Robyn S M; Anand, Amit; Nishimiya-Fujisawa, Chiemi; Kobayashi, Satoru; Kai, Toshie

2014-02-01

To preserve genome integrity, an evolutionarily conserved small RNA-based silencing mechanism involving PIWI proteins and PIWI-interacting RNAs (piRNAs) represses potentially deleterious transposons in animals. Although there has been extensive research into PIWI proteins in bilaterians, these proteins remain to be examined in ancient phyla. Here, we investigated the PIWI proteins Hywi and Hyli in the cnidarian Hydra, and found that both PIWI proteins are enriched in multipotent stem cells, germline stem cells, and in the female germline. Hywi and Hyli localize to the nuage, a perinuclear organelle that has been implicated in piRNA-mediated transposon silencing, together with other conserved nuage and piRNA pathway components. Our findings provide the first report of nuage protein localization patterns in a non-bilaterian. Hydra PIWI proteins possess symmetrical dimethylarginines: modified residues that are known to aid in PIWI protein localization to the nuage and proper piRNA loading. piRNA profiling suggests that transposons are the major targets of the piRNA pathway in Hydra. Our data suggest that piRNA biogenesis through the ping-pong amplification cycle occurs in Hydra and that Hywi and Hyli are likely to preferentially bind primary and secondary piRNAs, respectively. Presumptive piRNA clusters are unidirectionally transcribed and primarily give rise to piRNAs that are antisense to transposons. These results indicate that various conserved features of PIWI proteins, the piRNA pathway, and their associations with the nuage were likely established before the evolution of bilaterians. Copyright © 2013 Elsevier Inc. All rights reserved.

Popularity versus similarity in growing networks

NASA Astrophysics Data System (ADS)

Krioukov, Dmitri; Papadopoulos, Fragkiskos; Kitsak, Maksim; Serrano, Mariangeles; Boguna, Marian

2012-02-01

Preferential attachment is a powerful mechanism explaining the emergence of scaling in growing networks. If new connections are established preferentially to more popular nodes in a network, then the network is scale-free. Here we show that not only popularity but also similarity is a strong force shaping the network structure and dynamics. We develop a framework where new connections, instead of preferring popular nodes, optimize certain trade-offs between popularity and similarity. The framework admits a geometric interpretation, in which preferential attachment emerges from local optimization processes. As opposed to preferential attachment, the optimization framework accurately describes large-scale evolution of technological (Internet), social (web of trust), and biological (E.coli metabolic) networks, predicting the probability of new links in them with a remarkable precision. The developed framework can thus be used for predicting new links in evolving networks, and provides a different perspective on preferential attachment as an emergent phenomenon.

Preferential rifting of continents - A source of displaced terranes

NASA Technical Reports Server (NTRS)

Vink, G. E.; Morgan, W. J.; Zhao, W.-L.

1984-01-01

Lithospheric rifting, while prevalent in the continents, rarely occurs in oceanic regions. To explain this preferential rifting of continents, the total strength of different lithospheres is compared by integrating the limits of lithospheric stress with depth. Comparisons of total strength indicate that continental lithosphere is weaker than oceanic lithosphere by about a factor of three. Also, a thickened crust can halve the total strength of normal continental lithosphere. Because the weakest area acts as a stress guide, any rifting close to an ocean-continent boundary would prefer a continental pathway. This results in the formation of small continental fragments or microplates that, once accreted back to a continent during subduction, are seen as displaced terranes. In addition, the large crustal thicknesses associated with suture zones would make such areas likely locations for future rifting episodes. This results in the tendency of new oceans to open along the suture where a former ocean had closed.

Differential Disruption of Nucleocytoplasmic Trafficking Pathways by Rhinovirus 2A Proteases

PubMed Central

Watters, Kelly; Inankur, Bahar; Gardiner, Jaye C.; Warrick, Jay; Sherer, Nathan M.; Yin, John

2017-01-01

ABSTRACT The RNA rhinoviruses (RV) encode 2A proteases (2Apro) that contribute essential polyprotein processing and host cell shutoff functions during infection, including the cleavage of Phe/Gly-containing nucleoporin proteins (Nups) within nuclear pore complexes (NPC). Within the 3 RV species, multiple divergent genotypes encode diverse 2Apro sequences that act differentially on specific Nups. Since only subsets of Phe/Gly motifs, particularly those within Nup62, Nup98, and Nup153, are recognized by transport receptors (karyopherins) when trafficking large molecular cargos through the NPC, the processing preferences of individual 2Apro predict RV genotype-specific targeting of NPC pathways and cargos. To test this idea, transformed HeLa cell lines were created with fluorescent cargos (mCherry) for the importin α/β, transportin 1, and transportin 3 import pathways and the Crm1-mediated export pathway. Live-cell imaging of single cells expressing recombinant RV 2Apro (A16, A45, B04, B14, B52, C02, and C15) showed disruption of each pathway with measurably different efficiencies and reaction rates. The B04 and B52 proteases preferentially targeted Nups in the import pathways, while B04 and C15 proteases were more effective against the export pathway. Virus-type-specific trends were also observed during infection of cells with A16, B04, B14, and B52 viruses or their chimeras, as measured by NF-κB (p65/Rel) translocation into the nucleus and the rates of virus-associated cytopathic effects. This study provides new tools for evaluating the host cell response to RV infections in real time and suggests that differential 2Apro activities explain, in part, strain-dependent host responses and diverse RV disease phenotypes. IMPORTANCE Genetic variation among human rhinovirus types includes unexpected diversity in the genes encoding viral proteases (2Apro) that help these viruses achieve antihost responses. When the enzyme activities of 7 different 2Apro were measured comparatively in transformed cells programed with fluorescent reporter systems and by quantitative cell imaging, the cellular substrates, particularly in the nuclear pore complex, used by these proteases were indeed attacked at different rates and with different affinities. The importance of this finding is that it provides a mechanistic explanation for how different types (strains) of rhinoviruses may elicit different cell responses that directly or indirectly lead to distinct disease phenotypes. PMID:28179529

Integration of Multi-Tension Permeametry and Photogrammetric Textural Segmentation for Estimating Directional Permeability

DTIC Science & Technology

2010-04-01

this heterogeneity, for the purpose of predicting water flow and reactive transport behavior at the field scale, has proven quite difficult. This...potential (soil water pressure) at the outlet and at offset points in response injections at different inlet pressure heads. 13 Task 2: Development...preferential pathways (Wu et al., 1993). A viable solution to this problem is to supply water under tension using an inflatable borehole

Defining the computational structure of the motion detector in Drosophila

PubMed Central

Clark, Damon A.; Bursztyn, Limor; Horowitz, Mark; Schnitzer, Mark J.; Clandinin, Thomas R.

2011-01-01

SUMMARY Many animals rely on visual motion detection for survival. Motion information is extracted from spatiotemporal intensity patterns on the retina, a paradigmatic neural computation. A phenomenological model, the Hassenstein-Reichardt Correlator (HRC), relates visual inputs to neural and behavioral responses to motion, but the circuits that implement this computation remain unknown. Using cell-type specific genetic silencing, minimal motion stimuli, and in vivo calcium imaging, we examine two critical HRC inputs. These two pathways respond preferentially to light and dark moving edges. We demonstrate that these pathways perform overlapping but complementary subsets of the computations underlying the HRC. A numerical model implementing differential weighting of these operations displays the observed edge preferences. Intriguingly, these pathways are distinguished by their sensitivities to a stimulus correlation that corresponds to an illusory percept, “reverse phi”, that affects many species. Thus, this computational architecture may be widely used to achieve edge selectivity in motion detection. PMID:21689602

Self-renewal of a purified Tie2+ hematopoietic stem cell population relies on mitochondrial clearance.

PubMed

Ito, Kyoko; Turcotte, Raphaël; Cui, Jinhua; Zimmerman, Samuel E; Pinho, Sandra; Mizoguchi, Toshihide; Arai, Fumio; Runnels, Judith M; Alt, Clemens; Teruya-Feldstein, Julie; Mar, Jessica C; Singh, Rajat; Suda, Toshio; Lin, Charles P; Frenette, Paul S; Ito, Keisuke

2016-12-02

A single hematopoietic stem cell (HSC) is capable of reconstituting hematopoiesis and maintaining homeostasis by balancing self-renewal and cell differentiation. The mechanisms of HSC division balance, however, are not yet defined. Here we demonstrate, by characterizing at the single-cell level a purified and minimally heterogeneous murine Tie2 + HSC population, that these top hierarchical HSCs preferentially undergo symmetric divisions. The induction of mitophagy, a quality control process in mitochondria, plays an essential role in self-renewing expansion of Tie2 + HSCs. Activation of the PPAR (peroxisome proliferator-activated receptor)-fatty acid oxidation pathway promotes expansion of Tie2 + HSCs through enhanced Parkin recruitment in mitochondria. These metabolic pathways are conserved in human TIE2 + HSCs. Our data thus identify mitophagy as a key mechanism of HSC expansion and suggest potential methods of cell-fate manipulation through metabolic pathways. Copyright © 2016, American Association for the Advancement of Science.

Self-renewal of a purified Tie2+ hematopoietic stem cell population relies on mitochondrial clearance

PubMed Central

Ito, Kyoko; Turcotte, Raphaël; Cui, Jinhua; Zimmerman, Samuel E.; Pinho, Sandra; Mizoguchi, Toshihide; Arai, Fumio; Runnels, Judith M.; Alt, Clemens; Teruya-Feldstein, Julie; Mar, Jessica C.; Singh, Rajat; Suda, Toshio; Lin, Charles P.; Frenette, Paul S.; Ito, Keisuke

2016-01-01

A single hematopoietic stem cell (HSC) is capable of reconstituting hematopoiesis and maintaining homeostasis by balancing self-renewal and cell differentiation. The mechanisms of HSC division balance, however, are not yet defined. Here we demonstrate, by characterizing at the single-cell level a purified and minimally heterogeneous murine Tie2+ HSC population, that these top hierarchical HSCs preferentially undergo symmetric divisions. The induction of mitophagy, a quality control process in mitochondria, plays an essential role in self-renewing expansion of Tie2+ HSCs. Activation of the PPAR (peroxisome proliferator–activated receptor)–fatty acid oxidation pathway promotes expansion of Tie2+ HSCs through enhanced Parkin recruitment in mitochondria. These metabolic pathways are conserved in human TIE2+ HSCs. Our data thus identify mitophagy as a key mechanism of HSC expansion and suggest potential methods of cell-fate manipulation through metabolic pathways. PMID:27738012

A generalized theory of preferential linking

NASA Astrophysics Data System (ADS)

Hu, Haibo; Guo, Jinli; Liu, Xuan; Wang, Xiaofan

2014-12-01

There are diverse mechanisms driving the evolution of social networks. A key open question dealing with understanding their evolution is: How do various preferential linking mechanisms produce networks with different features? In this paper we first empirically study preferential linking phenomena in an evolving online social network, find and validate the linear preference. We propose an analyzable model which captures the real growth process of the network and reveals the underlying mechanism dominating its evolution. Furthermore based on preferential linking we propose a generalized model reproducing the evolution of online social networks, and present unified analytical results describing network characteristics for 27 preference scenarios. We study the mathematical structure of degree distributions and find that within the framework of preferential linking analytical degree distributions can only be the combinations of finite kinds of functions which are related to rational, logarithmic and inverse tangent functions, and extremely complex network structure will emerge even for very simple sublinear preferential linking. This work not only provides a verifiable origin for the emergence of various network characteristics in social networks, but bridges the micro individuals' behaviors and the global organization of social networks.

Time-dependent LXR/RXR pathway modulation characterizes capillary remodeling in inflammatory corneal neovascularization.

PubMed

Mukwaya, Anthony; Lennikov, Anton; Xeroudaki, Maria; Mirabelli, Pierfrancesco; Lachota, Mieszko; Jensen, Lasse; Peebo, Beatrice; Lagali, Neil

2018-05-01

Inflammation in the normally immune-privileged cornea can initiate a pathologic angiogenic response causing vision-threatening corneal neovascularization. Inflammatory pathways, however, are numerous, complex and are activated in a time-dependent manner. Effective resolution of inflammation and associated angiogenesis in the cornea requires knowledge of these pathways and their time dependence, which has, to date, remained largely unexplored. Here, using a model of endogenous resolution of inflammation-induced corneal angiogenesis, we investigate the time dependence of inflammatory genes in effecting capillary regression and the return of corneal transparency. Endogenous capillary regression was characterized by a progressive thinning and remodeling of angiogenic capillaries and inflammatory cell retreat in vivo in the rat cornea. By whole-genome longitudinal microarray analysis, early suppression of VEGF ligand-receptor signaling and inflammatory pathways preceded an unexpected later-phase preferential activation of LXR/RXR, PPARα/RXRα and STAT3 canonical pathways, with a concurrent attenuation of LPS/IL-1 inhibition of RXR function and Wnt/β-catenin signaling pathways. Potent downstream inflammatory cytokines such as Cxcl5, IL-1β, IL-6 and Ccl2 were concomitantly downregulated during the remodeling phase. Upstream regulators of the inflammatory pathways included Socs3, Sparc and ApoE. A complex and coordinated time-dependent interplay between pro- and anti-inflammatory signaling pathways highlights a potential anti-inflammatory role of LXR/RXR, PPARα/RXRα and STAT3 signaling pathways in resolving inflammatory corneal angiogenesis.

A combined crossed-beam and theoretical study of the reaction dynamics of O(3P) + C2H3 → C2H2 + OH: analysis of the nascent OH products with the preferential population of the Π(A') component.

PubMed

Park, Min-Jin; Jang, Su-Chan; Choi, Jong-Ho

2012-11-28

The gas-phase reaction dynamics of ground-state atomic oxygen [O((3)P) from the photo-dissociation of NO(2)] with vinyl radicals [C(2)H(3) from the supersonic flash pyrolysis of vinyl iodide, C(2)H(3)I] has been investigated using a combination of high-resolution laser-induced fluorescence spectroscopy in a crossed-beam configuration and ab initio calculations. Unlike the previous gas-phase bulk kinetic experiments by Baulch et al. [J. Phys. Chem. Ref. Data 34, 757 (2005)], a new exothermic channel of O((3)P) + C(2)H(3) → C(2)H(2) + OH (X (2)Π: υ" = 0) has been identified for the first time, and the population analysis shows bimodal nascent rotational distributions of OH products with low- and high-N" components with a ratio of 2.4:1. No spin-orbit propensities were observed, and the averaged ratios of Π(A('))∕Π(A") were determined to be 1.66 ± 0.27. On the basis of computations at the CBS-QB3 theory level and comparison with prior theory, the microscopic mechanisms responsible for the nascent populations can be understood in terms of two competing dynamical pathways: a direct abstraction process in the low-N" regime as the major pathway and an addition-complex forming process in the high-N" regime as the minor pathway. Particularly, during the bond cleavage process of the weakly bound van der Waals complex C(2)H(2)-OH, the characteristic pathway from the low dihedral-angle geometry was consistent with the observed preferential population of the Π(A') component in the nascent OH products. A molecular-level discussion of the reactivity, mechanism, and dynamical features of the title reaction are presented together with a comparison to gas-phase oxidation reactions of a series of prototypical hydrocarbon radicals.

Urinary metabolomics of young Italian autistic children supports abnormal tryptophan and purine metabolism.

PubMed

Gevi, Federica; Zolla, Lello; Gabriele, Stefano; Persico, Antonio M

2016-01-01

Autism spectrum disorder (ASD) is still diagnosed through behavioral observation, due to a lack of laboratory biomarkers, which could greatly aid clinicians in providing earlier and more reliable diagnoses. Metabolomics on human biofluids provides a sensitive tool to identify metabolite profiles potentially usable as biomarkers for ASD. Initial metabolomic studies, analyzing urines and plasma of ASD and control individuals, suggested that autistic patients may share some metabolic abnormalities, despite several inconsistencies stemming from differences in technology, ethnicity, age range, and definition of "control" status. ASD-specific urinary metabolomic patterns were explored at an early age in 30 ASD children and 30 matched controls (age range 2-7, M:F = 22:8) using hydrophilic interaction chromatography (HILIC)-UHPLC and mass spectrometry, a highly sensitive, accurate, and unbiased approach. Metabolites were then subjected to multivariate statistical analysis and grouped by metabolic pathway. Urinary metabolites displaying the largest differences between young ASD and control children belonged to the tryptophan and purine metabolic pathways. Also, vitamin B 6 , riboflavin, phenylalanine-tyrosine-tryptophan biosynthesis, pantothenate and CoA, and pyrimidine metabolism differed significantly. ASD children preferentially transform tryptophan into xanthurenic acid and quinolinic acid (two catabolites of the kynurenine pathway), at the expense of kynurenic acid and especially of melatonin. Also, the gut microbiome contributes to altered tryptophan metabolism, yielding increased levels of indolyl 3-acetic acid and indolyl lactate. The metabolic pathways most distinctive of young Italian autistic children largely overlap with those found in rodent models of ASD following maternal immune activation or genetic manipulations. These results are consistent with the proposal of a purine-driven cell danger response, accompanied by overproduction of epileptogenic and excitotoxic quinolinic acid, large reductions in melatonin synthesis, and gut dysbiosis. These metabolic abnormalities could underlie several comorbidities frequently associated to ASD, such as seizures, sleep disorders, and gastrointestinal symptoms, and could contribute to autism severity. Their diagnostic sensitivity, disease-specificity, and interethnic variability will merit further investigation.

Synergistic Toxicity of Polyglutamine-Expanded TATA-Binding Protein in Glia and Neuronal Cells: Therapeutic Implications for Spinocerebellar Ataxia 17

PubMed Central

Yang, Yang; Cui, Yiting; Tang, Beisha

2017-01-01

Spinocerebellar ataxia 17 (SCA17) is caused by polyglutamine (polyQ) repeat expansion in the TATA-binding protein (TBP) and is among a family of neurodegenerative diseases in which polyQ expansion leads to preferential neuronal loss in the brain. Although previous studies have demonstrated that expression of polyQ-expanded proteins in glial cells can cause neuronal injury via noncell-autonomous mechanisms, these studies investigated animal models that overexpress transgenic mutant proteins. Since glial cells are particularly reactive to overexpressed mutant proteins, it is important to investigate the in vivo role of glial dysfunction in neurodegeneration when mutant polyQ proteins are endogenously expressed. In the current study, we generated two conditional TBP-105Q knock-in mouse models that specifically express mutant TBP at the endogenous level in neurons or in astrocytes. We found that mutant TBP expression in neuronal cells or astrocytes alone only caused mild neurodegeneration, whereas severe neuronal toxicity requires the expression of mutant TBP in both neuronal and glial cells. Coculture of neurons and astrocytes further validated that mutant TBP in astrocytes promoted neuronal injury. We identified activated inflammatory signaling pathways in mutant TBP-expressing astrocytes, and blocking nuclear factor κB (NF-κB) signaling in astrocytes ameliorated neurodegeneration. Our results indicate that the synergistic toxicity of mutant TBP in neuronal and glial cells plays a critical role in SCA17 pathogenesis and that targeting glial inflammation could be a potential therapeutic approach for SCA17 treatment. SIGNIFICANCE STATEMENT Mutant TBP with polyglutamine expansion preferentially affects neuronal viability in SCA17 patients. Whether glia, the cells that support and protect neurons, contribute to neurodegeneration in SCA17 remains mostly unexplored. In this study, we provide both in vivo and in vitro evidence arguing that endogenous expression of mutant TBP in neurons and glia synergistically impacts neuronal survival. Hyperactivated inflammatory signaling pathways, particularly the NF-κB pathway, underlie glia-mediated neurotoxicity. Moreover, blocking NF-κB activity with small chemical inhibitors alleviated such neurotoxicity. Our study establishes glial dysfunction as an important component of SCA17 pathogenesis and suggests targeting glial inflammation as a potential therapeutic approach for SCA17 treatment. PMID:28821675

Frontosubthalamic Circuits for Control of Action and Cognition

PubMed Central

Herz, Damian M.; Brown, Peter; Forstmann, Birte U.; Zaghloul, Kareem

2016-01-01

The subthalamic nucleus (STN) of the basal ganglia appears to have a potent role in action and cognition. Anatomical and imaging studies show that different frontal cortical areas directly project to the STN via so-called hyperdirect pathways. This review reports some of the latest findings about such circuits, including simultaneous recordings from cortex and the STN in humans, single-unit recordings in humans, high-resolution fMRI, and neurocomputational modeling. We argue that a major function of the STN is to broadly pause behavior and cognition when stop signals, conflict signals, or surprise signals occur, and that the fronto-STN circuits for doing this, at least for stopping and conflict, are dissociable anatomically and in terms of their spectral reactivity. We also highlight recent evidence for synchronization of oscillations between prefrontal cortex and the STN, which may provide a preferential “window in time” for single neuron communication via long-range connections. PMID:27911752

Preferential assembly of heteromeric kainate and AMPA receptor amino terminal domains

PubMed Central

Lomash, Suvendu; Chittori, Sagar; Glasser, Carla

2017-01-01

Ion conductivity and the gating characteristics of tetrameric glutamate receptor ion channels are determined by their subunit composition. Competitive homo- and hetero-dimerization of their amino-terminal domains (ATDs) is a key step controlling assembly. Here we measured systematically the thermodynamic stabilities of homodimers and heterodimers of kainate and AMPA receptors using fluorescence-detected sedimentation velocity analytical ultracentrifugation. Measured affinities span many orders of magnitude, and complexes show large differences in kinetic stabilities. The association of kainate receptor ATD dimers is generally weaker than the association of AMPA receptor ATD dimers, but both show a general pattern of increased heterodimer stability as compared to the homodimers of their constituents, matching well physiologically observed receptor combinations. The free energy maps of AMPA and kainate receptor ATD dimers provide a framework for the interpretation of observed receptor subtype combinations and possible assembly pathways. PMID:29058671

Preferential assembly of heteromeric kainate and AMPA receptor amino terminal domains.

PubMed

Zhao, Huaying; Lomash, Suvendu; Chittori, Sagar; Glasser, Carla; Mayer, Mark L; Schuck, Peter

2017-10-23

Ion conductivity and the gating characteristics of tetrameric glutamate receptor ion channels are determined by their subunit composition. Competitive homo- and hetero-dimerization of their amino-terminal domains (ATDs) is a key step controlling assembly. Here we measured systematically the thermodynamic stabilities of homodimers and heterodimers of kainate and AMPA receptors using fluorescence-detected sedimentation velocity analytical ultracentrifugation. Measured affinities span many orders of magnitude, and complexes show large differences in kinetic stabilities. The association of kainate receptor ATD dimers is generally weaker than the association of AMPA receptor ATD dimers, but both show a general pattern of increased heterodimer stability as compared to the homodimers of their constituents, matching well physiologically observed receptor combinations. The free energy maps of AMPA and kainate receptor ATD dimers provide a framework for the interpretation of observed receptor subtype combinations and possible assembly pathways.

Mapping Inherited Fractures in the Critical Zone Using Seismic Anisotropy From Circular Surveys

NASA Astrophysics Data System (ADS)

Novitsky, Christopher G.; Holbrook, W. Steven; Carr, Bradley J.; Pasquet, Sylvain; Okaya, David; Flinchum, Brady A.

2018-04-01

Weathering and hydrological processes in Earth's shallow subsurface are influenced by inherited bedrock structures, such as bedding planes, faults, joints, and fractures. However, these structures are difficult to observe in soil-mantled landscapes. Steeply dipping structures with a dominant orientation are detectable by seismic anisotropy, with fast wave speeds along the strike of structures. We measured shallow ( 2-4 m) seismic anisotropy using "circle shots," geophones deployed in a circle around a central shot point, in a weathered granite terrain in the Laramie Range of Wyoming. The inferred remnant fracture orientations agree with brittle fracture orientations measured at tens of meters depth in boreholes, demonstrating that bedrock fractures persist through the weathering process into the shallow critical zone. Seismic anisotropy positively correlates with saprolite thickness, suggesting that inherited bedrock fractures may control saprolite thickness by providing preferential pathways for corrosive meteoric waters to access the deep critical zone.

Selective Cytotoxicity of Rhodium Metalloinsertors in Mismatch Repair-Deficient Cells†

PubMed Central

Ernst, Russell J.; Komor, Alexis C.; Barton, Jacqueline K.

2011-01-01

Mismatches in DNA occur naturally during replication and as a result of endogenous DNA damaging agents, but the mismatch repair (MMR) pathway acts to correct mismatches before subsequent rounds of replication. Rhodium metalloinsertors bind to DNA mismatches with high affinity and specificity and represent a promising strategy to target mismatches in cells. Here we examine the biological fate of rhodium metalloinsertors bearing dipyridylamine ancillary ligands in cells deficient in MMR versus those that are MMR-proficient. These complexes are shown to exhibit accelerated cellular uptake which permits the observation of various cellular responses, including disruption of the cell cycle, monitored by flow cytometry assays, and induction of necrosis, monitored by dye exclusion and caspase inhibition assays, that occur preferentially in the MMR-deficient cell line. These cellular responses provide insight into the mechanisms underlying the selective activity of this novel class of targeted anti-cancer agents. PMID:22103240

Thermoelectric properties of semiconductor nanowire networks

DOE PAGES

Roslyak, Oleksiy; Piryatinski, Andrei

2016-03-28

To examine the thermoelectric (TE) properties of a semiconductor nanowire (NW) network, we propose a theoretical approach mapping the TE network on a two-port network. In contrast to a conventional single-port (i.e., resistor)network model, our model allows for large scale calculations showing convergence of TE figure of merit, ZT, with an increasing number of junctions. Using this model, numerical simulations are performed for the Bi 2Te 3 branched nanowire (BNW) and Cayley tree NW (CTNW) network. We find that the phonon scattering at the network junctions plays a dominant role in enhancing the network ZT. Specifically, disordered BNW and CTNWmore » demonstrate an order of magnitude higher ZT enhancement compared to their ordered counterparts. Formation of preferential TE pathways in CTNW makes the network effectively behave as its BNW counterpart. In conclusion, we provide formalism for simulating large scale nanowire networks hinged upon experimentally measurable TE parameters of a single T-junction.« less

The influence of terracettes on surface hydrology and erosion on vegetated Alpine, mountain and steep-sloping environments

NASA Astrophysics Data System (ADS)

Kuhn, Nikolaus; (Phil) Greenwood, Philip

2014-05-01

Alpine and mountain slopes represent important pathways that link high altitude grazing areas to meadows and rangelands at lower elevations. Given the often acute gradient of mountain slopes, they represent a convenient and potentially highly efficient runoff conveyance route that facilitates the downslope transfer of fine-sediment and sediment-bound nutrients and contaminants during erosion events. Above a certain gradient, many slopes host small steps, or `terracettes`. As these are generally orientated across slope, their genesis is usually attributed to a combination of soil creep, coupled with (and often accentuated by) grazing animals. Motivated by the prevalence of these distinct landform features and lack of information on their role as runoff conveyance routes, this communication reports preliminary results from an investigation to explore the possibility that terracettes may act as preferential flow-paths, with an as yet undocumented ability to greatly influence surface hydrology in mountainous and steeply-sloping environments. A ca. 40 m2 area of vegetated terracettes and section of adjacent thalweg, with gradients ranging from approximately 25-35o, were scanned using an automated Topcon IS03 Total Station at a resolution of 0.1 * 0.1 m. Data were converted to a Digital Elevation Model (DEM) in ArcGIS 10 Geographical Information System (GIS), and queried using Spatial Analyst (Surface Hydrology; Flow Accumulation function) to identify slope-sections that could act as preferential flow-pathways during runoff events. These data were supplemented by information on soil physical properties that included grain size composition, bulk density and porosity, in order to establish spatial variations in soil characteristics associated with the vertical and horizontal terracette features. Combining the digital and in-situ data indicate that the technique is able to identify preferential surface flow-paths. Such information could greatly benefit the future management of grazing and rangelands in Alpine, mountain and steeply sloping environments. With higher resolution data covering larger areas, as well as the possibility of using fallout radionuclide data to establish sediment residence times on depositional areas, it is envisioned that runoff and transportation of fine-sediment and sediment-associated nutrients and contaminants down these flow pathways could be modeled, predicted and their effects mitigated and perhaps eventually reduced.

Increase in ubiquitin-protein conjugates concomitant with the increase in proteolysis in rat skeletal muscle during starvation and atrophy denervation

NASA Technical Reports Server (NTRS)

Wing, S. S.; Haas, A. L.; Goldberg, A. L.

1995-01-01

The rapid loss of skeletal-muscle protein during starvation and after denervation occurs primarily through increased rates of protein breakdown and activation of a non-lysosomal ATP-dependent proteolytic process. To investigate whether protein flux through the ubiquitin (Ub)-proteasome pathway is enhanced, as was suggested by related studies, we measured, using specific polyclonal antibodies, the levels of Ub-conjugated proteins in normal and atrophying muscles. The content of these critical intermediates had increased 50-250% after food deprivation in the extensor digitorum longus and soleus muscles 2 days after denervation. Like rates of proteolysis, the amount of Ub-protein conjugates and the fraction of Ub conjugated to proteins increased progressively during food deprivation and returned to normal within 1 day of refeeding. During starvation, muscles of adrenalectomized rats failed to increase protein breakdown, and they showed 50% lower levels of Ub-protein conjugates than those of starved control animals. The changes in the pools of Ub-conjugated proteins (the substrates for the 26S proteasome) thus coincided with and can account for the alterations in overall proteolysis. In this pathway, large multiubiquitinated proteins are preferentially degraded, and the Ub-protein conjugates that accumulated in atrophying muscles were of high molecular mass (> 100 kDa). When innervated and denervated gastrocnemius muscles were fractionated, a significant increase in ubiquitinated proteins was found in the myofibrillar fraction, the proteins of which are preferentially degraded on denervation, but not in the soluble fraction. Thus activation of this proteolytic pathway in atrophying muscles probably occurs initially by increasing Ub conjugation to cell proteins. The resulting accumulation of Ub-protein conjugates suggests that their degradation by the 26S proteasome complex subsequently becomes rate-limiting in these catabolic states.

The photochemistry in Photosystem II at 5 K is different in visible and far-red light.

PubMed

Mokvist, Fredrik; Sjöholm, Johannes; Mamedov, Fikret; Styring, Stenbjörn

2014-07-08

We have earlier shown that all electron transfer reactions in Photosystem II are operational up to 800 nm at room temperature [Thapper, A., et al. (2009) Plant Cell 21, 2391-2401]. This led us to suggest an alternative charge separation pathway for far-red excitation. Here we extend these studies to a very low temperature (5 K). Illumination of Photosystem II (PS II) with visible light at 5 K is known to result in oxidation of almost similar amounts of YZ and the Cyt b559/ChlZ/CarD2 pathway. This is reproduced here using laser flashes at 532 nm, and we find the partition ratio between the two pathways to be 1:0.8 at 5 K [the partition ratio is here defined as (yield of YZ/CaMn4 oxidation):(yield of Cyt b559/ChlZ/CarD2 oxidation)]. The result using far-red laser flashes is very different. We find partition ratios of 1.8 at 730 nm, 2.7 at 740 nm, and >2.7 at 750 nm. No photochemistry involving these pathways is observed above 750 nm at this temperature. Thus, far-red illumination preferentially oxidizes YZ, while the Cyt b559/ChlZ/CarD2 pathway is hardly touched. We propose that the difference in the partition ratio between visible and far-red light at 5 K reflects the formation of a different first stable charge pair. In visible light, the first stable charge pair is considered to be PD1+QA-. In contrast, we propose that the electron hole is residing on the ChlD1 molecule after illumination by far-red light at 5 K, resulting in the first stable charge pair being ChlD1+QA-. ChlD1 is much closer to YZ (11.3 Å) than to any component in the Cyt b559/ChlZ/CarD2 pathway (shortest ChlD1-CarD2 distance of 28.8 Å). This would then explain that far-red illumination preferentially drives efficient electron transfer from YZ. We also discuss mechanisms for accounting for the absorption of the far-red light and the existence of hitherto unobserved charge transfer states. The involvement of two or more of the porphyrin molecules in the core of the Photosystem II reaction center is proposed.

Multiple Genetic Pathways Involving Amino Acid Position 143 of HIV-1 Integrase Are Preferentially Associated with Specific Secondary Amino Acid Substitutions and Confer Resistance to Raltegravir and Cross-Resistance to Elvitegravir

PubMed Central

Frantzell, Arne; Fransen, Signe; Petropoulos, Christos J.

2013-01-01

Y143C,R substitutions in HIV-1 integrase define one of three primary raltegravir (RAL) resistance pathways. Here we describe clinical isolates with alternative substitutions at position 143 (Y143A, Y143G, Y143H, and Y143S [Y143A,G,H,S]) that emerge less frequently, and we compare the genotypic and phenotypic profiles of these viruses to Y143C,R viruses to reconcile the preferential selection of Y143C,R variants during RAL treatment. Integrase amino acid sequences and RAL susceptibility were characterized in 117 patient isolates submitted for drug resistance testing and contained Y143 amino acid changes. The influence of specific Y143 substitutions on RAL susceptibility and their preferential association with particular secondary substitutions were further defined by evaluating the composition of patient virus populations along with a large panel of site-directed mutants. Our observations demonstrate that the RAL resistance profiles of Y143A,G,H,S viruses and their association with specific secondary substitutions are similar to the well-established Y143C profile but distinct from the Y143R profile. Y143R viruses differ from Y143A,C,G,H,S viruses in that Y143R confers a greater reduction in RAL susceptibility as a single substitution, consistent with a lower resistance barrier. Among Y143A,C,G,H,S viruses, the higher prevalence of Y143C viruses is the result of a lower genetic barrier than that of the Y143A,G,S viruses and a lower resistance barrier than that of the Y143H viruses. In addition, Y143A,C,G,H,S viruses require multiple secondary substitutions to develop large reductions in RAL susceptibility. Patient-derived viruses containing Y143 substitutions exhibit cross-resistance to elvitegravir. PMID:23733474

Mouse mammary tumor virus-based vector transduces non-dividing cells, enters the nucleus via a TNPO3-independent pathway and integrates in a less biased fashion than other retroviruses.

PubMed

Konstantoulas, Constantine James; Indik, Stanislav

2014-04-30

Mouse mammary tumor virus (MMTV) is a complex, milk-born betaretrovirus, which preferentially infects dendritic cells (DC) in the gastrointestinal tract and then spreads to T and B lymphocytes and finally to the mammary gland. It is not clear how the prototypic betaretrovirus infects mucosal DCs and naïve lymphocytes as these cells are considered to be non-proliferative. Studies of MMTV biology have been hampered by the difficulty of obtaining sufficient virus/vector titers after transfection of a molecular clone in cultured cells. To surmount this barrier we developed a novel MMTV-based vector system with a split genome design containing potent posttranscriptional regulatory functions. Using this system, vector particles were produced to markedly greater titers (>1000-fold) than those obtained previously. The titers (>106 transduction units /ml) were comparable to those achieved with lentiviral or gammaretroviral vectors. Importantly, the vector transduced the enhanced green fluorescence protein gene into the chromosomes of non-dividing cells, such as cells arrested at the G2/M phase of the cell cycle and unstimulated hematopoietic progenitor cells, at an efficiency similar to that obtained with the HIV-1-based vector. In contrast to HIV-1, MMTV transductions were not affected by knocking down the expression of a factor involved in nuclear import of the HIV-1 pre-integration complexes, TNPO3. In contrast to HIV-1, the MMTV-based vector did not preferentially integrate in transcription units. Additionally, no preference for integration near transcription start sites, the regions preferentially targeted by gammaretroviral vectors, was observed. The vector derived from MMTV exhibits a random integration pattern. Overall, the betaretroviral vector system should facilitate molecular virology studies of the prototypic betaretrovirus as well as studies attempting to elucidate fundamental cellular processes such as nuclear import pathways. Random integration in cycling and non-cycling cells may be applicable in unbiased gene delivery.

From Free to Fee: Neoliberalising Preferential Policy Measures for Minority Education in China

ERIC Educational Resources Information Center

Yamada, Naomi C. F.

2015-01-01

In both China and in the United States, policies of "positive discrimination" were originally intended to lessen educational and economic inequalities, and to provide equal opportunities. As with affirmative action in the American context, China's "preferential policies" are broad-reaching, but are best known for taking ethnic…

Reactive oxygen species-mediated synergistic and preferential induction of cell death and reduction of clonogenic resistance in breast cancer cells by combined cisplatin and FK228.

PubMed

Pluchino, Lenora Ann; Choudhary, Shambhunath; Wang, Hwa-Chain Robert

2016-10-10

Safe and effective combination chemotherapy regimens against breast cancer are lacking. We used our cellular system, consisting of the non-cancerous human breast epithelial MCF10A cell line and its derived tumorigenic, oncogenic H-Ras-expressing, MCF10A-Ras cell line, to investigate the effectiveness of a combination chemotherapy regimen in treating breast cancer cells using two FDA-approved agents, cisplatin and FK228. Cisplatin and FK228 significantly, synergistically, and preferentially induced death and reduced drug resistance of MCF10A-Ras versus MCF10A cells. The ERK-Nox-ROS pathway played a major role in both synergistic cell death induction and GSH-level reduction, which contributed to the synergistic suppression of drug resistance in cells. Enhancement of the Ras-ERK-Nox pathway by combined cisplatin and FK228 significantly increased ROS levels, leading to induction of death, reduction of drug resistance, and induction of DNA damage and oxidation in cancerous MCF10A-Ras cells. Furthermore, synergistic induction of cell death and reduction of drug resistance by combined cisplatin and FK228 in breast cells is independent of their estrogen receptor status. Our study suggests that combined cisplatin and FK228 should be considered in clinical trials as a new regimen for therapeutic control of breast cancers. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Macropore system characteristics controls on non-reactive solute transport at different flow rates

NASA Astrophysics Data System (ADS)

Larsbo, Mats; Koestel, John

2014-05-01

Preferential flow and transport in macroporous soils are important pathways for the leaching of agrochemicals through soils. Preferential solute transport in soil is to a large extent determined by the macropore system characteristics and the water flow conditions. The importance of different characteristics of the macropore system is likely to vary with the flow conditions. The objective of this study was to determine which properties of the macropore system that control the shape of non-reactive tracer solute breakthrough curves at different steady-state flow rates. We sampled five undisturbed columns (20 cm high, 20 cm diameter) from the soil surface of four soils with clay contents between 21 and 50 %. Solute transport experiments were carried out under unsaturated conditions at 2, 4, 6, 8 and 12 mm h-1 flow rates. For each flow rate a pulse of potassium bromide solution was applied at the soil surface and the electrical conductivity was measured with high temporal resolution in the column effluent. We used the 5 % arrival time and the holdback factor to estimate the degree of preferential transport from the resulting breakthrough curves. Unsaturated hydraulic conductivities were measured at the soil surface of the columns using a tension disc infiltrometer. The macropore system was imaged by industrial X-ray computed tomography at a resolution of 125 μm in all directions. Measures of the macropore system characteristics including measures of pore continuity were calculated from these images using the ImageJ software. Results show that the degree of preferential transport is generally increasing with flow rate when larger pores become active in the transport. The degree of preferential flow was correlated to measures of macropore topology. This study show that conclusions drawn from experiments carried out at one flow rate should generally not be extrapolated to other flow rates.

Pluronic-based micelle encapsulation potentiates myricetin-induced cytotoxicity in human glioblastoma cells

PubMed Central

Tang, Xiang-Jun; Huang, Kuan-Ming; Gui, Hui; Wang, Jun-Jie; Lu, Jun-Ti; Dai, Long-Jun; Zhang, Li; Wang, Gang

2016-01-01

As one of the natural herbal flavonoids, myricetin has attracted much research interest, mainly owing to its remarkable anticancer properties and negligible side effects. It holds great potential to be developed as an ideal anticancer drug through improving its bioavailability. This study was performed to investigate the effects of Pluronic-based micelle encapsulation on myricetin-induced cytotoxicity and the mechanisms underlying its anticancer properties in human glioblastoma cells. Cell viability was assessed using a methylthiazol tetrazolium assay and a real-time cell analyzer. Immunoblotting and quantitative reverse transcriptase polymerase chain reaction techniques were used for determining the expression levels of related molecules in protein and mRNA. The results indicated that myricetin-induced cytotoxicity was highly potentiated by the encapsulation of myricetin. Mitochondrial apoptotic pathway was demonstrated to be involved in myricetin-induced glioblastoma cell death. The epidermal growth factor receptor (EGFR)/PI3K/Akt pathway located in the plasma membrane and cytosol and the RAS-ERK pathway located in mitochondria served as upstream and downstream targets, respectively, in myricetin-induced apoptosis. MiR-21 inhibitors interrupted the expression of EGFR, p-Akt, and K-Ras in the same fashion as myricetin-loaded mixed micelles (MYR-MCs) and miR-21 expression were dose-dependently inhibited by MYR-MCs, indicating the interaction of miR-21 with MYR-MCs. This study provided evidence supportive of further development of MYR-MC formulation for preferentially targeting mitochondria of glioblastoma cells. PMID:27757032

Particulate removal processes and hydraulics of porous gravel media filters

NASA Astrophysics Data System (ADS)

Minto, J. M.; Phoenix, V. R.; Dorea, C. C.; Haynes, H.; Sloan, W. T.

2013-12-01

Sustainable urban Drainage Systems (SuDS) are rapidly gaining acceptance as a low-cost tool for treating urban runoff pollutants close to source. Road runoff water in particular requires treatment due to the presence of high levels of suspended particles and heavy metals adsorbed to these particles. The aim of this research is to elucidate the particle removal processes that occur within gravel filters that have so far been considered as 'black-box' systems. Based on these findings, a better understanding will be attained on what influences gravel filter removal efficiency and how this changes throughout their design life; leading to a more rational design of this useful technology. This has been achieved by tying together three disparate research elements: tracer residence time distribution curves of filters during clogging; 3D magnetic resonance imaging (MRI) of clogging filters and computational fluid dynamics (CFD) modelling of complex filter pore networks. This research relates column average changes in particle removal efficiency and tracer residence time distributions (RTDs) due to clogging with non-invasive measurement of the spatial variability in particle deposition. The CFD modelling provides a link between observed deposition patterns, flow velocities and wall shear stresses as well as the explanations for the change in RTD with clogging and the effect on particle transport. Results show that, as a filter clogs, particles take a longer, more tortuous path through the filter. This is offset by a reduction in filter volume resulting in higher flow velocities and more rapid particle transport. Higher velocities result in higher shear stresses and the development of preferential pathways in which the velocity exceeds the deposition threshold and the overall efficiency of the filter decreases. Initial pore geometry is linked to the pattern of deposition and subsequent formation of preferential pathways. These results shed light on the 'black-box' internal clogging processes of gravel filters and are a considerable improvement on the inflow/outflow data most often available to monitor removal efficiency and clogging. Sub-section of the MRI derived geometry showing gravel (grey), pore space (blue), deposited particles (red) for 1) prior to clogging and 2) after clogging. The pore network skeleton (green) provided a reference point for comparing pore diameter change with clogging.

A Critical Role for the cccA Gene Product, Cytochrome c2, in Diverting Electrons from Aerobic Respiration to Denitrification in Neisseria gonorrhoeae

PubMed Central

Hopper, Amanda C.; Li, Ying

2013-01-01

Neisseria gonorrhoeae is a microaerophile that, when oxygen availability is limited, supplements aerobic respiration with a truncated denitrification pathway, nitrite reduction to nitrous oxide. We demonstrate that the cccA gene of Neisseria gonorrhoeae strain F62 (accession number NG0292) is expressed, but the product, cytochrome c2, accumulates to only low levels. Nevertheless, a cccA mutant reduced nitrite at about half the rate of the parent strain. We previously reported that cytochromes c4 and c5 transfer electrons to cytochrome oxidase cbb3 by two independent pathways and that the CcoP subunit of cytochrome oxidase cbb3 transfers electrons to nitrite. We show that mutants defective in either cytochrome c4 or c5 also reduce nitrite more slowly than the parent. By combining mutations in cccA (Δc2), cycA (Δc4), cycB (Δc5), and ccoP (ccoP-C368A), we demonstrate that cytochrome c2 is required for electron transfer from cytochrome c4 via the third heme group of CcoP to the nitrite reductase, AniA, and that cytochrome c5 transfers electrons to nitrite reductase by an independent pathway. We propose that cytochrome c2 forms a complex with cytochrome oxidase. If so, the redox state of cytochrome c2 might regulate electron transfer to nitrite or oxygen. However, our data are more consistent with a mechanism in which cytochrome c2 and the CcoQ subunit of cytochrome oxidase form alternative complexes that preferentially catalyze nitrite and oxygen reduction, respectively. Comparison with the much simpler electron transfer pathway for nitrite reduction in the meningococcus provides fascinating insights into niche adaptation within the pathogenic neisseriae. PMID:23543713

Nesfatin-1 inhibits ovarian epithelial carcinoma cell proliferation in vitro

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Yang; Pang, Xiaoyan; Dong, Mei

Highlights: •Nesfatin-1 inhibits the proliferation and growth of HO-8910 cells by G1 phase arrest. •Nesfatin-1 enhances HO-8910 cell apoptosis. •Nesfatin-1 inhibits HO-8910 cell proliferation via mTOR and RhoA/ROCK signaling pathway. •The first report of nesfatin-1-mediated proliferation in ovarian epithelial carcinoma. -- Abstract: Nesfatin-1, an 82-amino-acid peptide derived from a 396-amino-acid precursor protein nucleobindin 2 (NUCB2), was originally identified in hypothalamic nuclei involved in the regulation of food intake. It was recently reported that nesfatin-1 is a novel depot specific adipokine preferentially produced by subcutaneous tissue, with obesity- and food deprivation-regulated expression. Although a relation between ovarian cancer mortality and obesitymore » has been previously established, a role of nesfatin-1 in ovarian epithelial carcinoma remains unknown. The aim of the present study is to examine the effect of nesfatin-1 on ovary carcinoma cells proliferation. We found that nesfatin-1 inhibits the proliferation and growth of HO-8910 cells by G1 phase arrest, this inhibition could be abolished by nesfatin-1 neutralizing antibody. Nesfatin-1 enhances HO-8910 cell apoptosis, activation of mammalian target of rapamycin (mTOR) and RhoA/ROCK signaling pathway block the effects of nesfatin-1-induced apoptosis, therefore reverses the inhibition of HO-8910 cell proliferation by nesfatin-1. In conclusion, the present study demonstrated that nesfatin-1 can inhibit the proliferation in human ovarian epithelial carcinoma cell line HO-8910 cells through inducing apoptosis via mTOR and RhoA/ROCK signaling pathway. This study provides a novel regulatory signaling pathway of nesfatin-1-regulated ovarian epithelial carcinoma growth and may contribute to ovarian cancer prevention and therapy, especially in obese patients.« less

How does the wetting dynamics affect capillary trapping in heterogeneous soil: Neutron imaging study

NASA Astrophysics Data System (ADS)

Sacha, Jan; Snehota, Michal; Trtik, Pavel; Vontobel, Peter

2017-04-01

The wetting dynamics of the water infiltration into a porous soil system has a strong influence on the amount of entrapped air inside the soil. Simultaneously, a higher volume of entrapped air obstructs a water flow in the medium. This effect is more noticeable in soils with preferential pathways because the soil matrix has a higher capillary forces and therefore the air is accumulated in preferential pathways. In the presented study, two experiments were conducted on the same sample. The first experiment was performed under the constant water level condition (CWL) and the second experiment was carried out under the constant water flux condition (CWF) at the top of the sample. The sample was composed of coarse and medium coarse fractions of sand and fine porous ceramics. Materials were packed into the quartz glass column of the inner diameter of 29 mm. The coarse sand represented a highly conductive region connected from the top to the bottom of the sample with the exception of three thin (2-3 mm) separation layers made up of the medium coarse sand. Three discs of fine ceramics formed slow flow regions. Infiltration experiments were monitored by neutron radiography at two different beamlines to produce two-dimensional (2D) projections. The CWL experiment was monitored at NEUTRA station with an acquisition time of 16 seconds per projection and the CWF experiment was visualized at BOA station with an acquisition time of 0.25 seconds per projection. Both stations are located at the Paul Scherrer Institut, Switzerland. The acquired radiograms of the dry sample were subtracted from all subsequent radiograms to determine the water thickness in projections. From series of corrected radiograms taken at the different angles three-dimensional (3D) image was reconstructed for steady state stage of the CWL experiment and for the entire CWF experiment. Then the series of 3D images mapped the wetting of the porous system over the corresponding phase of infiltration process. The results show a higher steady state infiltration rate during the CWL experiment. In this case, the air was mostly pushed out from the sample by the moving wetting front. The infiltration rate was continuously decreasing during the infiltration up to the value of steady state infiltration rate. When the wetting front has reached the bottom of the sample the air was moving from matrix domain to preferential domain. Infiltration rate was still higher than during CWF. On the contrary, during the CWF the water infiltrated into the fine ceramics first and then into the medium coarse sand attracted by forces that were stronger in comparison to the coarse sand. Due to this effect a significant amount of air was trapped in preferential pathways, and consequently blocked the water flow primarily due to the presence of medium coarse sand regions.

Behavioural and biochemical responses following activation of midbrain dopamine pathways by receptor selective neurokinin agonists.

PubMed

Elliott, P J; Mason, G S; Stephens-Smith, M; Hagan, R M

1991-06-01

Preferential activation of mesolimbic and nigro-striatal dopamine (DA) pathways by receptor-selective and peptidase-resistant neurokinin (NK) agonists is reported. The DA cell body region of the mesolimbic pathway appears to be activated by NK agonists selective for NK-1 and NK-3 receptors whereas the DA cell bodies in the substantia nigra are under an excitatory NK-2 receptor-mediated influence. Stimulation of the mesolimbic DA pathway by NK-1 (Ava[L-Pro9,N-Me-Leu10]SP (7-11) [GR73632]) or NK-3 (Senktide) agonists increase locomotor activity. Additional studies showed that this elevated motor response observed after intra-VTA infusion of GR73632 was accompanied by a corresponding increase in DA turnover in the terminal fields of this pathway. Similarly, unilateral activation of the nigro-striatal DA pathway by NK-2 selective agonists (Ava (D-Pro9) SP (7-11) [GR51667] or [Lys3,Gly8,R-Lac-Leu9]NKA (3-10) [GR64349]) elicit contralateral rotational activity and an increase in DA turnover in the ipsilateral striatum. The rotational response was attenuated by prior administration of an NK-2 antagonist (cyclo (Gln, Trp, Phe, Gly, Leu, Met)] L-659877]) into the nigra. Peripheral injection of haloperidol, a DA antagonist, also blocked the NK-2 agonist induced rotations.

52 Genetic Loci Influencing Myocardial Mass

PubMed Central

van der Harst, Pim; van Setten, Jessica; Verweij, Niek; Vogler, Georg; Franke, Lude; Maurano, Matthew T.; Wang, Xinchen; Leach, Irene Mateo; Eijgelsheim, Mark; Sotoodehnia, Nona; Hayward, Caroline; Sorice, Rossella; Meirelles, Osorio; Lyytikäinen, Leo-Pekka; Polašek, Ozren; Tanaka, Toshiko; Arking, Dan E.; Ulivi, Sheila; Trompet, Stella; Müller-Nurasyid, Martina; Smith, Albert V.; Dörr, Marcus; Kerr, Kathleen F.; Magnani, Jared W.; Fabiola Del Greco, M.; Zhang, Weihua; Nolte, Ilja M.; Silva, Claudia T.; Padmanabhan, Sandosh; Tragante, Vinicius; Esko, Tõnu; Abecasis, Gonçalo R.; Adriaens, Michiel E.; Andersen, Karl; Barnett, Phil; Bis, Joshua C.; Bodmer, Rolf; Buckley, Brendan M.; Campbell, Harry; Cannon, Megan V.; Chakravarti, Aravinda; Chen, Lin Y.; Delitala, Alessandro; Devereux, Richard B.; Doevendans, Pieter A.; Dominiczak, Anna F.; Ferrucci, Luigi; Ford, Ian; Gieger, Christian; Harris, Tamara B.; Haugen, Eric; Heinig, Matthias; Hernandez, Dena G.; Hillege, Hans L.; Hirschhorn, Joel N.; Hofman, Albert; Hubner, Norbert; Hwang, Shih-Jen; Iorio, Annamaria; Kähönen, Mika; Kellis, Manolis; Kolcic, Ivana; Kooner, Ishminder K.; Kooner, Jaspal S.; Kors, Jan A.; Lakatta, Edward G.; Lage, Kasper; Launer, Lenore J.; Levy, Daniel; Lundby, Alicia; Macfarlane, Peter W.; May, Dalit; Meitinger, Thomas; Metspalu, Andres; Nappo, Stefania; Naitza, Silvia; Neph, Shane; Nord, Alex S.; Nutile, Teresa; Okin, Peter M.; Olsen, Jesper V.; Oostra, Ben A.; Penninger, Josef M.; Pennacchio, Len A.; Pers, Tune H.; Perz, Siegfried; Peters, Annette; Pinto, Yigal M.; Pfeufer, Arne; Pilia, Maria Grazia; Pramstaller, Peter P.; Prins, Bram P.; Raitakari, Olli T.; Raychaudhuri, Soumya; Rice, Ken M.; Rossin, Elizabeth J.; Rotter, Jerome I.; Schafer, Sebastian; Schlessinger, David; Schmidt, Carsten O.; Sehmi, Jobanpreet; Silljé, Herman H.W.; Sinagra, Gianfranco; Sinner, Moritz F.; Slowikowski, Kamil; Soliman, Elsayed Z.; Spector, Timothy D.; Spiering, Wilko; Stamatoyannopoulos, John A.; Stolk, Ronald P.; Strauch, Konstantin; Tan, Sian-Tsung; Tarasov, Kirill V.; Trinh, Bosco; Uitterlinden, Andre G.; van den Boogaard, Malou; van Duijn, Cornelia M.; van Gilst, Wiek H.; Viikari, Jorma S.; Visscher, Peter M.; Vitart, Veronique; Völker, Uwe; Waldenberger, Melanie; Weichenberger, Christian X.; Westra, Harm-Jan; Wijmenga, Cisca; Wolffenbuttel, Bruce H.; Yang, Jian; Bezzina, Connie R.; Munroe, Patricia B.; Snieder, Harold; Wright, Alan F.; Rudan, Igor; Boyer, Laurie A.; Asselbergs, Folkert W.; van Veldhuisen, Dirk J.; Stricker, Bruno H.; Psaty, Bruce M.; Ciullo, Marina; Sanna, Serena; Lehtimäki, Terho; Wilson, James F.; Bandinelli, Stefania; Alonso, Alvaro; Gasparini, Paolo; Jukema, J. Wouter; Kääb, Stefan; Gudnason, Vilmundur; Felix, Stephan B.; Heckbert, Susan R.; de Boer, Rudolf A.; Newton-Cheh, Christopher; Hicks, Andrew A.; Chambers, John C.; Jamshidi, Yalda; Visel, Axel; Christoffels, Vincent M.; Isaacs, Aaron; Samani, Nilesh J.; de Bakker, Paul I.W.

2017-01-01

BACKGROUND Myocardial mass is a key determinant of cardiac muscle function and hypertrophy. Myocardial depolarization leading to cardiac muscle contraction is reflected by the amplitude and duration of the QRS complex on the electrocardiogram (ECG). Abnormal QRS amplitude or duration reflect changes in myocardial mass and conduction, and are associated with increased risk of heart failure and death. OBJECTIVES This meta-analysis sought to gain insights into the genetic determinants of myocardial mass. METHODS We carried out a genome-wide association meta-analysis of 4 QRS traits in up to 73,518 individuals of European ancestry, followed by extensive biological and functional assessment. RESULTS We identified 52 genomic loci, of which 32 are novel, that are reliably associated with 1 or more QRS phenotypes at p < 1 × 10−8. These loci are enriched in regions of open chromatin, histone modifications, and transcription factor binding, suggesting that they represent regions of the genome that are actively transcribed in the human heart. Pathway analyses provided evidence that these loci play a role in cardiac hypertrophy. We further highlighted 67 candidate genes at the identified loci that are preferentially expressed in cardiac tissue and associated with cardiac abnormalities in Drosophila melanogaster and Mus musculus. We validated the regulatory function of a novel variant in the SCN5A/SCN10A locus in vitro and in vivo. CONCLUSIONS Taken together, our findings provide new insights into genes and biological pathways controlling myocardial mass and may help identify novel therapeutic targets. PMID:27659466

Grandparental help in Indonesia is directed preferentially towards needier descendants: a potential confounder when exploring grandparental influences on child health.

PubMed

Snopkowski, Kristin; Sear, Rebecca

2015-03-01

A considerable body of evidence has now demonstrated positive correlations between grandparental presence and child health outcomes. It is typically assumed that such correlations exist because grandparental investment in their grandchildren improves child health and wellbeing. However, less is known about how grandparents allocate help to adult children and grandchildren, particularly in lower income contexts. Here we use detailed quantitative data from the longitudinal Indonesia Family Life Survey (data collected in 1993, 1997, 2000, 2007; n = 16,250) to examine grandparental help in a society transitioning both demographically and economically. We test the hypothesis that grandparents direct help preferentially towards those adult children and grandchildren most in need of help. This hypothesis was supported for help provided by married grandparents and single grandmothers, who tended to: provide more help to their adult children when this generation had young children themselves, provide financial help if their adult children were poorer, and provide more household help if their adult daughters worked outside the home. One unexpected result was that help from maternal and paternal grandparents is positively correlated; if one set of grandparents is helping the other set is more likely to help, counter to our predictions. These results provide support for the hypothesis that grandparents preferentially invest in some descendants over others, where married grandparents and single grandmothers tend to invest in those adult children and grandchildren with the most need. Investigating the effect of grandparents on child health outcomes may therefore be confounded by grandparent's preferential investment in needier descendants. Copyright © 2015 Elsevier Ltd. All rights reserved.

The decoration of Nb-doped TiO2 microspheres by reduced graphene oxide for enhanced CO gas sensing

NASA Astrophysics Data System (ADS)

Liang, Feng; Chen, Shimin; Xie, Wei; Zou, Changwei

2018-03-01

Reduced graphene oxide (rGO) was used to improve the CO sensing properties of Nb-doped TiO2 (TiO2:Nb) microspheres by an improved ultrasonic spray pyrolysis deposition method. The responses of the sensor dramatically increased as the CO gas concentration increased from 100 to 1000 ppm, which indicated that rGO/TiO2:Nb-based sensor had a wide detection range for CO gas. Moreover, the conductivity of sensor based on the rGO/TiO2:Nb would be greatly improved than that of sensors without decoration by rGO. The enhanced gas sensing performance of the rGO/TiO2:Nb can be attributed to two reasons. Firstly, rGO could facilitate charge transport from TiO2 to graphene which provided a preferential pathway for the charge currents. Secondly, the decorated TiO2 by rGO could provide more active sites such as oxygen vacancy (VO) which could capture electrons from the conductance band and form a space-charge region.

Early Mesozoic rift basin architecture and sediment routing system in the Moroccan High Atlas

NASA Astrophysics Data System (ADS)

Perez, N.; Teixell, A.; Gomez, D.

2016-12-01

Late Permian to Triassic extensional systems associated with Pangea breakup governed the structural framework and rift basin architecture that was inherited by Cenozoic High Atlas Mountains in Morocco. U-Pb detrital zircon geochronologic and mapping results from Permo-Triassic deposits now incorporated into the High Atlas Mountains provide new constraints on the geometry and interconnectivity among synextensional depocenters. U-Pb detrital zircon data provide provenance constraints of Permo-Triassic deposits, highlighting temporal changes in sediment sources and revealing the spatial pattern of sediment routing along the rift. We also characterize the U-Pb detrital zircon geochronologic signature of distinctive interfingering fluvial, tidal, and aeolian facies that are preferentially preserved near the controlling normal faults. These results highlight complex local sediment mixing patterns potentially linked to the interplay between fault motion, eustatic, and erosion/transport processes. We compare our U-Pb geochronologic results with existing studies of Gondwanan and Laurentian cratonic blocks to investigate continent scale sediment routing pathways, and with analogous early Mesozoic extensional systems situated in South America (Mitu basin, Peru) and North America (Newark Basin) to assess sediment mixing patterns in rift basins.

Genome-wide DNA methylation profiling in infants born to gestational diabetes mellitus.

PubMed

Weng, Xiaoling; Liu, Fatao; Zhang, Hong; Kan, Mengyuan; Wang, Ting; Dong, Mingyue; Liu, Yun

2018-03-26

Offspring exposed to gestational diabetes mellitus (GDM) are at a high risk for metabolic diseases. The mechanisms behind the association between offspring exposed to GDM in utero and an increased risk of health consequences later in life remain unclear. The aim of this study was to clarify the changes in methylation levels in the foetuses of women with GDM and to explore the possible mechanisms linking maternal GDM with a high risk of metabolic diseases in offspring later in life. A genome-wide comparative methylome analysis on the umbilical cord blood of infants born to 30 women with GDM and 33 women with normal pregnancy was performed using Infinium HumanMethylation 450 BeadChip assays. A quantitative methylation analysis of 18 CpG dinucleotides was verified in the validation umbilical cord blood samples from 102 newborns exposed to GDM and 103 newborns who experienced normal pregnancy by MassARRAY EpiTYPER. A total of 4485 differentially methylated sites (DMSs), including 2150 hypermethylated sites and 2335 hypomethylated sites, with a mean β-value difference of >0.05, were identified by the 450k array. Good agreement was observed between the massarray validation data and the 450k array data (R 2 > 0.99; P < 0.0001). Thirty-seven CpGs (representing 20 genes) with a β-value difference of >0.15 between the GDM and healthy groups were identified and showed potential as clinical biomarkers for GDM. "hsa04940: Type I diabetes mellitus" was the most significant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, with a P-value = 3.20E-07 and 1.36E-02 in the hypermethylated and hypomethylated genepathway enrichment analyses, respectively. In the Gene Ontology (GO) pathway analyses, immune MHC-related pathways and neuron development-related pathways were significantly enriched. Our results suggest that GDM has epigenetic effects on genes that are preferentially involved in the Type I diabetes mellitus pathway, immune MHC (major histocompatibility complex)-related pathways and neuron development-related pathways, with consequences on fetal growth and development, and provide supportive evidence that DNA methylation is involved in fetal metabolic programming. Copyright © 2018. Published by Elsevier B.V.

Evidence of isotopic fractionation of natural uranium in cultured human cells

NASA Astrophysics Data System (ADS)

Paredes, Eduardo; Avazeri, Emilie; Malard, Véronique; Vidaud, Claude; Reiller, Pascal E.; Ortega, Richard; Nonell, Anthony; Isnard, Hélène; Chartier, Frédéric; Bresson, Carole

2016-12-01

The study of the isotopic fractionation of endogen elements and toxic heavy metals in living organisms for biomedical applications, and for metabolic and toxicological studies, is a cutting-edge research topic. This paper shows that human neuroblastoma cells incorporated small amounts of uranium (U) after exposure to 10 µM natural U, with preferential uptake of the 235U isotope with regard to 238U. Efforts were made to develop and then validate a procedure for highly accurate n(238U)/n(235U) determinations in microsamples of cells. We found that intracellular U is enriched in 235U by 0.38 ± 0.13‰ (2σ, n = 7) relative to the exposure solutions. These in vitro experiments provide clues for the identification of biological processes responsible for uranium isotopic fractionation and link them to potential U incorporation pathways into neuronal cells. Suggested incorporation processes are a kinetically controlled process, such as facilitated transmembrane diffusion, and the uptake through a high-affinity uranium transport protein involving the modification of the uranyl (UO22+) coordination sphere. These findings open perspectives on the use of isotopic fractionation of metals in cellular models, offering a probe to track uptake/transport pathways and to help decipher associated cellular metabolic processes.

The Neural Basis of Vocal Pitch Imitation in Humans.

PubMed

Belyk, Michel; Pfordresher, Peter Q; Liotti, Mario; Brown, Steven

2016-04-01

Vocal imitation is a phenotype that is unique to humans among all primate species, and so an understanding of its neural basis is critical in explaining the emergence of both speech and song in human evolution. Two principal neural models of vocal imitation have emerged from a consideration of nonhuman animals. One hypothesis suggests that putative mirror neurons in the inferior frontal gyrus pars opercularis of Broca's area may be important for imitation. An alternative hypothesis derived from the study of songbirds suggests that the corticostriate motor pathway performs sensorimotor processes that are specific to vocal imitation. Using fMRI with a sparse event-related sampling design, we investigated the neural basis of vocal imitation in humans by comparing imitative vocal production of pitch sequences with both nonimitative vocal production and pitch discrimination. The strongest difference between these tasks was found in the putamen bilaterally, providing a striking parallel to the role of the analogous region in songbirds. Other areas preferentially activated during imitation included the orofacial motor cortex, Rolandic operculum, and SMA, which together outline the corticostriate motor loop. No differences were seen in the inferior frontal gyrus. The corticostriate system thus appears to be the central pathway for vocal imitation in humans, as predicted from an analogy with songbirds.

Inappropriate activation of the androgen receptor by nonsteroids: involvement of the Src kinase pathway and its therapeutic implications.

PubMed

Desai, Sonal J; Ma, Ai-Hong; Tepper, Clifford G; Chen, Hong-Wu; Kung, Hsing-Jien

2006-11-01

The inappropriate activation of androgen receptor (AR) by nonsteroids is considered a potential mechanism in the emergence of hormone-refractory prostate tumors, but little is known about the properties of these "pseudoactivated" AR. Here, we present the first comprehensive analysis closely examining the properties of AR activated by the neuropeptide bombesin that distinguish it from androgen-activated AR. We show that bombesin-activated AR (a) is required for bombesin-induced growth of LNCaP cells, (b) has a transcriptional profile overlapping with, but not identical to, androgen-activated AR, (c) activates prostate-specific antigen by preferentially binding to its proximal promoter, and (d) assembles a distinct coactivator complex. Significantly, we found that Src kinase is critical for bombesin-induced AR-mediated activity and is required for translocation and transactivation of AR. Additionally, we identify c-Myc, a Src target gene, to be activated by bombesin and a potential coactivator of AR-mediated activity specific to bombesin-induced signaling. Because Src kinase is often activated by other nonsteroids, such as other neuropeptides, growth factors, chemokines, and cytokines, our findings have general applicability and provide rationale for investigating the efficacy of the Src kinase pathway as a target for the prevention of relapsed prostate cancers.

Evidence of isotopic fractionation of natural uranium in cultured human cells

PubMed Central

Paredes, Eduardo; Avazeri, Emilie; Malard, Véronique; Vidaud, Claude; Reiller, Pascal E.; Ortega, Richard; Nonell, Anthony; Isnard, Hélène; Chartier, Frédéric; Bresson, Carole

2016-01-01

The study of the isotopic fractionation of endogen elements and toxic heavy metals in living organisms for biomedical applications, and for metabolic and toxicological studies, is a cutting-edge research topic. This paper shows that human neuroblastoma cells incorporated small amounts of uranium (U) after exposure to 10 µM natural U, with preferential uptake of the 235U isotope with regard to 238U. Efforts were made to develop and then validate a procedure for highly accurate n(238U)/n(235U) determinations in microsamples of cells. We found that intracellular U is enriched in 235U by 0.38 ± 0.13‰ (2σ, n = 7) relative to the exposure solutions. These in vitro experiments provide clues for the identification of biological processes responsible for uranium isotopic fractionation and link them to potential U incorporation pathways into neuronal cells. Suggested incorporation processes are a kinetically controlled process, such as facilitated transmembrane diffusion, and the uptake through a high-affinity uranium transport protein involving the modification of the uranyl (UO22+) coordination sphere. These findings open perspectives on the use of isotopic fractionation of metals in cellular models, offering a probe to track uptake/transport pathways and to help decipher associated cellular metabolic processes. PMID:27872304

Evidence of isotopic fractionation of natural uranium in cultured human cells.

PubMed

Paredes, Eduardo; Avazeri, Emilie; Malard, Véronique; Vidaud, Claude; Reiller, Pascal E; Ortega, Richard; Nonell, Anthony; Isnard, Hélène; Chartier, Frédéric; Bresson, Carole

2016-12-06

The study of the isotopic fractionation of endogen elements and toxic heavy metals in living organisms for biomedical applications, and for metabolic and toxicological studies, is a cutting-edge research topic. This paper shows that human neuroblastoma cells incorporated small amounts of uranium (U) after exposure to 10 µM natural U, with preferential uptake of the 235 U isotope with regard to 238 U. Efforts were made to develop and then validate a procedure for highly accurate n( 238 U)/n( 235 U) determinations in microsamples of cells. We found that intracellular U is enriched in 235 U by 0.38 ± 0.13‰ (2σ, n = 7) relative to the exposure solutions. These in vitro experiments provide clues for the identification of biological processes responsible for uranium isotopic fractionation and link them to potential U incorporation pathways into neuronal cells. Suggested incorporation processes are a kinetically controlled process, such as facilitated transmembrane diffusion, and the uptake through a high-affinity uranium transport protein involving the modification of the uranyl (UO 2 2+ ) coordination sphere. These findings open perspectives on the use of isotopic fractionation of metals in cellular models, offering a probe to track uptake/transport pathways and to help decipher associated cellular metabolic processes.

Genetic and Genomic Insights into the Role of Benzoate-Catabolic Pathway Redundancy in Burkholderia xenovorans LB400†

PubMed Central

Denef, V. J.; Klappenbach, J. A.; Patrauchan, M. A.; Florizone, C.; Rodrigues, J. L. M.; Tsoi, T. V.; Verstraete, W.; Eltis, L. D.; Tiedje, J. M.

2006-01-01

Transcriptomic and proteomic analyses of Burkholderia xenovorans LB400, a potent polychlorinated biphenyl (PCB) degrader, have implicated growth substrate- and phase-dependent expression of three benzoate-catabolizing pathways: a catechol ortho cleavage (ben-cat) pathway and two benzoyl-coenzyme A pathways, encoded by gene clusters on the large chromosome (boxC) and the megaplasmid (boxM). To elucidate the significance of this apparent redundancy, we constructed mutants with deletions of the ben-cat pathway (the ΔbenABCD::kan mutant), the boxC pathway (the ΔboxABC::kan mutant), and both pathways (the ΔbenABCDΔ boxABC::kan mutant). All three mutants oxidized benzoate in resting-cell assays. However, the ΔbenABCD::kan and ΔbenABCD ΔboxABC::kan mutants grew at reduced rates on benzoate and displayed increased lag phases. By contrast, growth on succinate, on 4-hydroxybenzoate, and on biphenyl was unaffected. Microarray and proteomic analyses revealed that cells of the ΔbenABCD::kan mutant growing on benzoate expressed both box pathways. Overall, these results indicate that all three pathways catabolize benzoate. Deletion of benABCD abolished the ability of LB400 to grow using 3-chlorobenzoate. None of the benzoate pathways could degrade 2- or 4-chlorobenzoate, indicating that the pathway redundancy does not directly contribute to LB400's PCB-degrading capacities. Finally, an extensive sigmaE-regulated oxidative stress response not present in wild-type LB400 grown on benzoate was detected in these deletion mutants, supporting our earlier suggestion that the box pathways are preferentially active under reduced oxygen tension. Our data further substantiate the expansive network of tightly interconnected and complexly regulated aromatic degradation pathways in LB400. PMID:16391095

Chewing the fat: lipid metabolism and homeostasis during M. tuberculosis infection.

PubMed

Lovewell, Rustin R; Sassetti, Christopher M; VanderVen, Brian C

2016-02-01

The interplay between Mycobacterium tuberculosis lipid metabolism, the immune response and lipid homeostasis in the host creates a complex and dynamic pathogen-host interaction. Advances in imaging and metabolic analysis techniques indicate that M. tuberculosis preferentially associates with foamy cells and employs multiple physiological systems to utilize exogenously derived fatty-acids and cholesterol. Moreover, novel insights into specific host pathways that control lipid accumulation during infection, such as the PPARγ and LXR transcriptional regulators, have begun to reveal mechanisms by which host immunity alters the bacterial micro-environment. As bacterial lipid metabolism and host lipid regulatory pathways are both important, yet inherently complex, components of active tuberculosis, delineating the heterogeneity in lipid trafficking within disease states remains a major challenge for therapeutic design. Copyright © 2015. Published by Elsevier Ltd.

Methods of expressing and detecting activity of expansin in plant cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hood, Elizabeth E.; Yoon, Sangwoong

A method of expressing heterologous expansin in a plant cell is provided where a nucleic acid molecule encoding expansin is introduced into the plant cell and in an embodiment is operably linked to a promoter preferentially expressing in the seed tissue of the plant, and in another embodiment is linked to a promoter preferentially expressing in the embryo tissue of the seed. An embodiment provides the nucleic acid molecule is operably linked to a second nucleic acid molecule that directs expression to the endoplasmic reticulum, vacuole or cell wall. Plants and plant parts expressing expansin are provided. An assay formore » detection of expansin activity is also provided.« less

Non-invasive flow path characterization in a mining-impacted wetland

USGS Publications Warehouse

Bethune, James; Randell, Jackie; Runkel, Robert L.; Singha, Kamini

2015-01-01

Time-lapse electrical resistivity (ER) was used to capture the dilution of a seasonal pulse of acid mine drainage (AMD) contamination in the subsurface of a wetland downgradient of the abandoned Pennsylvania mine workings in central Colorado. Data were collected monthly from mid-July to late October of 2013, with an additional dataset collected in June of 2014. Inversion of the ER data shows the development through time of multiple resistive anomalies in the subsurface, which corroborating data suggest are driven by changes in total dissolved solids (TDS) localized in preferential flow pathways. Sensitivity analyses on a synthetic model of the site suggest that the anomalies would need to be at least several meters in diameter to be adequately resolved by the inversions. The existence of preferential flow paths would have a critical impact on the extent of attenuation mechanisms at the site, and their further characterization could be used to parameterize reactive transport models in developing quantitative predictions of remediation strategies.

Controlled CO preferential oxidation

DOEpatents

Meltser, Mark A.; Hoch, Martin M.

1997-01-01

Method for controlling the supply of air to a PROX reactor for the preferential oxidation in the presence of hydrogen wherein the concentration of the hydrogen entering and exiting the PROX reactor is monitored, the difference therebetween correlated to the amount of air needed to minimize such difference, and based thereon the air supply to the PROX reactor adjusted to provide such amount and minimize such difference.

Submicron structures provide preferential spots for carbon and nitrogen sequestration in soils

PubMed Central

Vogel, Cordula; Mueller, Carsten W.; Höschen, Carmen; Buegger, Franz; Heister, Katja; Schulz, Stefanie; Schloter, Michael; Kögel-Knabner, Ingrid

2014-01-01

The sequestration of carbon and nitrogen by clay-sized particles in soils is well established, and clay content or mineral surface area has been used to estimate the sequestration potential of soils. Here, via incubation of a sieved (<2 mm) topsoil with labelled litter, we find that only some of the clay-sized surfaces bind organic matter (OM). Surprisingly, <19% of the visible mineral areas show an OM attachment. OM is preferentially associated with organo-mineral clusters with rough surfaces. By combining nano-scale secondary ion mass spectrometry and isotopic tracing, we distinguish between new labelled and pre-existing OM and show that new OM is preferentially attached to already present organo-mineral clusters. These results, which provide evidence that only a limited proportion of the clay-sized surfaces contribute to OM sequestration, revolutionize our view of carbon sequestration in soils and the widely used carbon saturation estimates. PMID:24399306

Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function.

PubMed

Pattaro, Cristian; Teumer, Alexander; Gorski, Mathias; Chu, Audrey Y; Li, Man; Mijatovic, Vladan; Garnaas, Maija; Tin, Adrienne; Sorice, Rossella; Li, Yong; Taliun, Daniel; Olden, Matthias; Foster, Meredith; Yang, Qiong; Chen, Ming-Huei; Pers, Tune H; Johnson, Andrew D; Ko, Yi-An; Fuchsberger, Christian; Tayo, Bamidele; Nalls, Michael; Feitosa, Mary F; Isaacs, Aaron; Dehghan, Abbas; d'Adamo, Pio; Adeyemo, Adebowale; Dieffenbach, Aida Karina; Zonderman, Alan B; Nolte, Ilja M; van der Most, Peter J; Wright, Alan F; Shuldiner, Alan R; Morrison, Alanna C; Hofman, Albert; Smith, Albert V; Dreisbach, Albert W; Franke, Andre; Uitterlinden, Andre G; Metspalu, Andres; Tonjes, Anke; Lupo, Antonio; Robino, Antonietta; Johansson, Åsa; Demirkan, Ayse; Kollerits, Barbara; Freedman, Barry I; Ponte, Belen; Oostra, Ben A; Paulweber, Bernhard; Krämer, Bernhard K; Mitchell, Braxton D; Buckley, Brendan M; Peralta, Carmen A; Hayward, Caroline; Helmer, Catherine; Rotimi, Charles N; Shaffer, Christian M; Müller, Christian; Sala, Cinzia; van Duijn, Cornelia M; Saint-Pierre, Aude; Ackermann, Daniel; Shriner, Daniel; Ruggiero, Daniela; Toniolo, Daniela; Lu, Yingchang; Cusi, Daniele; Czamara, Darina; Ellinghaus, David; Siscovick, David S; Ruderfer, Douglas; Gieger, Christian; Grallert, Harald; Rochtchina, Elena; Atkinson, Elizabeth J; Holliday, Elizabeth G; Boerwinkle, Eric; Salvi, Erika; Bottinger, Erwin P; Murgia, Federico; Rivadeneira, Fernando; Ernst, Florian; Kronenberg, Florian; Hu, Frank B; Navis, Gerjan J; Curhan, Gary C; Ehret, George B; Homuth, Georg; Coassin, Stefan; Thun, Gian-Andri; Pistis, Giorgio; Gambaro, Giovanni; Malerba, Giovanni; Montgomery, Grant W; Eiriksdottir, Gudny; Jacobs, Gunnar; Li, Guo; Wichmann, H-Erich; Campbell, Harry; Schmidt, Helena; Wallaschofski, Henri; Völzke, Henry; Brenner, Hermann; Kroemer, Heyo K; Kramer, Holly; Lin, Honghuang; Leach, I Mateo; Ford, Ian; Guessous, Idris; Rudan, Igor; Prokopenko, Inga; Borecki, Ingrid; Heid, Iris M; Kolcic, Ivana; Persico, Ivana; Jukema, J Wouter; Wilson, James F; Felix, Janine F; Divers, Jasmin; Lambert, Jean-Charles; Stafford, Jeanette M; Gaspoz, Jean-Michel; Smith, Jennifer A; Faul, Jessica D; Wang, Jie Jin; Ding, Jingzhong; Hirschhorn, Joel N; Attia, John; Whitfield, John B; Chalmers, John; Viikari, Jorma; Coresh, Josef; Denny, Joshua C; Karjalainen, Juha; Fernandes, Jyotika K; Endlich, Karlhans; Butterbach, Katja; Keene, Keith L; Lohman, Kurt; Portas, Laura; Launer, Lenore J; Lyytikäinen, Leo-Pekka; Yengo, Loic; Franke, Lude; Ferrucci, Luigi; Rose, Lynda M; Kedenko, Lyudmyla; Rao, Madhumathi; Struchalin, Maksim; Kleber, Marcus E; Cavalieri, Margherita; Haun, Margot; Cornelis, Marilyn C; Ciullo, Marina; Pirastu, Mario; de Andrade, Mariza; McEvoy, Mark A; Woodward, Mark; Adam, Martin; Cocca, Massimiliano; Nauck, Matthias; Imboden, Medea; Waldenberger, Melanie; Pruijm, Menno; Metzger, Marie; Stumvoll, Michael; Evans, Michele K; Sale, Michele M; Kähönen, Mika; Boban, Mladen; Bochud, Murielle; Rheinberger, Myriam; Verweij, Niek; Bouatia-Naji, Nabila; Martin, Nicholas G; Hastie, Nick; Probst-Hensch, Nicole; Soranzo, Nicole; Devuyst, Olivier; Raitakari, Olli; Gottesman, Omri; Franco, Oscar H; Polasek, Ozren; Gasparini, Paolo; Munroe, Patricia B; Ridker, Paul M; Mitchell, Paul; Muntner, Paul; Meisinger, Christa; Smit, Johannes H; Kovacs, Peter; Wild, Philipp S; Froguel, Philippe; Rettig, Rainer; Mägi, Reedik; Biffar, Reiner; Schmidt, Reinhold; Middelberg, Rita P S; Carroll, Robert J; Penninx, Brenda W; Scott, Rodney J; Katz, Ronit; Sedaghat, Sanaz; Wild, Sarah H; Kardia, Sharon L R; Ulivi, Sheila; Hwang, Shih-Jen; Enroth, Stefan; Kloiber, Stefan; Trompet, Stella; Stengel, Benedicte; Hancock, Stephen J; Turner, Stephen T; Rosas, Sylvia E; Stracke, Sylvia; Harris, Tamara B; Zeller, Tanja; Zemunik, Tatijana; Lehtimäki, Terho; Illig, Thomas; Aspelund, Thor; Nikopensius, Tiit; Esko, Tonu; Tanaka, Toshiko; Gyllensten, Ulf; Völker, Uwe; Emilsson, Valur; Vitart, Veronique; Aalto, Ville; Gudnason, Vilmundur; Chouraki, Vincent; Chen, Wei-Min; Igl, Wilmar; März, Winfried; Koenig, Wolfgang; Lieb, Wolfgang; Loos, Ruth J F; Liu, Yongmei; Snieder, Harold; Pramstaller, Peter P; Parsa, Afshin; O'Connell, Jeffrey R; Susztak, Katalin; Hamet, Pavel; Tremblay, Johanne; de Boer, Ian H; Böger, Carsten A; Goessling, Wolfram; Chasman, Daniel I; Köttgen, Anna; Kao, W H Linda; Fox, Caroline S

2016-01-21

Reduced glomerular filtration rate defines chronic kidney disease and is associated with cardiovascular and all-cause mortality. We conducted a meta-analysis of genome-wide association studies for estimated glomerular filtration rate (eGFR), combining data across 133,413 individuals with replication in up to 42,166 individuals. We identify 24 new and confirm 29 previously identified loci. Of these 53 loci, 19 associate with eGFR among individuals with diabetes. Using bioinformatics, we show that identified genes at eGFR loci are enriched for expression in kidney tissues and in pathways relevant for kidney development and transmembrane transporter activity, kidney structure, and regulation of glucose metabolism. Chromatin state mapping and DNase I hypersensitivity analyses across adult tissues demonstrate preferential mapping of associated variants to regulatory regions in kidney but not extra-renal tissues. These findings suggest that genetic determinants of eGFR are mediated largely through direct effects within the kidney and highlight important cell types and biological pathways.

New evidence for grain specific C4 photosynthesis in wheat

PubMed Central

Rangan, Parimalan; Furtado, Agnelo; Henry, Robert J

2016-01-01

The C4 photosynthetic pathway evolved to allow efficient CO2 capture by plants where effective carbon supply may be limiting as in hot or dry environments, explaining the high growth rates of C4 plants such as maize. Important crops such as wheat and rice are C3 plants resulting in efforts to engineer them to use the C4 pathway. Here we show the presence of a C4 photosynthetic pathway in the developing wheat grain that is absent in the leaves. Genes specific for C4 photosynthesis were identified in the wheat genome and found to be preferentially expressed in the photosynthetic pericarp tissue (cross- and tube-cell layers) of the wheat caryopsis. The chloroplasts exhibit dimorphism that corresponds to chloroplasts of mesophyll- and bundle sheath-cells in leaves of classical C4 plants. Breeding to optimize the relative contributions of C3 and C4 photosynthesis may adapt wheat to climate change, contributing to wheat food security. PMID:27530078

Defining the computational structure of the motion detector in Drosophila.

PubMed

Clark, Damon A; Bursztyn, Limor; Horowitz, Mark A; Schnitzer, Mark J; Clandinin, Thomas R

2011-06-23

Many animals rely on visual motion detection for survival. Motion information is extracted from spatiotemporal intensity patterns on the retina, a paradigmatic neural computation. A phenomenological model, the Hassenstein-Reichardt correlator (HRC), relates visual inputs to neural activity and behavioral responses to motion, but the circuits that implement this computation remain unknown. By using cell-type specific genetic silencing, minimal motion stimuli, and in vivo calcium imaging, we examine two critical HRC inputs. These two pathways respond preferentially to light and dark moving edges. We demonstrate that these pathways perform overlapping but complementary subsets of the computations underlying the HRC. A numerical model implementing differential weighting of these operations displays the observed edge preferences. Intriguingly, these pathways are distinguished by their sensitivities to a stimulus correlation that corresponds to an illusory percept, "reverse phi," that affects many species. Thus, this computational architecture may be widely used to achieve edge selectivity in motion detection. Copyright © 2011 Elsevier Inc. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hintermeier, Peter H.; Eckstein, Sebastian; Mei, Donghai

Hydronium ions in the pores of zeolite H-ZSM5 show high catalytic activity in the elimination of water from cyclohexanol in aqueous phase. Substitution induces subtle changes in rates and reaction pathways, which are concluded to be related to steric effects. Exploring the reaction pathways of 2-, 3-, and 4-methylcyclohexanol (2-McyOH, 3-McyOH, and 4-McyOH), 2- and 4-ethylcyclohexanol (2-EcyOH and 4-EcyOH), 2- n-propylcyclohexanol (2-PcyOH), and cyclohexanol (CyOH) it is shown that the E2 character increases with closer positioning of the alkyl and hydroxyl groups. Thus, 4-McyOH dehydration proceeds via an E1-type elimination, while cis-2-McyOH preferentially reacts via an E2 pathway. The entropymore » of activation decreased with increasing alkyl chain length (ca. 20 J mol -1 K -1 per CH 2 unit) for 2-substituted alcohols, which is concluded to result from constraints influencing the configurational entropy of the transition states.« less

Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function

PubMed Central

Pattaro, Cristian; Teumer, Alexander; Gorski, Mathias; Chu, Audrey Y.; Li, Man; Mijatovic, Vladan; Garnaas, Maija; Tin, Adrienne; Sorice, Rossella; Li, Yong; Taliun, Daniel; Olden, Matthias; Foster, Meredith; Yang, Qiong; Chen, Ming-Huei; Pers, Tune H.; Johnson, Andrew D.; Ko, Yi-An; Fuchsberger, Christian; Tayo, Bamidele; Nalls, Michael; Feitosa, Mary F.; Isaacs, Aaron; Dehghan, Abbas; d'Adamo, Pio; Adeyemo, Adebowale; Dieffenbach, Aida Karina; Zonderman, Alan B.; Nolte, Ilja M.; van der Most, Peter J.; Wright, Alan F.; Shuldiner, Alan R.; Morrison, Alanna C.; Hofman, Albert; Smith, Albert V.; Dreisbach, Albert W.; Franke, Andre; Uitterlinden, Andre G.; Metspalu, Andres; Tonjes, Anke; Lupo, Antonio; Robino, Antonietta; Johansson, Åsa; Demirkan, Ayse; Kollerits, Barbara; Freedman, Barry I.; Ponte, Belen; Oostra, Ben A.; Paulweber, Bernhard; Krämer, Bernhard K.; Mitchell, Braxton D.; Buckley, Brendan M.; Peralta, Carmen A.; Hayward, Caroline; Helmer, Catherine; Rotimi, Charles N.; Shaffer, Christian M.; Müller, Christian; Sala, Cinzia; van Duijn, Cornelia M.; Saint-Pierre, Aude; Ackermann, Daniel; Shriner, Daniel; Ruggiero, Daniela; Toniolo, Daniela; Lu, Yingchang; Cusi, Daniele; Czamara, Darina; Ellinghaus, David; Siscovick, David S.; Ruderfer, Douglas; Gieger, Christian; Grallert, Harald; Rochtchina, Elena; Atkinson, Elizabeth J.; Holliday, Elizabeth G.; Boerwinkle, Eric; Salvi, Erika; Bottinger, Erwin P.; Murgia, Federico; Rivadeneira, Fernando; Ernst, Florian; Kronenberg, Florian; Hu, Frank B.; Navis, Gerjan J.; Curhan, Gary C.; Ehret, George B.; Homuth, Georg; Coassin, Stefan; Thun, Gian-Andri; Pistis, Giorgio; Gambaro, Giovanni; Malerba, Giovanni; Montgomery, Grant W.; Eiriksdottir, Gudny; Jacobs, Gunnar; Li, Guo; Wichmann, H-Erich; Campbell, Harry; Schmidt, Helena; Wallaschofski, Henri; Völzke, Henry; Brenner, Hermann; Kroemer, Heyo K.; Kramer, Holly; Lin, Honghuang; Leach, I. Mateo; Ford, Ian; Guessous, Idris; Rudan, Igor; Prokopenko, Inga; Borecki, Ingrid; Heid, Iris M.; Kolcic, Ivana; Persico, Ivana; Jukema, J. Wouter; Wilson, James F.; Felix, Janine F.; Divers, Jasmin; Lambert, Jean-Charles; Stafford, Jeanette M.; Gaspoz, Jean-Michel; Smith, Jennifer A.; Faul, Jessica D.; Wang, Jie Jin; Ding, Jingzhong; Hirschhorn, Joel N.; Attia, John; Whitfield, John B.; Chalmers, John; Viikari, Jorma; Coresh, Josef; Denny, Joshua C.; Karjalainen, Juha; Fernandes, Jyotika K.; Endlich, Karlhans; Butterbach, Katja; Keene, Keith L.; Lohman, Kurt; Portas, Laura; Launer, Lenore J.; Lyytikäinen, Leo-Pekka; Yengo, Loic; Franke, Lude; Ferrucci, Luigi; Rose, Lynda M.; Kedenko, Lyudmyla; Rao, Madhumathi; Struchalin, Maksim; Kleber, Marcus E.; Cavalieri, Margherita; Haun, Margot; Cornelis, Marilyn C.; Ciullo, Marina; Pirastu, Mario; de Andrade, Mariza; McEvoy, Mark A.; Woodward, Mark; Adam, Martin; Cocca, Massimiliano; Nauck, Matthias; Imboden, Medea; Waldenberger, Melanie; Pruijm, Menno; Metzger, Marie; Stumvoll, Michael; Evans, Michele K.; Sale, Michele M.; Kähönen, Mika; Boban, Mladen; Bochud, Murielle; Rheinberger, Myriam; Verweij, Niek; Bouatia-Naji, Nabila; Martin, Nicholas G.; Hastie, Nick; Probst-Hensch, Nicole; Soranzo, Nicole; Devuyst, Olivier; Raitakari, Olli; Gottesman, Omri; Franco, Oscar H.; Polasek, Ozren; Gasparini, Paolo; Munroe, Patricia B.; Ridker, Paul M.; Mitchell, Paul; Muntner, Paul; Meisinger, Christa; Smit, Johannes H.; Abecasis, Goncalo R.; Adair, Linda S.; Alexander, Myriam; Altshuler, David; Amin, Najaf; Arking, Dan E.; Arora, Pankaj; Aulchenko, Yurii; Bakker, Stephan J. L.; Bandinelli, Stefania; Barroso, Ines; Beckmann, Jacques S.; Beilby, John P.; Bergman, Richard N.; Bergmann, Sven; Bis, Joshua C.; Boehnke, Michael; Bonnycastle, Lori L.; Bornstein, Stefan R.; Bots, Michiel L.; Bragg-Gresham, Jennifer L.; Brand, Stefan-Martin; Brand, Eva; Braund, Peter S.; Brown, Morris J.; Burton, Paul R.; Casas, Juan P.; Caulfield, Mark J.; Chakravarti, Aravinda; Chambers, John C.; Chandak, Giriraj R.; Chang, Yen-Pei C.; Charchar, Fadi J.; Chaturvedi, Nish; Shin Cho, Yoon; Clarke, Robert; Collins, Francis S.; Collins, Rory; Connell, John M.; Cooper, Jackie A.; Cooper, Matthew N.; Cooper, Richard S.; Corsi, Anna Maria; Dörr, Marcus; Dahgam, Santosh; Danesh, John; Smith, George Davey; Day, Ian N. M.; Deloukas, Panos; Denniff, Matthew; Dominiczak, Anna F.; Dong, Yanbin; Doumatey, Ayo; Elliott, Paul; Elosua, Roberto; Erdmann, Jeanette; Eyheramendy, Susana; Farrall, Martin; Fava, Cristiano; Forrester, Terrence; Fowkes, F. Gerald R.; Fox, Ervin R.; Frayling, Timothy M.; Galan, Pilar; Ganesh, Santhi K.; Garcia, Melissa; Gaunt, Tom R.; Glazer, Nicole L.; Go, Min Jin; Goel, Anuj; Grässler, Jürgen; Grobbee, Diederick E.; Groop, Leif; Guarrera, Simonetta; Guo, Xiuqing; Hadley, David; Hamsten, Anders; Han, Bok-Ghee; Hardy, Rebecca; Hartikainen, Anna-Liisa; Heath, Simon; Heckbert, Susan R.; Hedblad, Bo; Hercberg, Serge; Hernandez, Dena; Hicks, Andrew A.; Hilton, Gina; Hingorani, Aroon D.; Bolton, Judith A Hoffman; Hopewell, Jemma C.; Howard, Philip; Humphries, Steve E.; Hunt, Steven C.; Hveem, Kristian; Ikram, M. Arfan; Islam, Muhammad; Iwai, Naoharu; Jarvelin, Marjo-Riitta; Jackson, Anne U.; Jafar, Tazeen H.; Janipalli, Charles S.; Johnson, Toby; Kathiresan, Sekar; Khaw, Kay-Tee; Kim, Hyung-Lae; Kinra, Sanjay; Kita, Yoshikuni; Kivimaki, Mika; Kooner, Jaspal S.; Kumar, M. J. Kranthi; Kuh, Diana; Kulkarni, Smita R.; Kumari, Meena; Kuusisto, Johanna; Kuznetsova, Tatiana; Laakso, Markku; Laan, Maris; Laitinen, Jaana; Lakatta, Edward G.; Langefeld, Carl D.; Larson, Martin G.; Lathrop, Mark; Lawlor, Debbie A.; Lawrence, Robert W.; Lee, Jong-Young; Lee, Nanette R.; Levy, Daniel; Li, Yali; Longstreth, Will T.; Luan, Jian'an; Lucas, Gavin; Ludwig, Barbara; Mangino, Massimo; Mani, K. Radha; Marmot, Michael G.; Mattace-Raso, Francesco U. S.; Matullo, Giuseppe; McArdle, Wendy L.; McKenzie, Colin A.; Meitinger, Thomas; Melander, Olle; Meneton, Pierre; Meschia, James F.; Miki, Tetsuro; Milaneschi, Yuri; Mohlke, Karen L.; Mooser, Vincent; Morken, Mario A.; Morris, Richard W.; Mosley, Thomas H.; Najjar, Samer; Narisu, Narisu; Newton-Cheh, Christopher; Nguyen, Khanh-Dung Hoang; Nilsson, Peter; Nyberg, Fredrik; O'Donnell, Christopher J.; Ogihara, Toshio; Ohkubo, Takayoshi; Okamura, Tomonori; Ong, RickTwee-Hee; Ongen, Halit; Onland-Moret, N. Charlotte; O'Reilly, Paul F.; Org, Elin; Orru, Marco; Palmas, Walter; Palmen, Jutta; Palmer, Lyle J.; Palmer, Nicholette D.; Parker, Alex N.; Peden, John F.; Peltonen, Leena; Perola, Markus; Pihur, Vasyl; Platou, Carl G. P.; Plump, Andrew; Prabhakaran, Dorairajan; Psaty, Bruce M.; Raffel, Leslie J.; Rao, Dabeeru C.; Rasheed, Asif; Ricceri, Fulvio; Rice, Kenneth M.; Rosengren, Annika; Rotter, Jerome I.; Rudock, Megan E.; Sõber, Siim; Salako, Tunde; Saleheen, Danish; Salomaa, Veikko; Samani, Nilesh J.; Schwartz, Steven M.; Schwarz, Peter E. H.; Scott, Laura J.; Scott, James; Scuteri, Angelo; Sehmi, Joban S.; Seielstad, Mark; Seshadri, Sudha; Sharma, Pankaj; Shaw-Hawkins, Sue; Shi, Gang; Shrine, Nick R. G.; Sijbrands, Eric J. G.; Sim, Xueling; Singleton, Andrew; Sjögren, Marketa; Smith, Nicholas L.; Artigas, Maria Soler; Spector, Tim D.; Staessen, Jan A.; Stancakova, Alena; Steinle, Nanette I.; Strachan, David P.; Stringham, Heather M.; Sun, Yan V.; Swift, Amy J.; Tabara, Yasuharu; Tai, E-Shyong; Talmud, Philippa J.; Taylor, Andrew; Terzic, Janos; Thelle, Dag S.; Tobin, Martin D.; Tomaszewski, Maciej; Tripathy, Vikal; Tuomilehto, Jaakko; Tzoulaki, Ioanna; Uda, Manuela; Ueshima, Hirotsugu; Uiterwaal, Cuno S. P. M.; Umemura, Satoshi; van der Harst, Pim; van der Schouw, Yvonne T.; van Gilst, Wiek H.; Vartiainen, Erkki; Vasan, Ramachandran S.; Veldre, Gudrun; Verwoert, Germaine C.; Viigimaa, Margus; Vinay, D. G.; Vineis, Paolo; Voight, Benjamin F.; Vollenweider, Peter; Wagenknecht, Lynne E.; Wain, Louise V.; Wang, Xiaoling; Wang, Thomas J.; Wareham, Nicholas J.; Watkins, Hugh; Weder, Alan B.; Whincup, Peter H.; Wiggins, Kerri L.; Witteman, Jacqueline C. M.; Wong, Andrew; Wu, Ying; Yajnik, Chittaranjan S.; Yao, Jie; Young, J. H.; Zelenika, Diana; Zhai, Guangju; Zhang, Weihua; Zhang, Feng; Zhao, Jing Hua; Zhu, Haidong; Zhu, Xiaofeng; Zitting, Paavo; Zukowska-Szczechowska, Ewa; Okada, Yukinori; Wu, Jer-Yuarn; Gu, Dongfeng; Takeuchi, Fumihiko; Takahashi, Atsushi; Maeda, Shiro; Tsunoda, Tatsuhiko; Chen, Peng; Lim, Su-Chi; Wong, Tien-Yin; Liu, Jianjun; Young, Terri L.; Aung, Tin; Teo, Yik-Ying; Kim, Young Jin; Kang, Daehee; Chen, Chien-Hsiun; Tsai, Fuu-Jen; Chang, Li-Ching; Fann, S. -J. Cathy; Mei, Hao; Hixson, James E.; Chen, Shufeng; Katsuya, Tomohiro; Isono, Masato; Albrecht, Eva; Yamamoto, Kazuhiko; Kubo, Michiaki; Nakamura, Yusuke; Kamatani, Naoyuki; Kato, Norihiro; He, Jiang; Chen, Yuan-Tsong; Tanaka, Toshihiro; Reilly, Muredach P; Schunkert, Heribert; Assimes, Themistocles L.; Hall, Alistair; Hengstenberg, Christian; König, Inke R.; Laaksonen, Reijo; McPherson, Ruth; Thompson, John R.; Thorsteinsdottir, Unnur; Ziegler, Andreas; Absher, Devin; Chen, Li; Cupples13, L. Adrienne; Halperin, Eran; Li, Mingyao; Musunuru, Kiran; Preuss, Michael; Schillert, Arne; Thorleifsson, Gudmar; Wells, George A.; Holm, Hilma; Roberts, Robert; Stewart, Alexandre F. R.; Fortmann, Stephen; Go, Alan; Hlatky, Mark; Iribarren, Carlos; Knowles, Joshua; Myers, Richard; Quertermous, Thomas; Sidney, Steven; Risch, Neil; Tang, Hua; Blankenberg, Stefan; Schnabel, Renate; Sinning, Christoph; Lackner, Karl J.; Tiret, Laurence; Nicaud, Viviane; Cambien, Francois; Bickel, Christoph; Rupprecht, Hans J.; Perret, Claire; Proust, Carole; Münzel, Thomas F.; Barbalic, Maja; Chen, Ida Yii-Der; Demissie-Banjaw, Serkalem; Folsom, Aaron; Lumley, Thomas; Marciante, Kristin; Taylor, Kent D.; Volcik, Kelly; Gretarsdottir, Solveig; Gulcher, Jeffrey R.; Kong, Augustine; Stefansson, Kari; Thorgeirsson, Gudmundur; Andersen, Karl; Fischer, Marcus; Grosshennig, Anika; Linsel-Nitschke, Patrick; Stark, Klaus; Schreiber, Stefan; Aherrahrou, Zouhair; Bruse, Petra; Doering, Angela; Klopp, Norman; Diemert, Patrick; Loley, Christina; Medack, Anja; Nahrstedt, Janja; Peters, Annette; Wagner, Arnika K.; Willenborg, Christina; Böhm, Bernhard O.; Dobnig, Harald; Grammer, Tanja B.; Hoffmann, Michael M.; Meinitzer, Andreas; Winkelmann, Bernhard R.; Pilz, Stefan; Renner, Wilfried; Scharnagl, Hubert; Stojakovic, Tatjana; Tomaschitz, Andreas; Winkler, Karl; Guiducci, Candace; Burtt, Noel; Gabriel, Stacey B.; Dandona, Sonny; Jarinova, Olga; Qu, Liming; Wilensky, Robert; Matthai, William; Hakonarson, Hakon H.; Devaney, Joe; Burnett, Mary Susan; Pichard, Augusto D.; Kent, Kenneth M.; Satler, Lowell; Lindsay, Joseph M.; Waksman, Ron; Knouff, Christopher W.; Waterworth, Dawn M.; Walker, Max C.; Epstein, Stephen E.; Rader, Daniel J.; Nelson, Christopher P.; Wright, Benjamin J.; Balmforth, Anthony J.; Ball, Stephen G.; Loehr, Laura R.; Rosamond, Wayne D.; Benjamin, Emelia; Haritunians, Talin; Couper, David; Murabito, Joanne; Wang, Ying A.; Stricker, Bruno H.; Chang, Patricia P.; Willerson, James T.; Felix, Stephan B.; Watzinger, Norbert; Aragam, Jayashri; Zweiker, Robert; Lind, Lars; Rodeheffer, Richard J.; Greiser, Karin Halina; Deckers, Jaap W.; Stritzke, Jan; Ingelsson, Erik; Kullo, Iftikhar; Haerting, Johannes; Reffelmann, Thorsten; Redfield, Margaret M.; Werdan, Karl; Mitchell, Gary F.; Arnett, Donna K.; Gottdiener, John S.; Blettner, Maria; Friedrich, Nele; Kovacs, Peter; Wild, Philipp S.; Froguel, Philippe; Rettig, Rainer; Mägi, Reedik; Biffar, Reiner; Schmidt, Reinhold; Middelberg, Rita P. S.; Carroll, Robert J.; Penninx, Brenda W.; Scott, Rodney J.; Katz, Ronit; Sedaghat, Sanaz; Wild, Sarah H.; Kardia, Sharon L. R.; Ulivi, Sheila; Hwang, Shih-Jen; Enroth, Stefan; Kloiber, Stefan; Trompet, Stella; Stengel, Benedicte; Hancock, Stephen J.; Turner, Stephen T.; Rosas, Sylvia E.; Stracke, Sylvia; Harris, Tamara B.; Zeller, Tanja; Zemunik, Tatijana; Lehtimäki, Terho; Illig, Thomas; Aspelund, Thor; Nikopensius, Tiit; Esko, Tonu; Tanaka, Toshiko; Gyllensten, Ulf; Völker, Uwe; Emilsson, Valur; Vitart, Veronique; Aalto, Ville; Gudnason, Vilmundur; Chouraki, Vincent; Chen, Wei-Min; Igl, Wilmar; März, Winfried; Koenig, Wolfgang; Lieb, Wolfgang; Loos, Ruth J. F.; Liu, Yongmei; Snieder, Harold; Pramstaller, Peter P.; Parsa, Afshin; O'Connell, Jeffrey R.; Susztak, Katalin; Hamet, Pavel; Tremblay, Johanne; de Boer, Ian H.; Böger, Carsten A.; Goessling, Wolfram; Chasman, Daniel I.; Köttgen, Anna; Kao, W. H. Linda; Fox, Caroline S.

2016-01-01

Reduced glomerular filtration rate defines chronic kidney disease and is associated with cardiovascular and all-cause mortality. We conducted a meta-analysis of genome-wide association studies for estimated glomerular filtration rate (eGFR), combining data across 133,413 individuals with replication in up to 42,166 individuals. We identify 24 new and confirm 29 previously identified loci. Of these 53 loci, 19 associate with eGFR among individuals with diabetes. Using bioinformatics, we show that identified genes at eGFR loci are enriched for expression in kidney tissues and in pathways relevant for kidney development and transmembrane transporter activity, kidney structure, and regulation of glucose metabolism. Chromatin state mapping and DNase I hypersensitivity analyses across adult tissues demonstrate preferential mapping of associated variants to regulatory regions in kidney but not extra-renal tissues. These findings suggest that genetic determinants of eGFR are mediated largely through direct effects within the kidney and highlight important cell types and biological pathways. PMID:26831199

Anther-preferential expressing gene PMR is essential for the mitosis of pollen development in rice.

PubMed

Liu, Yaqin; Xu, Ya; Ling, Sheng; Liu, Shasha; Yao, Jialing

2017-06-01

Phenotype identification, expression examination, and function prediction declared that the anther-preferential expressing gene PMR may participate in regulation of male gametophyte development in rice. Male germline development in flowering plants produces the pair of sperm cells for double fertilization and the pollen mitosis is a key process of it. Although the structural features of male gametophyte have been defined, the molecular mechanisms regulating the mitotic cell cycle are not well elucidated in rice. Here, we reported an anther-preferential expressing gene in rice, PMR (Pollen Mitosis Relative), playing an essential role in male gametogenesis. When PMR gene was suppressed via RNAi, the mitosis of microspore was severely damaged, and the plants formed unmatured pollens containing only one or two nucleuses at the anthesis, ultimately leading to serious reduction of pollen fertility and seed-setting. The CRISPR mutants, pmr-1 and pmr-2, both showed the similar defects as the PMR-RNAi lines. Further analysis revealed that PMR together with its co-expressing genes were liable to participate in the regulation of DNA metabolism in the nucleus, and affected the activities of some enzymes related to the cell cycle. We finally discussed that unknown protein PMR contained the PHD, SWIB and Plus-3 domains and they might have coordinating functions in regulation pathway of the pollen mitosis in rice.

Phosphodiesterase-10A Inverse Changes in Striatopallidal and Striatoentopeduncular Pathways of a Transgenic Mouse Model of DYT1 Dystonia.

PubMed

D'Angelo, Vincenza; Castelli, Valentina; Giorgi, Mauro; Cardarelli, Silvia; Saverioni, Ilaria; Palumbo, Francesca; Bonsi, Paola; Pisani, Antonio; Giampà, Carmela; Sorge, Roberto; Biagioni, Stefano; Fusco, Francesca R; Sancesario, Giuseppe

2017-02-22

We report that changes of phosphodiesterase-10A (PDE10A) can map widespread functional imbalance of basal ganglia circuits in a mouse model of DYT1 dystonia overexpressing mutant torsinA. PDE10A is a key enzyme in the catabolism of second messenger cAMP and cGMP, whose synthesis is stimulated by D1 receptors and inhibited by D2 receptors preferentially expressed in striatoentopeducuncular/substantia nigra or striatopallidal pathways, respectively. PDE10A was studied in control mice (NT) and in mice carrying human wild-type torsinA (hWT) or mutant torsinA (hMT). Quantitative analysis of PDE10A expression was assessed in different brain areas by rabbit anti-PDE10A antibody immunohistochemistry and Western blotting. PDE10A-dependent cAMP hydrolyzing activity and PDE10A mRNA were also assessed. Striatopallidal neurons were identified by rabbit anti-enkephalin antibody.In NT mice, PDE10A is equally expressed in medium spiny striatal neurons and in their projections to entopeduncular nucleus/substantia nigra and to external globus pallidus. In hMT mice, PDE10A content selectively increases in enkephalin-positive striatal neuronal bodies; moreover, PDE10A expression and activity in hMT mice, compared with NT mice, significantly increase in globus pallidus but decrease in entopeduncular nucleus/substantia nigra. Similar changes of PDE10A occur in hWT mice, but such changes are not always significant. However, PDE10A mRNA expression appears comparable among NT, hWT, and hMT mice.In DYT1 transgenic mice, the inverse changes of PDE10A in striatoentopeduncular and striatopallidal projections might result over time in an imbalance between direct and indirect pathways for properly focusing movement. The decrease of PDE10A in the striatoentopeduncular/nigral projections might lead to increased intensity and duration of D1-stimulated cAMP/cGMP signaling; conversely, the increase of PDE10A in the striatopallidal projections might lead to increased intensity and duration of D2-inhibited cAMP/cGMP signaling. SIGNIFICANCE STATEMENT In DYT1 transgenic mouse model of dystonia, PDE10A, a key enzyme in cAMP and cGMP catabolism, is downregulated in striatal projections to entopeduncular nucleus/substantia nigra, preferentially expressing D1 receptors that stimulate cAMP/cGMP synthesis. Conversely, in DYT1 mice, PDE10A is upregulated in striatal projections to globus pallidus, preferentially expressing D2 receptors that inhibit cAMP/cGMP synthesis. The inverse changes to PDE10A in striatoentopeduncular/substantia nigra and striatopallidal pathways might tightly interact downstream to dopamine receptors, likely resulting over time to increased intensity and duration respectively of D1-stimulated and D2-inhibited cAMP/cGMP signals. Therefore, PDE10A changes in the DYT1 model of dystonia can upset the functional balance of basal ganglia circuits, affecting direct and indirect pathways simultaneously. Copyright © 2017 the authors 0270-6474/17/372113-13$15.00/0.

A Close Look at the Structure of the TiO2-APTES Interface in Hybrid Nanomaterials and Its Degradation Pathway: An Experimental and Theoretical Study

PubMed Central

2016-01-01

The surface functionalization of TiO2-based materials with alkylsilanes is attractive in several cutting-edge applications, such as photovoltaics, sensors, and nanocarriers for the controlled release of bioactive molecules. (3-Aminopropyl)triethoxysilane (APTES) is able to self-assemble to form monolayers on TiO2 surfaces, but its adsorption geometry and solar-induced photodegradation pathways are not well understood. We here employ advanced experimental (XPS, NEXAFS, AFM, HR-TEM, and FT-IR) and theoretical (plane-wave DFT) tools to investigate the preferential interaction mode of APTES on anatase TiO2. We demonstrate that monomeric APTES chemisorption should proceed through covalent Si–O–Ti bonds. Although dimerization of the silane through Si–O–Si bonds is possible, further polymerization on the surface is scarcely probable. Terminal amino groups are expected to be partially involved in strong charge-assisted hydrogen bonds with surface hydroxyl groups of TiO2, resulting in a reduced propensity to react with other species. Solar-induced mineralization proceeds through preferential cleavage of the alkyl groups, leading to the rapid loss of the terminal NH2 moieties, whereas the Si-bearing head of APTES undergoes slower oxidation and remains bound to the surface. The suitability of employing the silane as a linker with other chemical species is discussed in the context of controlled degradation of APTES monolayers for drug release and surface patterning. PMID:28191270

Hydrology of paraglacial catchments: preferential flow sustaining biodiversity hotspots in a changing climate

NASA Astrophysics Data System (ADS)

Grocott, M.; Kettridge, N.; Bradley, C.; Milner, A.

2015-12-01

Groundwater-fed streams are important biodiversity hotspots on paraglacial floodplains supporting a rich and abundant fauna. However, paraglacial systems in arctic, sub-arctic, and alpine regions are changing profoundly as a consequence of climate change. Glacial retreat, increasing permafrost melt, declining winter snowpacks, earlier spring melt, and shifting summer precipitation patterns are modifying the water balance in these areas and increasing environmental vulnerability. Here, we determine the hydrological functioning of groundwater-fed stream networks in Denali National Park, Alaska, demonstrating the importance of hillslope runoff through talus deposits and the significance of preferential flow pathways (PFPs) in supporting the stream networks. We used geochemical (major ions) and stable isotopic (δ2H & δ18O) tracers to identify key water sources, determine flow paths, and highlight spatial and temporal variations in the relative contributions of individual water sources and pathways to streamflow. Multiple flow paths are shown to support streams, with the relative contribution of water sources varying on both inter-annual and seasonal scales. Hydrograph separations confirm hillslope runoff as a key contributor of flow to groundwater fed stream networks. Further, they establish the importance of talus deposits on valley sides as conduits of flow, and their potential importance as headwater aquifers. The implications are that the effects of changing climates within paraglacial environments on hillslope runoff sources will have a greater impact on these biodiversity hotspots than up-valley glacial retreat and associated changes.

Use of geophysical methods to characterize groundwater in karstic rocks near Puerto Morelos, Yucatan Peninsula, Mexico

NASA Astrophysics Data System (ADS)

cerda Garcia, C. G.; Carpenter, P. J.; Leal-Bautista, R. M.

2017-12-01

Geophysical surveys were used to determine the depth of the freshwater/saltwater interface and groundwater preferential flow pathways along the Ruta de los Cenotes, near Puerto Morelos (northeast part of the Yucatán peninsula). The Yucatán Peninsula is a limestone platform that allows quick recharge of the aquifer, the main supply of water for this region. The water in the aquifer is divided into freshwater and saltwater zones. A Schlumberger resistivity sounding along the road near one cenote suggests the water table is 5 meters deep and the freshwater/saltwater interface is 38 meters deep. A time-domain electromagnetic (TEM) sounding suggests the freshwater/saltwater interface is 45 meters deep. The depth of the interface determines the volume of fresh water available. Preferential flow pathways in the vadose and saturated zones are karst conduits where groundwater percolates downward in the vadose zone. These were identified using resistivity profiling and spontaneous self-potential (SP) geophysical methods. Interpretation of SP profile Line SP1, located 3 m south of the cenote, suggests two fractures, which appear to extend south as far as SP profile Line SP2, 15 m south of the cenote; both lines are parallel to each other. SP anomalies suggest water flow along these fractures. The use of noninvasive geophysical methods, specifically SP, resistivity and TEM are useful for exploring the karst system in the Yucatán peninsula.

A Hybrid Analytical/Numerical Model for the Characterization of Preferential Flow Path with Non-Darcy Flow

PubMed Central

Wang, Sen; Feng, Qihong; Han, Xiaodong

2013-01-01

Due to the long-term fluid-solid interactions in waterflooding, the tremendous variation of oil reservoir formation parameters will lead to the widespread evolution of preferential flow paths, thereby preventing the further enhancement of recovery efficiency because of unstable fingering and premature breakthrough. To improve oil recovery, the characterization of preferential flow paths is essential and imperative. In efforts that have been previously documented, fluid flow characteristics within preferential paths are assumed to obey Darcy's equation. However, the occurrence of non-Darcy flow behavior has been increasingly suggested. To examine this conjecture, the Forchheimer number with the inertial coefficient estimated from different empirical formulas is applied as the criterion. Considering a 10% non-Darcy effect, the fluid flow in a preferential path may do experience non-Darcy behavior. With the objective of characterizing the preferential path with non-Darcy flow, a hybrid analytical/numerical model has been developed to investigate the pressure transient response, which dynamically couples a numerical model describing the non-Darcy effect of a preferential flow path with an analytical reservoir model. The characteristics of the pressure transient behavior and the sensitivities of corresponding parameters have also been discussed. In addition, an interpretation approach for pressure transient testing is also proposed, in which the Gravitational Search Algorithm is employed as a non-linear regression technology to match measured pressure with this hybrid model. Examples of applications from different oilfields are also presented to illustrate this method. This cost-effective approach provides more accurate characterization of a preferential flow path with non-Darcy flow, which will lay a solid foundation for the design and operation of conformance control treatments, as well as several other Enhanced Oil Recovery projects. PMID:24386224

Structure-Function Analysis of the Drosophila melanogaster Caudal Transcription Factor Provides Insights into Core Promoter-preferential Activation.

PubMed

Shir-Shapira, Hila; Sharabany, Julia; Filderman, Matan; Ideses, Diana; Ovadia-Shochat, Avital; Mannervik, Mattias; Juven-Gershon, Tamar

2015-07-10

Regulation of RNA polymerase II transcription is critical for the proper development, differentiation, and growth of an organism. The RNA polymerase II core promoter is the ultimate target of a multitude of transcription factors that control transcription initiation. Core promoters encompass the RNA start site and consist of functional elements such as the TATA box, initiator, and downstream core promoter element (DPE), which confer specific properties to the core promoter. We have previously discovered that Drosophila Caudal, which is a master regulator of genes involved in development and differentiation, is a DPE-specific transcriptional activator. Here, we show that the mouse Caudal-related homeobox (Cdx) proteins (mCdx1, mCdx2, and mCdx4) are also preferential core promoter transcriptional activators. To elucidate the mechanism that enables Caudal to preferentially activate DPE transcription, we performed structure-function analysis. Using a systematic series of deletion mutants (all containing the intact DNA-binding homeodomain) we discovered that the C-terminal region of Caudal contributes to the preferential activation of the fushi tarazu (ftz) Caudal target gene. Furthermore, the region containing both the homeodomain and the C terminus of Caudal was sufficient to confer core promoter-preferential activation to the heterologous GAL4 DNA-binding domain. Importantly, we discovered that Drosophila CREB-binding protein (dCBP) is a co-activator for Caudal-regulated activation of ftz. Strikingly, dCBP conferred the ability to preferentially activate the DPE-dependent ftz reporter to mini-Caudal proteins that were unable to preferentially activate ftz transcription themselves. Taken together, it is the unique combination of dCBP and Caudal that enables the co-activation of ftz in a core promoter-preferential manner. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Initial targets and cellular responses to PDT

NASA Astrophysics Data System (ADS)

Rodriguez, Myriam E.; Azizuddin, Kashif; Chiu, Song-mao; Delos Santos, Grace; Joseph, Sheeba; Xue, Liang-yan; Oleinick, Nancy L.

2007-02-01

Pc 4, a photosensitizer first synthesized at Case Western Reserve University and now in clinical trial at University Hospitals of Cleveland, has been shown to bind preferentially and with high affinity to mitochondrial and endoplasmic reticulum membranes. Upon photoirradiation of Pc 4-loaded cells, membrane components are photodamaged. In most cancer cells, apoptosis is triggered by the initial photodamage; however, in cells deficient in one of the critical intermediates of apoptosis, this process does not occur, although the cells remain as sensitive to the lethal effects of Pc 4-PDT as the apoptosis-competent cells, when cell death is determined by colony formation. Here we report that an alternative death process, autophagy, is induced in all cells tested and becomes the dominant pathway for elimination of lethally damaged cells when apoptosis is compromised. The anti-apoptotic protein Bcl-2, when overexpressed, protects only apoptosis-competent cells against loss of clonogenicity, while the autophagy inhibitor 3-methyladenine provides a markedly greater protection to apoptosis-deficient cells. The results suggest that the primary determinant of cell death is not the final pathway for elimination of the cells but the initial photodamage to critical membrane targets. In attempts to identify those targets, we have studied the role of different membrane phospholipids in the localization of Pc 4. Cardiolipin (CL) is a phospholipid found exclusively in the mitochondrial inner membrane and at the contact sites between the inner and outer membranes. Previous fluorescence resonance energy transfer studies revealed colocalization of Pc 4 and CL, which points to CL as a possible binding site and target for Pc 4. Unilamellar liposomes with different lipid compositions were used as membrane models to test the affinity of Pc 4. As revealed by the binding constants, Pc 4 does not display preferential binding to CL in these systems. Moreover, binding affinities appear to be independent of lipid composition. Localization of Pc 4 in mitochondrial membranes is likely determined by proteins or other factors not replicated in the liposomes. Studies in cells with modified CL content could report modified binding affinities.

A combined crossed-beam and theoretical study of the reaction dynamics of O(3P) + C2H3 → C2H2 + OH: Analysis of the nascent OH products with the preferential population of the Π(A') component

NASA Astrophysics Data System (ADS)

Park, Min-Jin; Jang, Su-Chan; Choi, Jong-Ho

2012-11-01

The gas-phase reaction dynamics of ground-state atomic oxygen [O(3P) from the photo-dissociation of NO2] with vinyl radicals [C2H3 from the supersonic flash pyrolysis of vinyl iodide, C2H3I] has been investigated using a combination of high-resolution laser-induced fluorescence spectroscopy in a crossed-beam configuration and ab initio calculations. Unlike the previous gas-phase bulk kinetic experiments by Baulch et al. [J. Phys. Chem. Ref. Data 34, 757 (2005)], 10.1063/1.1748524, a new exothermic channel of O(3P) + C2H3 → C2H2 + OH (X 2Π: υ″ = 0) has been identified for the first time, and the population analysis shows bimodal nascent rotational distributions of OH products with low- and high-N″ components with a ratio of 2.4:1. No spin-orbit propensities were observed, and the averaged ratios of Π(A')/Π(A″) were determined to be 1.66 ± 0.27. On the basis of computations at the CBS-QB3 theory level and comparison with prior theory, the microscopic mechanisms responsible for the nascent populations can be understood in terms of two competing dynamical pathways: a direct abstraction process in the low-N″ regime as the major pathway and an addition-complex forming process in the high-N″ regime as the minor pathway. Particularly, during the bond cleavage process of the weakly bound van der Waals complex C2H2—OH, the characteristic pathway from the low dihedral-angle geometry was consistent with the observed preferential population of the Π(A') component in the nascent OH products. A molecular-level discussion of the reactivity, mechanism, and dynamical features of the title reaction are presented together with a comparison to gas-phase oxidation reactions of a series of prototypical hydrocarbon radicals.

Co-Administration of an Excipient Oligonucleotide Helps Delineate Pathways of Productive and Nonproductive Uptake of Phosphorothioate Antisense Oligonucleotides in the Liver.

PubMed

Donner, Aaron J; Wancewicz, Edward V; Murray, Heather M; Greenlee, Sarah; Post, Noah; Bell, Melanie; Lima, Walt F; Swayze, Eric E; Seth, Punit P

2017-08-01

Phosphorothioate (PS) modified antisense oligonucleotides (ASOs) have progressed rapidly in the clinic for treating a variety of disease indications. We previously demonstrated that the activity of PS ASOs in the liver can be enhanced by co-infusion of an excipient oligonucleotide (EON). It was posited that the EON saturates a nonproductive uptake pathway(s) thereby permitting accumulation of the PS ASO in a productive tissue compartment. In this report, we measured PS ASO activity following administration by bolus, infusion or co-fusion with EON within hepatocytes and nonparenchymal cells (NPCs), of the liver. This revealed that while ASOs accumulate preferentially in NPCs, they are intrinsically more active in hepatocytes. Furthermore, we show that the EON enhances ASO potency when infused up to 72 h before or after administration of the active ASO suggesting that the EON can saturate and displace the ASO from nonproductive to productive compartments. Physical presence of the EON in tissues was required for optimal potentiation suggesting that there is a dynamic distribution of the ASO and EON between the compartments. Lastly, using a candidate approach, we confirmed Stabilin-2 as a molecular pathway for ASO uptake in sinusoidal endothelial cells and the ASGR as a pathway for ASO uptake into hepatocytes in the liver.

Transcriptomic analysis of genes in the nitrogen recycling pathway of meat-type chickens divergently selected for feed efficiency.

PubMed

Aggrey, S E; Lee, J; Karnuah, A B; Rekaya, R

2014-04-01

The understanding of the dynamics of ammonia detoxification and excretion in uricotelic species is lagging behind ureotelic species. The relative expression of genes involved in nitrogen recycling and feed efficiency in chickens is unknown. The objective of this study was to investigate the transcriptomics differences in key genes in the nitrogen (N) metabolism and purine biosynthesis pathway in a chicken population divergently selected for low (LRFI) or high (HRFI) residual feed intake at days 35 and 42 using duodenum, liver, pectoralis major (P. major) and kidney. There was a significant positive correlation between RFI and fecal N. The purine salvage pathway was activated in the LRFI compared with HRFI at days 42. The birds in the LRFI population attained greater feed efficiency by having lower FI, increasing their protein retention and producing adequate glutamine to maintain growth compared with the HRFI line. To maintain growth, excess N is deaminated mostly to generate purine nucleotides. Generating purine nucleotides primarily from the purine biosynthesis pathway is energetically costly, and to preserve energy, they preferentially generate nucleotides from the purine salvage pathway. The LRFI birds need to generate sufficient nucleotides to maintain growth despite reduced FI that then results in reduced fecal N. © 2013 Stichting International Foundation for Animal Genetics.

Evidence for the Existence in Arabidopsis thaliana of the Proteasome Proteolytic Pathway

PubMed Central

Polge, Cécile; Jaquinod, Michel; Holzer, Frances; Bourguignon, Jacques; Walling, Linda; Brouquisse, Renaud

2009-01-01

Heavy metals are known to generate reactive oxygen species that lead to the oxidation and fragmentation of proteins, which become toxic when accumulated in the cell. In this study, we investigated the role of the proteasome during cadmium stress in the leaves of Arabidopsis thaliana plants. Using biochemical and proteomics approaches, we present the first evidence of an active proteasome pathway in plants. We identified and characterized the peptidases acting sequentially downstream from the proteasome in animal cells as follows: tripeptidyl-peptidase II, thimet oligopeptidase, and leucine aminopeptidase. We investigated the proteasome proteolytic pathway response in the leaves of 6-week-old A. thaliana plants grown hydroponically for 24, 48, and 144 h in the presence or absence of 50 μm cadmium. The gene expression and proteolytic activity of the proteasome and the different proteases of the pathway were found to be up-regulated in response to cadmium. In an in vitro assay, oxidized bovine serum albumin and lysozyme were more readily degraded in the presence of 20 S proteasome and tripeptidyl-peptidase II than their nonoxidized form, suggesting that oxidized proteins are preferentially degraded by the Arabidopsis 20 S proteasome pathway. These results show that, in response to cadmium, the 20 S proteasome proteolytic pathway is up-regulated at both RNA and activity levels in Arabidopsis leaves and may play a role in degrading oxidized proteins generated by the stress. PMID:19822524

Runoff sources and flowpaths in a partially burned, upland boreal catchment underlain by permafrost

USGS Publications Warehouse

Koch, Joshua C.; Kikuchi, Colin P.; Wickland, Kimberly P.; Schuster, Paul

2014-01-01

Boreal soils in permafrost regions contain vast quantities of frozen organic material that is released to terrestrial and aquatic environments via subsurface flowpaths as permafrost thaws. Longer flowpaths may allow chemical reduction of solutes, nutrients, and contaminants, with implications for greenhouse gas emissions and aqueous export. Predicting boreal catchment runoff is complicated by soil heterogeneities related to variability in active layer thickness, soil type, fire history, and preferential flow potential. By coupling measurements of permeability, infiltration potential, and water chemistry with a stream chemistry end member mixing model, we tested the hypothesis that organic soils and burned slopes are the primary sources of runoff, and that runoff from burned soils is greater due to increased hydraulic connectivity. Organic soils were more permeable than mineral soils, and 25% of infiltration moved laterally upon reaching the organic-mineral soil boundary on unburned hillslopes. A large portion of the remaining water infiltrated into deeper, less permeable soils. In contrast, burned hillslopes displayed poorly defined soil horizons, allowing rapid, mineral-rich runoff through preferential pathways at various depths. On the catchment scale, mineral/organic runoff ratios averaged 1.6 and were as high as 5.2 for an individual storm. Our results suggest that burned soils are the dominant source of water and solutes reaching the stream in summer, whereas unburned soils may provide longer term storage and residence times necessary for production of anaerobic compounds. These results are relevant to predicting how boreal catchment drainage networks and stream export will evolve given continued warming and altered fire regimes.

Loss of function of folylpolyglutamate synthetase 1 reduces lignin content and improves cell wall digestibility in Arabidopsis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Srivastava, Avinash C.; Chen, Fang; Ray, Tui

One-carbon (C1) metabolism is important for synthesizing a range of biologically important compounds that are essential for life. In plants, the C1 pathway is crucial for the synthesis of a large number of secondary metabolites, including lignin. Tetrahydrofolate and its derivatives, collectively referred to as folates, are crucial co-factors for C1 metabolic pathway enzymes. Given the link between the C1 and phenylpropanoid pathways, we evaluated whether folylpolyglutamate synthetase (FPGS), an enzyme that catalyzes the addition of a glutamate tail to folates to form folylpolyglutamates, can be a viable target for reducing cell wall recalcitrance in plants. Consistent with its rolemore » in lignocellulosic formation, FPGS1 was preferentially expressed in vascular tissues. Total lignin was low in fpgs1 plants leading to higher saccharification efficiency of the mutant. The decrease in total lignin in fpgs1 was mainly due to lower guaiacyl (G) lignin levels. Glycome profiling revealed subtle alterations in the cell walls of fpgs1. Further analyses of hemicellulosic polysaccharides by NMR showed that the degree of methylation of 4-O-methyl glucuronoxylan was reduced in the fpgs1 mutant. Microarray analysis and real-time qRT-PCR revealed that transcripts of a number of genes in the C1 and lignin pathways had altered expression in fpgs1 mutants. Consistent with the transcript changes of C1-related genes, a significant reduction in S-adenosyl-l-methionine content was detected in the fpgs1 mutant. The modified expression of the various methyltransferases and lignin-related genes indicate possible feedback regulation of C1 pathway-mediated lignin biosynthesis. In conclusion, our observations provide genetic and biochemical support for the importance of folylpolyglutamates in the lignocellulosic pathway and reinforces previous observations that targeting a single FPGS isoform for down-regulation leads to reduced lignin in plants. Because fpgs1 mutants had no dramatic defects in above ground biomass, selective down-regulation of individual components of C1 metabolism is an approach that should be explored further for the improvement of lignocellulosic feedstocks.« less

Elucidation of Altered Pathways in Tumor-Initiating Cells of Triple-Negative Breast Cancer: A Useful Cell Model System for Drug Screening.

PubMed

Christensen, Anne G; Ehmsen, Sidse; Terp, Mikkel G; Batra, Richa; Alcaraz, Nicolas; Baumbach, Jan; Noer, Julie B; Moreira, José; Leth-Larsen, Rikke; Larsen, Martin R; Ditzel, Henrik J

2017-08-01

A limited number of cancer cells within a tumor are thought to have self-renewing and tumor-initiating capabilities that produce the remaining cancer cells in a heterogeneous tumor mass. Elucidation of central pathways preferentially used by tumor-initiating cells/cancer stem cells (CSCs) may allow their exploitation as potential cancer therapy targets. We used single cell cloning to isolate and characterize four isogenic cell clones from a triple-negative breast cancer cell line; two exhibited mesenchymal-like and two epithelial-like characteristics. Within these pairs, one, but not the other, resulted in tumors in immunodeficient NOD/Shi-scid/IL-2 Rγ null mice and efficiently formed mammospheres. Quantitative proteomics and phosphoproteomics were used to map signaling pathways associated with the tumor-initiating ability. Signaling associated with apoptosis was suppressed in tumor-initiating versus nontumorigenic counterparts with pro-apoptotic proteins, such as Bcl2-associated agonist of cell death (BAD), FAS-associated death domain protein (FADD), and myeloid differentiation primary response protein (MYD88), downregulated in tumor-initiating epithelial-like cells. Functional studies confirmed significantly lower apoptosis in tumor-initiating versus nontumorigenic cells. Moreover, central pathways, including β-catenin and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB)-related signaling, exhibited increased activation in the tumor-initiating cells. To evaluate the CSC model as a tool for drug screening, we assessed the effect of separately blocking NF-κB and Wnt/β-catenin signaling and found markedly reduced mammosphere formation, particularly for tumor-initiating cells. Similar reduction was also observed using patient-derived primary cancer cells. Furthermore, blocking NF-κB signaling in mice transplanted with tumor-initiating cells significantly reduced tumor outgrowth. Our study demonstrates that suppressed apoptosis, activation of pathways associated with cell viability, and CSCs are the major differences between tumor-initiating and nontumorigenic cells independent of their epithelial-like/mesenchymal-like phenotype. These altered pathways may provide targets for future drug development to eliminate CSCs, and the cell model may be a useful tool in such drug screenings. Stem Cells 2017;35:1898-1912. © 2017 AlphaMed Press.

Loss of function of folylpolyglutamate synthetase 1 reduces lignin content and improves cell wall digestibility in Arabidopsis

DOE PAGES

Srivastava, Avinash C.; Chen, Fang; Ray, Tui; ...

2015-12-21

One-carbon (C1) metabolism is important for synthesizing a range of biologically important compounds that are essential for life. In plants, the C1 pathway is crucial for the synthesis of a large number of secondary metabolites, including lignin. Tetrahydrofolate and its derivatives, collectively referred to as folates, are crucial co-factors for C1 metabolic pathway enzymes. Given the link between the C1 and phenylpropanoid pathways, we evaluated whether folylpolyglutamate synthetase (FPGS), an enzyme that catalyzes the addition of a glutamate tail to folates to form folylpolyglutamates, can be a viable target for reducing cell wall recalcitrance in plants. Consistent with its rolemore » in lignocellulosic formation, FPGS1 was preferentially expressed in vascular tissues. Total lignin was low in fpgs1 plants leading to higher saccharification efficiency of the mutant. The decrease in total lignin in fpgs1 was mainly due to lower guaiacyl (G) lignin levels. Glycome profiling revealed subtle alterations in the cell walls of fpgs1. Further analyses of hemicellulosic polysaccharides by NMR showed that the degree of methylation of 4-O-methyl glucuronoxylan was reduced in the fpgs1 mutant. Microarray analysis and real-time qRT-PCR revealed that transcripts of a number of genes in the C1 and lignin pathways had altered expression in fpgs1 mutants. Consistent with the transcript changes of C1-related genes, a significant reduction in S-adenosyl-l-methionine content was detected in the fpgs1 mutant. The modified expression of the various methyltransferases and lignin-related genes indicate possible feedback regulation of C1 pathway-mediated lignin biosynthesis. In conclusion, our observations provide genetic and biochemical support for the importance of folylpolyglutamates in the lignocellulosic pathway and reinforces previous observations that targeting a single FPGS isoform for down-regulation leads to reduced lignin in plants. Because fpgs1 mutants had no dramatic defects in above ground biomass, selective down-regulation of individual components of C1 metabolism is an approach that should be explored further for the improvement of lignocellulosic feedstocks.« less

Modeling preferential water flow and solute transport in unsaturated soil using the active region model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sheng, F.; Wang, K.; Zhang, R.

2009-03-15

Preferential flow and solute transport are common processes in the unsaturated soil, in which distributions of soil water content and solute concentrations are often characterized as fractal patterns. An active region model (ARM) was recently proposed to describe the preferential flow and transport patterns. In this study, ARM governing equations were derived to model the preferential soil water flow and solute transport processes. To evaluate the ARM equations, dye infiltration experiments were conducted, in which distributions of soil water content and Cl{sup -} concentration were measured. Predicted results using the ARM and the mobile-immobile region model (MIM) were compared withmore » the measured distributions of soil water content and Cl{sup -} concentration. Although both the ARM and the MIM are two-region models, they are fundamental different in terms of treatments of the flow region. The models were evaluated based on the modeling efficiency (ME). The MIM provided relatively poor prediction results of the preferential flow and transport with negative ME values or positive ME values less than 0.4. On the contrary, predicted distributions of soil water content and Cl- concentration using the ARM agreed reasonably well with the experimental data with ME values higher than 0.8. The results indicated that the ARM successfully captured the macroscopic behavior of preferential flow and solute transport in the unsaturated soil.« less

Polyamines and plant stress - Activation of putrescine biosynthesis by osmotic shock

NASA Technical Reports Server (NTRS)

Flores, H. E.; Galston, A. W.

1982-01-01

The putrescine content of oat leaf cells and protoplasts increases up to 60-fold within 6 hours of exposure to osmotic stress (0.4 to 0.6 molar sorbitol). Barley, corn, wheat, and wild oat leaves show a similar response. Increased arginine decarboxylase activity parallels the rise in putrescine, whereas ornithine decarboxylase remains unchanged. DL-alpha-Difluoromethylarginine, a specific irreversible inhibitor of arginine decarboxylase, prevents the stress-induced rise in increase in arginine decarboxylase activity and putrescine synthesis, indicating the preferential activation of this pathway.

DOE Office of Scientific and Technical Information (OSTI.GOV)

French, Jarrod B.; Ealick, Steven E.

Many plants, fungi, and bacteria catabolize allantoin as a mechanism for nitrogen assimilation. Recent reports have shown that in plants and some bacteria the product of hydrolysis of allantoin by allantoinase is the unstable intermediate ureidoglycine. While this molecule can spontaneously decay, genetic analysis of some bacterial genomes indicates that an aminotransferase may be present in the pathway. Here we present evidence that Klebsiella pneumoniae HpxJ is an aminotransferase that preferentially converts ureidoglycine and an {alpha}-keto acid into oxalurate and the corresponding amino acid. We determined the crystal structure of HpxJ, allowing us to present an explanation for substrate specificity.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schachtl, Eva; Yoo, Jong Suk; Gutiérrez, Oliver Y.

The reaction network and elementary steps of the hydrogenation of phenanthrene are explored on parent and Ni-promoted MoS2/c-Al2O3. Two pathways were identified, i.e., Path 1: Phenanthrene _ 9,10-dihydrophenanthrene (DiHPhe)?1,2,3,4,4a,9,10,10a-octahydro-phenanthrene (asymOHPhe), and Path 2: Phenanthrene ?1,2,3,4-tetrahydrophenanthrene (TetHPhe)?1,2,3,4,5,6,7,8-octahydrophenan threne. The steps TetHPhe?asymOHPhe (hydrogenation), and DiHPhe?TetHPhe (hydrogenationisomerization) become notable at phenanthrene conversions above 20%. The reaction preferentially proceeds via Path 1 (90% selectivity) on MoS2/Al2O3. Ni promotion (Ni/(Ni + Mo) molar ratio of 0.3 at the edges on MoS2) increases the hydrogenation activity per active edge twofold and leads to 50% selectivity to both pathways. The reaction orders in H2 vary from _0.8more » on MoS2/Al2O3 to _1.2 on Ni-MoS2/Al2O3, whereas the reaction orders in phenanthrene (_0.6) hardly depend on Ni promotion. The reaction orders in H2S are zero on MoS2/Al2O3 and slightly negative on Ni-MoS2/Al2O3. DFT calculations indicate that phenanthrene is preferentially adsorbed parallel to the basal planes, while H is located at the edges perpendicular to the basal planes. Theory also suggests that Ni atoms, incorporated preferentially on the S-edges, increase the stability of hydrogenated intermediates. Hydrogenation of phenanthrene proceeds through quasi-equilibrated adsorption of the reactants followed by consecutive addition of hydrogen pairs to the adsorbed hydrocarbon. The rate determining steps for the formation of DiHPhe and TetHPhe are the addition of the first and second hydrogen pair, respectively. The concentration of SH groups (activated H at the edges) increases with Ni promotion linearly correlating the rates of Path 1 and Path 2, albeit with different functions. The enhancing effect of Ni on Path 2 is attributed to accelerated hydrogen addition to adsorbed hydrocarbons without important changes in their coverages.« less

Aerobic glycolysis during brain activation: adrenergic regulation and influence of norepinephrine on astrocytic metabolism.

PubMed

Dienel, Gerald A; Cruz, Nancy F

2016-07-01

Aerobic glycolysis occurs during brain activation and is characterized by preferential up-regulation of glucose utilization compared with oxygen consumption even though oxygen level and delivery are adequate. Aerobic glycolysis is a widespread phenomenon that underlies energetics of diverse brain activities, such as alerting, sensory processing, cognition, memory, and pathophysiological conditions, but specific cellular functions fulfilled by aerobic glycolysis are poorly understood. Evaluation of evidence derived from different disciplines reveals that aerobic glycolysis is a complex, regulated phenomenon that is prevented by propranolol, a non-specific β-adrenoceptor antagonist. The metabolic pathways that contribute to excess utilization of glucose compared with oxygen include glycolysis, the pentose phosphate shunt pathway, the malate-aspartate shuttle, and astrocytic glycogen turnover. Increased lactate production by unidentified cells, and lactate dispersal from activated cells and lactate release from the brain, both facilitated by astrocytes, are major factors underlying aerobic glycolysis in subjects with low blood lactate levels. Astrocyte-neuron lactate shuttling with local oxidation is minor. Blockade of aerobic glycolysis by propranolol implicates adrenergic regulatory processes including adrenal release of epinephrine, signaling to brain via the vagus nerve, and increased norepinephrine release from the locus coeruleus. Norepinephrine has a powerful influence on astrocytic metabolism and glycogen turnover that can stimulate carbohydrate utilization more than oxygen consumption, whereas β-receptor blockade 're-balances' the stoichiometry of oxygen-glucose or -carbohydrate metabolism by suppressing glucose and glycogen utilization more than oxygen consumption. This conceptual framework may be helpful for design of future studies to elucidate functional roles of preferential non-oxidative glucose utilization and glycogen turnover during brain activation. Aerobic glycolysis, the preferential up-regulation of glucose utilization (CMRglc ) compared with oxygen consumption (CMRO2 ) during brain activation, is blocked by propranolol. Epinephrine release from the adrenal gland stimulates vagus nerve signaling to the locus coeruleus, enhancing norepinephrine release in the brain, and regulation of astrocytic and neuronal metabolism to stimulate CMRglc more than CMRO2 . Propranolol suppresses CMRglc more than CMRO2 . © 2016 International Society for Neurochemistry.

Dynamics of Phosphorus export from small forested catchments in low mountain ranges in Germany

NASA Astrophysics Data System (ADS)

Julich, Stefan; Julich, Dorit; Benning, Raphael; Feger, Karl-Heinz

2017-04-01

Phosphorus (P) plays an important role in the nutrition of forest ecosystem. The transport of P in forest soils predominantly occurs along preferential water flow pathways bypassing large parts of the soil matrix. Therefore, rapid flow processes by preferential flow and/or during storm events may lead to significant P losses from forest soils. However only little knowledge about the dynamics, magnitude and driving processes of P exports into surface water exist. In this contribution, we present the results of two studies where two small forested catchments have been monitored for a period around 3 years. Both catchments are situated in low mountain ranges in Saxony (catchment size 21 ha) and Thuringia (catchment size 5 ha) representing medium P contents in the topsoil of 1142 mg kg-1 and 834 mg kg-1 respectively. During the regular sampling (monthly to weekly sampling frequency), the mean Total-P concentrations of 23 μg L-1(Thuringian Site) and 8 μg L-1(Saxonian Site) have been measured. However, during single storm events Total-P concentrations increased considerably with maximum concentrations of 134 μg L-1(Thuringian Site) and 203 μg L-1(Saxonian Site). Our findings indicate that during storm events, especially after longer dry periods, significant amounts of phosphorus can be exported from forest ecosystems. Comparison of discharge-concentration patterns of Total-P, Nitrogen and DOC, as well as dye tracer experiments, suggest that preferential flow along biopores and stone surfaces, and the interface between mineral soil and litter layer are main pathways of export from forests. For the site in Saxony we calculated mean annual export rates of 32.8 to 33.5 g ha-1 a-1 based on the weekly sampling with different load calculation methods (flow weighted methods up to linear regression models). If the events are included into the annual load calculation the mean annual export fluxes increase from 47.8 to 58.6 g ha-1 a-1 based on the different load calculation methods. This implies that the estimation of P-exports from forested catchments need to be based on appropriate monitoring schemes and load estimation methods.

Deconvoluting the complexity of autophagy and Parkinson's disease for potential therapeutic purpose

PubMed Central

Ouyang, Liang; Liu, Bo

2015-01-01

Parkinson's disease (PD) is a neurodegenerative disorder characterized by the preferential death of dopaminergic neurons. In the past two decades, great progress has been made toward understanding the pathogenesis of PD; however, its precise pathogenesis still remains unclear. Recently, accumulating evidence has suggested that macroautophagy (herein referred to as autophagy) is tightly linked to PD. Dysregulation of autophagic pathways has been observed in the brains of PD patients and in animal models of PD. More importantly, a number of PD-associated proteins, such as α-synuclein, LRRK2, Parkin and PINK1 have been further revealed to be involved in autophagy. Thus, it is now acknowledged that constitutive autophagy is essential for neuronal survival and that dysregulation of autophagy leads to PD. In this review, we focus on summarizing the relationships amongst PD-associated proteins, autophagy and PD. Moreover, we also demonstrate some autophagy-modulating compounds and autophagic microRNAs in PD models, which may provide better promising strategies for potential PD therapy. PMID:26415234

Internuclear separation dependent ionization of the valence orbitals of I2 by strong laser fields.

PubMed

Chen, H; Tagliamonti, V; Gibson, G N

2012-11-09

Using a pump-dump-probe technique and Fourier-transform spectroscopy, we study the internuclear separation R dependence and relative strength of the ionization rates of the π and σ electrons of I2, whose valence orbitals are σ(g)(2)π(u)(4)π(g)(4)σ(u)(0). We find that ionization of the highest occupied molecular orbital (HOMO)-2 (σ(g)) has a strong dependence on R while the HOMO and HOMO-1 do not. Surprisingly, the ionization rate of the HOMO-2 exceeds the combined ionization rate of the less bound orbitals and this branching ratio increases with R. Since our technique produces target molecules that are highly aligned with the laser polarization, the σ orbitals will be preferentially ionized and undergo enhanced ionization at larger R compared to the π orbitals. Nevertheless, it is highly unusual that an inner orbital provides the dominant strong field ionization pathway in a small molecule.

Internuclear Separation Dependent Ionization of the Valence Orbitals of I2 by Strong Laser Fields

NASA Astrophysics Data System (ADS)

Chen, H.; Tagliamonti, V.; Gibson, G. N.

2012-11-01

Using a pump-dump-probe technique and Fourier-transform spectroscopy, we study the internuclear separation R dependence and relative strength of the ionization rates of the π and σ electrons of I2, whose valence orbitals are σg2πu4πg4σu0. We find that ionization of the highest occupied molecular orbital (HOMO)-2 (σg) has a strong dependence on R while the HOMO and HOMO-1 do not. Surprisingly, the ionization rate of the HOMO-2 exceeds the combined ionization rate of the less bound orbitals and this branching ratio increases with R. Since our technique produces target molecules that are highly aligned with the laser polarization, the σ orbitals will be preferentially ionized and undergo enhanced ionization at larger R compared to the π orbitals. Nevertheless, it is highly unusual that an inner orbital provides the dominant strong field ionization pathway in a small molecule.

Dorsolateral Striatum Engagement Interferes with Early Discrimination Learning.

PubMed

Bergstrom, Hadley C; Lipkin, Anna M; Lieberman, Abby G; Pinard, Courtney R; Gunduz-Cinar, Ozge; Brockway, Emma T; Taylor, William W; Nonaka, Mio; Bukalo, Olena; Wills, Tiffany A; Rubio, F Javier; Li, Xuan; Pickens, Charles L; Winder, Danny G; Holmes, Andrew

2018-05-22

In current models, learning the relationship between environmental stimuli and the outcomes of actions involves both stimulus-driven and goal-directed systems, mediated in part by the DLS and DMS, respectively. However, though these models emphasize the importance of the DLS in governing actions after extensive experience has accumulated, there is growing evidence of DLS engagement from the onset of training. Here, we used in vivo photosilencing to reveal that DLS recruitment interferes with early touchscreen discrimination learning. We also show that the direct output pathway of the DLS is preferentially recruited and causally involved in early learning and find that silencing the normal contribution of the DLS produces plasticity-related alterations in a PL-DMS circuit. These data provide further evidence suggesting that the DLS is recruited in the construction of stimulus-elicited actions that ultimately automate behavior and liberate cognitive resources for other demands, but with a cost to performance at the outset of learning. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Influence of Polymer-Clay Interfacial Interactions on the Ignition Time of Polymer/Clay Nanocomposites

PubMed Central

Zope, Indraneel S.; Yu, Zhong-Zhen

2017-01-01

Metal ions present on smectite clay (montmorillonite) platelets have preferential reactivity towards peroxy/alkoxy groups during polyamide 6 (PA6) thermal decomposition. This changes the decomposition pathway and negatively affects the ignition response of PA6. To restrict these interfacial interactions, high-temperature-resistant polymers such as polyetherimide (PEI) and polyimide (PI) were used to coat clay layers. PEI was deposited on clay by solution-precipitation, whereas PI was deposited through a solution-imidization-precipitation technique before melt blending with PA6. The absence of polymer-clay interfacial interactions has resulted in a similar time-to-ignition of PA6/PEI-clay (133 s) and PA6/PI-clay (139 s) composites as neat PA6 (140 s). On the contrary, PA6 with conventional ammonium-based surfactant modified clay has showed a huge drop in time-to-ignition (81 s), as expected. The experimental evidences provided herein reveal the role of the catalytic activity of clay during the early stages of polymer decomposition. PMID:28800095

Furanodiene Induces Extrinsic and Intrinsic Apoptosis in Doxorubicin-Resistant MCF-7 Breast Cancer Cells via NF-κB-Independent Mechanism.

PubMed

Zhong, Zhang-Feng; Yu, Hai-Bing; Wang, Chun-Ming; Qiang, Wen-An; Wang, Sheng-Peng; Zhang, Jin-Ming; Yu, Hua; Cui, Liao; Wu, Tie; Li, De-Qiang; Wang, Yi-Tao

2017-01-01

Chemotherapy is used as a primary approach in cancer treatment after routine surgery. However, chemo-resistance tends to occur when chemotherapy is used clinically, resulting in poor prognosis and recurrence. Currently, Chinese medicine may provide insight into the design of new therapies to overcome chemo-resistance. Furanodiene, as a heat-sensitive sesquiterpene, is isolated from the essential oil of Rhizoma Curcumae . Even though mounting evidence claiming that furanodiene possesses anti-cancer activities in various types of cancers, the underlying mechanisms against chemo-resistant cancer are not fully clear. Our study found that furanodiene could display anti-cancer effects by inhibiting cell viability, inducing cell cytotoxicity, and suppressing cell proliferation in doxorubicin-resistant MCF-7 breast cancer cells. Furthermore, furanodiene preferentially causes apoptosis by interfering with intrinsic/extrinsic-dependent and NF-κB-independent pathways in doxorubicin-resistant MCF-7 cells. These observations also prompt that furanodiene may be developed as a promising natural product for multidrug-resistant cancer therapy in the future.

Evolution of the human-specific microRNA miR-941

PubMed Central

Hu, Hai Yang; He, Liu; Fominykh, Kseniya; Yan, Zheng; Guo, Song; Zhang, Xiaoyu; Taylor, Martin S.; Tang, Lin; Li, Jie; Liu, Jianmei; Wang, Wen; Yu, Haijing; Khaitovich, Philipp

2012-01-01

MicroRNA-mediated gene regulation is important in many physiological processes. Here we explore the roles of a microRNA, miR-941, in human evolution. We find that miR-941 emerged de novo in the human lineage, between six and one million years ago, from an evolutionarily volatile tandem repeat sequence. Its copy-number remains polymorphic in humans and shows a trend for decreasing copy-number with migration out of Africa. Emergence of miR-941 was accompanied by accelerated loss of miR-941-binding sites, presumably to escape regulation. We further show that miR-941 is highly expressed in pluripotent cells, repressed upon differentiation and preferentially targets genes in hedgehog- and insulin-signalling pathways, thus suggesting roles in cellular differentiation. Human-specific effects of miR-941 regulation are detectable in the brain and affect genes involved in neurotransmitter signalling. Taken together, these results implicate miR-941 in human evolution, and provide an example of rapid regulatory evolution in the human linage. PMID:23093182

Chemotherapeutic tumor microparticles combining low-dose irradiation reprogram tumor-promoting macrophages through a tumor-repopulating cell-curtailing pathway

PubMed Central

Sun, Yanling; Zheng, Zu'an; Zhang, Huafeng; Yu, Yuandong; Ma, Jingwei; Tang, Ke; Xu, Pingwei; Ji, Tiantian; Liang, Xiaoyu; Chen, Degao; Jin, Xun; Zhang, Tianzhen; Long, Zhixiong; Liu, Yuying; Huang, Bo

2017-01-01

ABSTRACT Stem cell-like tumor-repopulating cells (TRCs) have a critical role in establishing a tumor immunosuppressive microenvironment. However, means to enhance antitumor immunity by disrupting TRCs are absent. Our previous studies have shown that tumor cell-derived microparticles (T-MPs) preferentially abrogate TRCs by delivering antitumor drugs into nuclei of TRCs. Here, we show that low dose irradiation (LDI) enhances the effect of cisplatin-packaging T-MPs (Cis-MPs) on TRCs, leading to inhibiting tumor growth in different tumor models. This antitumor effect is not due to the direct killing of tumor cells but is T cell-dependent and relies on macrophages for their efficacy. The underlying mechanism is involved in therapeutic reprograming macrophages from tumor-promotion to tumor-inhibition by disrupting TRCs and curtailing their vicious education on macrophages. These findings provide a novel strategy to reset macrophage polarization and confer their function more like M1 than M2 types with highly promising potential clinical applications. PMID:28680743

Cell-Intrinsic Glycogen Metabolism Supports Early Glycolytic Reprogramming Required for Dendritic Cell Immune Responses.

PubMed

Thwe, Phyu M; Pelgrom, Leonard; Cooper, Rachel; Beauchamp, Saritha; Reisz, Julie A; D'Alessandro, Angelo; Everts, Bart; Amiel, Eyal

2017-09-05

Dendritic cell (DC) activation by Toll-like receptor (TLR) agonists causes rapid glycolytic reprogramming that is required to meet the metabolic demands of their immune activation. Recent efforts in the field have identified an important role for extracellular glucose sourcing to support DC activation. However, the contributions of intracellular glucose stores to these processes have not been well characterized. We demonstrate that DCs possess intracellular glycogen stores and that cell-intrinsic glycogen metabolism supports the early effector functions of TLR-activated DCs. Inhibition of glycogenolysis significantly attenuates TLR-mediated DC maturation and impairs their ability to initiate lymphocyte activation. We further report that DCs exhibit functional compartmentalization of glucose- and glycogen-derived carbons, where these substrates preferentially contribute to distinct metabolic pathways. This work provides novel insights into nutrient homeostasis in DCs, demonstrating that differential utilization of glycogen and glucose metabolism regulates their optimal immune function. Copyright © 2017 Elsevier Inc. All rights reserved.

Alcohol-abuse drug disulfiram targets cancer via p97 segregase adapter NPL4

PubMed Central

Skrott, Zdenek; Mistrik, Martin; Andersen, Klaus Kaae; Friis, Søren; Majera, Dusana; Gursky, Jan; Ozdian, Tomas; Bartkova, Jirina; Turi, Zsofia; Moudry, Pavel; Kraus, Marianne; Michalova, Martina; Vaclavkova, Jana; Dzubak, Petr; Vrobel, Ivo; Pouckova, Pavla; Sedlacek, Jindrich; Miklovicova, Andrea; Kutt, Anne; Li, Jing; Mattova, Jana; Driessen, Christoph; Dou, Q. Ping; Olsen, Jørgen; Hajduch, Marian; Cvek, Boris; Deshaies, Raymond J.; Bartek, Jiri

2017-01-01

Cancer incidence is rising and this global challenge is further exacerbated by tumour resistance to available medicines. A promising approach to such unmet need for improved cancer treatment is drug repurposing. Here we highlight the potential for repurposing disulfiram (Antabuse), an old alcohol-aversion drug effective against diverse cancer types in preclinical studies. Our nationwide epidemiological study reveals that patients who continuously used disulfiram have a lower risk of death from cancer compared to those who stopped using the drug at their diagnosis. Moreover, we identify ditiocarb-copper complex as the metabolite of disulfiram responsible for anticancer effects, and provide methods to detect its preferential accumulation in tumours and candidate biomarkers for impact in cells and tissues. Finally, our functional and biophysical analyses reveal the long-sought molecular target of disulfiram’s tumour suppressing effects as NPL4, an adapter of p97/VCP segregase essential for protein turnover involved in multiple regulatory and stress-response cellular pathways. PMID:29211715

Influence of Polymer-Clay Interfacial Interactions on the Ignition Time of Polymer/Clay Nanocomposites.

PubMed

Zope, Indraneel S; Dasari, Aravind; Yu, Zhong-Zhen

2017-08-11

Metal ions present on smectite clay (montmorillonite) platelets have preferential reactivity towards peroxy/alkoxy groups during polyamide 6 (PA6) thermal decomposition. This changes the decomposition pathway and negatively affects the ignition response of PA6. To restrict these interfacial interactions, high-temperature-resistant polymers such as polyetherimide (PEI) and polyimide (PI) were used to coat clay layers. PEI was deposited on clay by solution-precipitation, whereas PI was deposited through a solution-imidization-precipitation technique before melt blending with PA6. The absence of polymer-clay interfacial interactions has resulted in a similar time-to-ignition of PA6/PEI-clay (133 s) and PA6/PI-clay (139 s) composites as neat PA6 (140 s). On the contrary, PA6 with conventional ammonium-based surfactant modified clay has showed a huge drop in time-to-ignition (81 s), as expected. The experimental evidences provided herein reveal the role of the catalytic activity of clay during the early stages of polymer decomposition.

Therapeutic effects of telomerase in mice with pulmonary fibrosis induced by damage to the lungs and short telomeres.

PubMed

Povedano, Juan Manuel; Martinez, Paula; Serrano, Rosa; Tejera, Águeda; Gómez-López, Gonzalo; Bobadilla, Maria; Flores, Juana Maria; Bosch, Fátima; Blasco, Maria A

2018-01-30

Pulmonary fibrosis is a fatal lung disease characterized by fibrotic foci and inflammatory infiltrates. Short telomeres can impair tissue regeneration and are found both in hereditary and sporadic cases. We show here that telomerase expression using AAV9 vectors shows therapeutic effects in a mouse model of pulmonary fibrosis owing to a low-dose bleomycin insult and short telomeres. AAV9 preferentially targets regenerative alveolar type II cells (ATII). AAV9- Tert -treated mice show improved lung function and lower inflammation and fibrosis at 1-3 weeks after viral treatment, and improvement or disappearance of the fibrosis at 8 weeks after treatment. AAV9- Tert treatment leads to longer telomeres and increased proliferation of ATII cells, as well as lower DNA damage, apoptosis, and senescence. Transcriptome analysis of ATII cells confirms downregulation of fibrosis and inflammation pathways. We provide a proof-of-principle that telomerase activation may represent an effective treatment for pulmonary fibrosis provoked or associated with short telomeres. © 2018, Povedano et al.

Therapeutic effects of telomerase in mice with pulmonary fibrosis induced by damage to the lungs and short telomeres

PubMed Central

Serrano, Rosa; Tejera, Águeda; Gómez-López, Gonzalo; Bobadilla, Maria; Flores, Juana Maria; Bosch, Fátima

2018-01-01

Pulmonary fibrosis is a fatal lung disease characterized by fibrotic foci and inflammatory infiltrates. Short telomeres can impair tissue regeneration and are found both in hereditary and sporadic cases. We show here that telomerase expression using AAV9 vectors shows therapeutic effects in a mouse model of pulmonary fibrosis owing to a low-dose bleomycin insult and short telomeres. AAV9 preferentially targets regenerative alveolar type II cells (ATII). AAV9-Tert-treated mice show improved lung function and lower inflammation and fibrosis at 1–3 weeks after viral treatment, and improvement or disappearance of the fibrosis at 8 weeks after treatment. AAV9-Tert treatment leads to longer telomeres and increased proliferation of ATII cells, as well as lower DNA damage, apoptosis, and senescence. Transcriptome analysis of ATII cells confirms downregulation of fibrosis and inflammation pathways. We provide a proof-of-principle that telomerase activation may represent an effective treatment for pulmonary fibrosis provoked or associated with short telomeres. PMID:29378675

Characterization of Preferential Flow Path in Fractured Rock Using Heat-pulse Flowmeter

NASA Astrophysics Data System (ADS)

Lee, Tsai-Ping; Lin, Ming-Hsuan; Chuang, Po-Yu; Chia, Yeeping

2015-04-01

Rigorous thinking on how to dispose radioactive wastes safely is essential to mankind and living environment. The concepts of multiple barriers and deep geologic disposal remain the preferred option to retard the radionuclide migration in most countries. However, the investigation of preferential groundwater flow path in a fractured rock is a challenge to the characterization of potential disposal site. Heat-pulse flowmeter is a developing logging tool for measuring the vertical flow velocity in a borehole under a constant pumping or injection rate and provides a promising direct measurement method for determining the vertical distribution of hydraulic conductivity of formation. As heat-pulse flowmeter is a potential technique to measure low-velocity borehole flow, we adopted it to test the feasibility of detecting permeable fractures. Besides, a new magnetic tracer made by nano-iron particles is developed to identify the possible flow path precisely and to verify the permeable section detected by the heat-pulse flowmeter. The magnetic tracer was received by a magnet array and can also be detected by a sensor of electric conductivity. The test site is located in the Heshe of Taiwan. Eight wells were established in a fractured sandy siltstone for characterizing the fracture network. The test wells are 25 to 45 m depth and opened ranging from 15 to 45 m. Prior to the heat-pulse flowmeter measurement, we also performed surface geological investigation, pumping test, geophysical logging, and salt tracer test. Field measurements using heat-pulse flowmeter were then conducted at a constant pumping rate. The measurement interval is 50 to 100 cm in depth but improved to 25 cm near the relatively permeable zone. Based on the results of heat-pulse flowmeter, several permeable sections were identified. The magnetic tracer tests were then conducted to verify the potential preferential flow pathway between adjacent wells. Test results indicated that water flow in borehole is produced primarily from a few fractures. However, the large aperture and high density of fractures did not certainly correlate well to the permeable section. Integration of heat-pulse flowmeter measurement with other in-situ tests, it is possible to identify the exact location of the highly permeable fractures.

Popularity versus similarity in growing networks.

PubMed

Papadopoulos, Fragkiskos; Kitsak, Maksim; Serrano, M Ángeles; Boguñá, Marián; Krioukov, Dmitri

2012-09-27

The principle that 'popularity is attractive' underlies preferential attachment, which is a common explanation for the emergence of scaling in growing networks. If new connections are made preferentially to more popular nodes, then the resulting distribution of the number of connections possessed by nodes follows power laws, as observed in many real networks. Preferential attachment has been directly validated for some real networks (including the Internet), and can be a consequence of different underlying processes based on node fitness, ranking, optimization, random walks or duplication. Here we show that popularity is just one dimension of attractiveness; another dimension is similarity. We develop a framework in which new connections optimize certain trade-offs between popularity and similarity, instead of simply preferring popular nodes. The framework has a geometric interpretation in which popularity preference emerges from local optimization. As opposed to preferential attachment, our optimization framework accurately describes the large-scale evolution of technological (the Internet), social (trust relationships between people) and biological (Escherichia coli metabolic) networks, predicting the probability of new links with high precision. The framework that we have developed can thus be used for predicting new links in evolving networks, and provides a different perspective on preferential attachment as an emergent phenomenon.

Are preferential flow paths perpetuated by microbial activity in the soil matrix? A review

NASA Astrophysics Data System (ADS)

Morales, Verónica L.; Parlange, J.-Yves; Steenhuis, Tammo S.

2010-10-01

SummaryRecently, the interactions between soil structure and microbes have been associated with water transport, retention and preferential or column flow development. Of particular significance is the potential impact of microbial extracellular polymeric substances (EPS) on soil porosity (i.e., hydraulic conductivity reduction or bioclogging) and of exudates from biota, including bacteria, fungi, roots and earthworms on the degree of soil water repellency. These structural and surface property changes create points of wetting instability, which under certain infiltrating conditions can often result in the formation of persistent preferential flow paths. Moreover, distinct differences in physical and chemical properties between regions of water flow (preferential flow paths) and no-flow (soil matrix) provide a unique set of environmental living conditions for adaptable microorganisms to exist. In this review, special consideration is given to: (1) the functional significance of microbial activity in the host porous medium in terms of feedback mechanisms instigated by irregular water availability and (2) the related physical and chemical conditions that force the organization and formation of unique microbial habitats in unsaturated soils that prompt and potentially perpetuate the formation of preferential flow paths in the vadose zone.

OsCHX14 is Involved in the K+ Homeostasis in Rice (Oryza sativa) Flowers.

PubMed

Chen, Yi; Ma, Jingkun; Miller, Anthony J; Luo, Bingbing; Wang, Mei; Zhu, Zhen; Ouwerkerk, Pieter B F

2016-07-01

Previously we showed in the osjar1 mutants that the lodicule senescence which controls the closing of rice flowers was delayed. This resulted in florets staying open longer when compared with the wild type. The gene OsJAR1 is silenced in osjar1 mutants and is a key member of the jasmonic acid (JA) signaling pathway. We found that K concentrations in lodicules and flowers of osjar1-2 were significantly elevated compared with the wild type, indicating that K + homeostasis may play a role in regulating the closure of rice flowers. The cation/H + exchanger (CHX) family from rice was screened for potential K + transporters involved as many members of this family in Arabidopsis were exclusively or preferentially expressed in flowers. Expression profiling confirmed that among 17 CHX genes in rice, OsCHX14 was the only member that showed an expression polymorphism, not only in osjar1 mutants but also in RNAi (RNA interference) lines of OsCOI1, another key member of the JA signaling pathway. This suggests that the expression of OsCHX14 is regulated by the JA signaling pathway. Green fluorescent protein (GFP)-tagged OsCHX14 protein was preferentially localized to the endoplasmic reticulum. Promoter-β-glucuronidase (GUS) analysis of transgenic rice revealed that OsCHX14 is mainly expressed in lodicules and the region close by throughout the flowering process. Characterization in yeast and Xenopus laevis oocytes verified that OsCHX14 is able to transport K + , Rb + and Cs + in vivo. Our data suggest that OsCHX14 may play an important role in K + homeostasis during flowering in rice. © The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

WNT2B2 mRNA, up-regulated in primary gastric cancer, is a positive regulator of the WNT- beta-catenin-TCF signaling pathway.

PubMed

Katoh, M; Kirikoshi, H; Terasaki, H; Shiokawa, K

2001-12-21

Genetic alterations of WNT signaling molecules lead to carcinogenesis through activation of the beta-catenin-TCF signaling pathway. We have previously cloned and characterized WNT2B/WNT13 gene on human chromosome 1p13, which is homologous to proto-oncogene WNT2 on human chromosome 7q31. WNT2B1 and WNT2B2 mRNAs, generated from the WNT2B gene due to alternative splicing of the alternative promoter type, encode almost identical polypeptides with divergence in the N-terminal region. WNT2B2 mRNA rather than WNT2B1 mRNA is preferentially expressed in NT2 cells with the potential of neuronal differentiation. Here, we describe our investigations of expression of WNT2B mRNAs in various types of human primary cancer. Matched tumor/normal expression array analysis revealed that WNT2B mRNAs were significantly up-regulated in 2 of 8 cases of primary gastric cancer. WNT2B2 mRNA rather than WNT2B1 mRNA was found to be preferentially up-regulated in a case of primary gastric cancer (signet ring cell carcinoma). Function of WNT2B1 mRNA and that of WNT2B2 mRNA were investigated by using Xenopus axis duplication assay. Injection of synthetic WNT2B1 mRNA into the ventral marginal zone of fertilized Xenopus eggs at the 4-cell stage did not induce axis duplication. In contrast, ventral injection of synthetic WNT2B2 mRNA induced axis duplication in 90% of embryos (complete axis duplication, 24%). These results strongly suggest that WNT2B2 up-regulation in some cases of gastric cancer might lead to carcinogenesis through activation of the beta-catenin-TCF signaling pathway.

Low-energy collision induced dissociation (low-energy CID), collision induced dissociation (CID) and higher-energy collision dissociation (HCD) mass spectrometry for structural elucidation of saccharides and clarification of their dissolution mechanism in DMAc/LiCl.

PubMed

Bayat, Parisa; Lesage, Denis; Cole, Richard B

2018-05-29

The dissolution mechanism of oligosaccharides in N,N-dimethylacetamide/lithium chloride (DMAc/LiCl), a solvent used for cellulose dissolution, and the capabilities of low-energy collision induced dissociation (low-energy CID), collision induced dissociation (CID) and higher-energy collision dissociation (HCD) for structural analysis of carbohydrates were investigated. Comparing the spectra obtained using three techniques shows that, generally, when working with mono-lithiated sugars, CID spectra provide more structurally informative fragments, and glycosidic bond cleavage is the main pathway. However, when working with di-lithiated sugars, HCD spectra can be more informative providing predominately cross-ring cleavage fragments. This is because HCD is a non-resonant activation technique and it allows a higher amount of energy to be deposited in a short time, giving access to more endothermic decomposition pathways as well as consecutive fragmentations. The difference in preferred dissociation pathways of mono-lithiated and di-lithiated sugars indicates that the presence of the second lithium strongly influences the relative rate constants for cross-ring cleavages (rearrangement) vs. direct glycosidic bond cleavages, and disfavors the latter. Regarding the dissolution mechanism of sugars in DMAc/LiCl, CID and HCD experiments on di-lithiated and tri-lithiated sugars reveal that intensities of product ions containing two Li + or three Li + , respectively, are higher than those bearing only one Li + . In addition, comparing the fragmentation spectra (both HCD and CID) of LiCl adducted lithiated sugar and NaCl adducted sodiated sugar shows that while, in the latter case, loss of NaCl is dominant, in the former case, loss of HCl occurs preferentially. The compiled evidence implies that there is a strong and direct interaction between lithium and the saccharide during the dissolution process in the DMAc/LiCl solvent system. This article is protected by copyright. All rights reserved.

Internal electron transfer between hemes and Cu(II) bound at cysteine beta93 promotes methemoglobin reduction by carbon monoxide.

PubMed

Bonaventura, C; Godette, G; Tesh, S; Holm, D E; Bonaventura, J; Crumbliss, A L; Pearce, L L; Peterson, J

1999-02-26

Previous studies showed that CO/H2O oxidation provides electrons to drive the reduction of oxidized hemoglobin (metHb). We report here that Cu(II) addition accelerates the rate of metHb beta chain reduction by CO by a factor of about 1000. A mechanism whereby electron transfer occurs via an internal pathway coupling CO/H2O oxidation to Fe(III) and Cu(II) reduction is suggested by the observation that the copper-induced rate enhancement is inhibited by blocking Cys-beta93 with N-ethylmaleimide. Furthermore, this internal electron-transfer pathway is more readily established at low Cu(II) concentrations in Hb Deer Lodge (beta2His --> Arg) and other species lacking His-beta2 than in Hb A0. This difference is consistent with preferential binding of Cu(II) in Hb A0 to a high affinity site involving His-beta2, which is ineffective in promoting electron exchange between Cu(II) and the beta heme iron. Effective electron transfer is thus affected by Hb type but is not governed by the R left arrow over right arrow T conformational equilibrium. The beta hemes in Cu(II)-metHb are reduced under CO at rates close to those observed for cytochrome c oxidase, where heme and copper are present together in the oxygen-binding site and where internal electron transfer also occurs.

Stabilization of Two Radicals with One Metal: A Stepwise Coupling Model for Copper-Catalyzed Radical–Radical Cross-Coupling

PubMed Central

Qi, Xiaotian; Zhu, Lei; Bai, Ruopeng; Lan, Yu

2017-01-01

Transition metal-catalyzed radical–radical cross-coupling reactions provide innovative methods for C–C and C–heteroatom bond construction. A theoretical study was performed to reveal the mechanism and selectivity of the copper-catalyzed C–N radical–radical cross-coupling reaction. The concerted coupling pathway, in which a C–N bond is formed through the direct nucleophilic addition of a carbon radical to the nitrogen atom of the Cu(II)–N species, is demonstrated to be kinetically unfavorable. The stepwise coupling pathway, which involves the combination of a carbon radical with a Cu(II)–N species before C–N bond formation, is shown to be probable. Both the Mulliken atomic spin density distribution and frontier molecular orbital analysis on the Cu(II)–N intermediate show that the Cu site is more reactive than that of N; thus, the carbon radical preferentially react with the metal center. The chemoselectivity of the cross-coupling is also explained by the differences in electron compatibility of the carbon radical, the nitrogen radical and the Cu(II)–N intermediate. The higher activation free energy for N–N radical–radical homo-coupling is attributed to the mismatch of Cu(II)–N species with the nitrogen radical because the electrophilicity for both is strong. PMID:28272407

Intracranial delivery of Interleukin-17A via adeno-associated virus fails to induce physical and learning disabilities and neuroinflammation in mice but improves glucose metabolism through AKT signaling pathway

PubMed Central

Yang, Junling; Kou, Jinghong; Lim, Jeong-Eun; Lalonde, Robert; Fukuchi, Ken-ichiro

2015-01-01

Interleukin-17A (IL-17A) is generally considered as one of the pathogenic factors involved in multiple sclerosis (MS). Indirect evidence for this is that IL-17A-producing T helper 17 (Th17) cells preferentially accumulate in lesions of MS and experimental autoimmune encephalomyelitis (EAE). However, a direct involvement of IL-17A in MS pathogenesis is still an open question. In this study, we overexpressed IL-17A in the brains of mice (IL-17A-in-Brain mice) via recombinant adeno-associated virus serotype 5 (rAAV5)-mediated gene delivery. In spite of high levels of IL-17A expression in the brain and blood, IL-17A-in-Brain mice exhibit no inflammatory responses and no abnormalities in motor coordination and spatial orientation. Unexpectedly, IL-17A-in-Brain mice show decreases in body weight and adipose tissue mass and an improvement in glucose tolerance and insulin sensitivity. IL-17A enhances glucose uptake in PC12 cells by activation of AKT. Our results provide direct evidence for the first time that IL-17A overexpression in the central nervous system does not cause physical and learning disabilities and neuroinflammation and suggest that IL-17A may regulate glucose metabolism through the AKT signaling pathway. PMID:26562537

Evolution of Chloroplast Transcript Processing in Plasmodium and Its Chromerid Algal Relatives

PubMed Central

Dorrell, Richard G.; Drew, James; Nisbet, R. Ellen R.; Howe, Christopher J.

2014-01-01

It is well understood that apicomplexan parasites, such as the malaria pathogen Plasmodium, are descended from free-living algae, and maintain a vestigial chloroplast that has secondarily lost all genes of photosynthetic function. Recently, two fully photosynthetic relatives of parasitic apicomplexans have been identified, the ‘chromerid’ algae Chromera velia and Vitrella brassicaformis, which retain photosynthesis genes within their chloroplasts. Elucidating the processes governing gene expression in chromerid chloroplasts might provide valuable insights into the origins of parasitism in the apicomplexans. We have characterised chloroplast transcript processing pathways in C. velia, V. brassicaformis and P. falciparum with a focus on the addition of an unusual, 3′ poly(U) tail. We demonstrate that poly(U) tails in chromerids are preferentially added to transcripts that encode proteins that are directly involved in photosynthetic electron transfer, over transcripts for proteins that are not involved in photosynthesis. To our knowledge, this represents the first chloroplast transcript processing pathway to be associated with a particular functional category of genes. In contrast, Plasmodium chloroplast transcripts are not polyuridylylated. We additionally present evidence that poly(U) tail addition in chromerids is involved in the alternative processing of polycistronic precursors covering multiple photosynthesis genes, and appears to be associated with high levels of transcript abundance. We propose that changes to the chloroplast transcript processing machinery were an important step in the loss of photosynthesis in ancestors of parasitic apicomplexans. PMID:24453981

A thaumatin-like protein of Ocimum basilicum confers tolerance to fungal pathogen and abiotic stress in transgenic Arabidopsis

PubMed Central

Misra, Rajesh Chandra; Sandeep; Kamthan, Mohan; Kumar, Santosh; Ghosh, Sumit

2016-01-01

Plant often responds to fungal pathogens by expressing a group of proteins known as pathogenesis-related proteins (PRs). The expression of PR is mediated through pathogen-induced signal-transduction pathways that are fine-tuned by phytohormones such as methyl jasmonate (MeJA). Here, we report functional characterization of an Ocimum basilicum PR5 family member (ObTLP1) that was identified from a MeJA-responsive expression sequence tag collection. ObTLP1 encodes a 226 amino acid polypeptide that showed sequence and structural similarities with a sweet-tasting protein thaumatin of Thaumatococcus danielli and also with a stress-responsive protein osmotin of Nicotiana tabacum. The expression of ObTLP1 in O. basilicum was found to be organ-preferential under unstressed condition, and responsive to biotic and abiotic stresses, and multiple phytohormone elicitations. Bacterially-expressed recombinant ObTLP1 inhibited mycelial growth of the phytopathogenic fungi, Scleretonia sclerotiorum and Botrytis cinerea; thereby, suggesting its antifungal activity. Ectopic expression of ObTLP1 in Arabidopsis led to enhanced tolerance to S. sclerotiorum and B. cinerea infections, and also to dehydration and salt stress. Moreover, induced expression of the defense marker genes suggested up-regulation of the defense-response pathways in ObTLP1-expressing Arabidopsis upon fungal challenge. Thus, ObTLP1 might be useful for providing tolerance to the fungal pathogens and abiotic stresses in crops. PMID:27150014

A thaumatin-like protein of Ocimum basilicum confers tolerance to fungal pathogen and abiotic stress in transgenic Arabidopsis.

PubMed

Misra, Rajesh Chandra; Sandeep; Kamthan, Mohan; Kumar, Santosh; Ghosh, Sumit

2016-05-06

Plant often responds to fungal pathogens by expressing a group of proteins known as pathogenesis-related proteins (PRs). The expression of PR is mediated through pathogen-induced signal-transduction pathways that are fine-tuned by phytohormones such as methyl jasmonate (MeJA). Here, we report functional characterization of an Ocimum basilicum PR5 family member (ObTLP1) that was identified from a MeJA-responsive expression sequence tag collection. ObTLP1 encodes a 226 amino acid polypeptide that showed sequence and structural similarities with a sweet-tasting protein thaumatin of Thaumatococcus danielli and also with a stress-responsive protein osmotin of Nicotiana tabacum. The expression of ObTLP1 in O. basilicum was found to be organ-preferential under unstressed condition, and responsive to biotic and abiotic stresses, and multiple phytohormone elicitations. Bacterially-expressed recombinant ObTLP1 inhibited mycelial growth of the phytopathogenic fungi, Scleretonia sclerotiorum and Botrytis cinerea; thereby, suggesting its antifungal activity. Ectopic expression of ObTLP1 in Arabidopsis led to enhanced tolerance to S. sclerotiorum and B. cinerea infections, and also to dehydration and salt stress. Moreover, induced expression of the defense marker genes suggested up-regulation of the defense-response pathways in ObTLP1-expressing Arabidopsis upon fungal challenge. Thus, ObTLP1 might be useful for providing tolerance to the fungal pathogens and abiotic stresses in crops.

Characterization of TCE DNAPL and Dissolved Phase Transport in Karst Media

NASA Astrophysics Data System (ADS)

Carmona, M.; Padilla, I. Y.

2015-12-01

Trichloroethylene (TCE) contaminated sites are a threat to the environment and human health. Of particular concerns is the contamination of karst groundwater systems (KGWSs). Their heterogeneous character, rapid flow through conduits, high permeability zones, and strong storage capacity in the rock porous-matrix pose a high risk of exposure over large areas and temporal scales. To achieve effective remedial actions for TCE removal, it is important to understand and quantify the fate and transport process of trichloroethylene in these systems. This research studies the fate, transport, and distribution of TCE Non-Aqueous Phase Liquids (NAPLs) and associated dissolved species in KGWSs. Experiments are conducted in a karstified limestone physical model, a limestone rock mimicking a saturated confined karst aquifer. After injecting TCE solvent into a steady groundwater flow field, samples are taken spatially and temporally and analyzed for TCE NAPL and dissolved phases. Data analysis shows the rapid detection of TCE NAPL and high aqueous concentrations along preferential pathway, even at distances far away from the injection point. Temporal distribution curves exhibit spatial variations related to the limestone rock heterogeneity. Rapid response to TCE concentrations is associated with preferential flow paths. Slow response with long tailing indicates rate-limited diffusive transport in the rock matrix. Overall, results indicate that karstified limestone has a high capacity to rapidly transport pure and dissolved TCE along preferential flow paths, and to store and slowly release TCE over long periods of time.

Brain Cancer Stem Cells Display Preferential Sensitivity to Akt Inhibition

PubMed Central

Eyler, Christine E.; Foo, Wen-Chi; LaFiura, Katherine M.; McLendon, Roger E.; Hjelmeland, Anita B.; Rich, Jeremy N.

2009-01-01

Malignant brain tumors are among the most lethal cancers, and conventional therapies are largely limited to palliation. Novel therapies targeted against specific molecular pathways may offer improved efficacy and reduced toxicity compared to conventional therapies, but initial clinical trials of molecular targeted agents in brain cancer therapy have been frequently disappointing. In brain tumors and other cancers, subpopulations of tumor cells have recently been characterized by their ability to self-renew and initiate tumors. Although these cancer stem cells, or tumor initiating cells, are often only present in small numbers in human tumors, mounting evidence suggests that cancer stem cells contribute to tumor maintenance and therapeutic resistance. Thus, the development of therapies that target cancer stem cell signal transduction and biologies may improve brain tumor patient survival. We now demonstrate that populations enriched for cancer stem cells are preferentially sensitive to an inhibitor of Akt, a prominent cell survival and invasion signaling node. Treatment with an Akt inhibitor more potently reduced the numbers of viable brain cancer stem cells relative to matched non-stem cancer cells associated with a preferential induction of apoptosis and a suppression of neurosphere formation. Akt inhibition also reduced the motility and invasiveness of all tumor cells but had a greater impact on cancer stem cell behaviors. Furthermore, inhibition of Akt activity in cancer stem cells increased survival of immunocompromised mice bearing human glioma xenografts in vivo. Together, these results suggest that Akt inhibitors may function as effective anti-cancer stem cell therapies. PMID:18802038

Susceptibility to enhanced chemical migration from depression-focused preferential flow, High Plains aquifer

USGS Publications Warehouse

Gurdak, Jason J.; Walvoord, Michelle Ann; McMahon, Peter B.

2008-01-01

Aquifer susceptibility to contamination is controlled in part by the inherent hydrogeologic properties of the vadose zone, which includes preferential-flow pathways. The purpose of this study was to investigate the importance of seasonal ponding near leaky irrigation wells as a mechanism for depression-focused preferential flow and enhanced chemical migration through the vadose zone of the High Plains aquifer. Such a mechanism may help explain the widespread presence of agrichemicals in recently recharged groundwater despite estimates of advective chemical transit times through the vadose zone from diffuse recharge that exceed the historical period of agriculture. Using a combination of field observations, vadose zone flow and transport simulations, and probabilistic neural network modeling, we demonstrated that vadose zone transit times near irrigation wells range from 7 to 50 yr, which are one to two orders of magnitude faster than previous estimates based on diffuse recharge. These findings support the concept of fast and slow transport zones and help to explain the previous discordant findings of long vadose zone transit times and the presence of agrichemicals at the water table. Using predictions of aquifer susceptibility from probabilistic neural network models, we delineated approximately 20% of the areal extent of the aquifer to have conditions that may promote advective chemical transit times to the water table of <50 yr if seasonal ponding and depression-focused flow exist. This aquifer-susceptibility map may help managers prioritize areas for groundwater monitoring or implementation of best management practices.

Emergence of Soft Communities from Geometric Preferential Attachment

PubMed Central

Zuev, Konstantin; Boguñá, Marián; Bianconi, Ginestra; Krioukov, Dmitri

2015-01-01

All real networks are different, but many have some structural properties in common. There seems to be no consensus on what the most common properties are, but scale-free degree distributions, strong clustering, and community structure are frequently mentioned without question. Surprisingly, there exists no simple generative mechanism explaining all the three properties at once in growing networks. Here we show how latent network geometry coupled with preferential attachment of nodes to this geometry fills this gap. We call this mechanism geometric preferential attachment (GPA), and validate it against the Internet. GPA gives rise to soft communities that provide a different perspective on the community structure in networks. The connections between GPA and cosmological models, including inflation, are also discussed. PMID:25923110

Bioaccumulation of hydroxylated polychlorinated biphenyls and pentachlorophenol in the serum of northern elephant seal pups (Mirounga angustirostris)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Louis, Caroline, E-mail: caroline.louis@uclouvain.be; Covaci, Adrian; Stas, Marie

Northern elephant seals (NES) (Mirounga angustirostris) from the Año Nuevo State Reserve (CA, USA) were sampled at 1-, 4-, 7- and 10-week post-weaning. Concentrations of hydroxylated polychlorinated biphenyls (HO-PCBs) and their parent PCBs were measured in the serum of each individual. The ΣHO-PCB concentrations in the serum increased significantly between early and late fast (from 282±20 to 529±31 pg/mL). This increase might result from a mobilisation of HO-PCBs transferred from the mother during gestation and/or lactation and stored in the pup's liver. Food deprivation has been shown to exacerbate biotransformation capacities in mammals, birds and fish. The HO-penta-CBs was themore » predominant homologue group, followed by HO-hexa-CBs and HO-hepta-CBs. No preferential pathway for the metabolism of HO-PCBs (HO-direct insertion or NIH-shift of a chlorine atom) could be evidenced. The concentrations of pentachlorophenol (PCP) in the serum of weaned NES increased from 103±7 pg/mL at early fast to 246±41 pg/mL at late fast, which is within the range of PCP concentrations usually encountered in marine mammals. - Highlights: • Σ HO-PCB concentrations in serum significantly increased between early and late fast. • The HO-penta-CBs were the predominant homologue group measured in serum. • No preferential pathway for the metabolism of HO-PCBs could be evidenced. • PCP concentrations in serum significantly increased between early and late fast.« less

Leveraging increased cytoplasmic nucleoside kinase activity to target mtDNA and oxidative phosphorylation in AML.

PubMed

Liyanage, Sanduni U; Hurren, Rose; Voisin, Veronique; Bridon, Gaëlle; Wang, Xiaoming; Xu, ChangJiang; MacLean, Neil; Siriwardena, Thirushi P; Gronda, Marcela; Yehudai, Dana; Sriskanthadevan, Shrivani; Avizonis, Daina; Shamas-Din, Aisha; Minden, Mark D; Bader, Gary D; Laposa, Rebecca; Schimmer, Aaron D

2017-05-11

Mitochondrial DNA (mtDNA) biosynthesis requires replication factors and adequate nucleotide pools from the mitochondria and cytoplasm. We performed gene expression profiling analysis of 542 human acute myeloid leukemia (AML) samples and identified 55% with upregulated mtDNA biosynthesis pathway expression compared with normal hematopoietic cells. Genes that support mitochondrial nucleotide pools, including mitochondrial nucleotide transporters and a subset of cytoplasmic nucleoside kinases, were also increased in AML compared with normal hematopoietic samples. Knockdown of cytoplasmic nucleoside kinases reduced mtDNA levels in AML cells, demonstrating their contribution in maintaining mtDNA. To assess cytoplasmic nucleoside kinase pathway activity, we used a nucleoside analog 2'3'-dideoxycytidine (ddC), which is phosphorylated to the activated antimetabolite, 2'3'-dideoxycytidine triphosphate by cytoplasmic nucleoside kinases. ddC is a selective inhibitor of the mitochondrial DNA polymerase γ. ddC was preferentially activated in AML cells compared with normal hematopoietic progenitor cells. ddC treatment inhibited mtDNA replication, oxidative phosphorylation, and induced cytotoxicity in a panel of AML cell lines. Furthermore, ddC preferentially inhibited mtDNA replication in a subset of primary human leukemia cells and selectively targeted leukemia cells while sparing normal progenitor cells. In animal models of human AML, treatment with ddC decreased mtDNA, electron transport chain proteins, and induced tumor regression without toxicity. ddC also targeted leukemic stem cells in secondary AML xenotransplantation assays. Thus, AML cells have increased cytidine nucleoside kinase activity that regulates mtDNA biogenesis and can be leveraged to selectively target oxidative phosphorylation in AML. © 2017 by The American Society of Hematology.

Leveraging increased cytoplasmic nucleoside kinase activity to target mtDNA and oxidative phosphorylation in AML

PubMed Central

Liyanage, Sanduni U.; Hurren, Rose; Voisin, Veronique; Bridon, Gaëlle; Wang, Xiaoming; Xu, ChangJiang; MacLean, Neil; Siriwardena, Thirushi P.; Gronda, Marcela; Yehudai, Dana; Sriskanthadevan, Shrivani; Avizonis, Daina; Shamas-Din, Aisha; Minden, Mark D.; Bader, Gary D.; Laposa, Rebecca

2017-01-01

Mitochondrial DNA (mtDNA) biosynthesis requires replication factors and adequate nucleotide pools from the mitochondria and cytoplasm. We performed gene expression profiling analysis of 542 human acute myeloid leukemia (AML) samples and identified 55% with upregulated mtDNA biosynthesis pathway expression compared with normal hematopoietic cells. Genes that support mitochondrial nucleotide pools, including mitochondrial nucleotide transporters and a subset of cytoplasmic nucleoside kinases, were also increased in AML compared with normal hematopoietic samples. Knockdown of cytoplasmic nucleoside kinases reduced mtDNA levels in AML cells, demonstrating their contribution in maintaining mtDNA. To assess cytoplasmic nucleoside kinase pathway activity, we used a nucleoside analog 2′3′-dideoxycytidine (ddC), which is phosphorylated to the activated antimetabolite, 2′3′-dideoxycytidine triphosphate by cytoplasmic nucleoside kinases. ddC is a selective inhibitor of the mitochondrial DNA polymerase γ. ddC was preferentially activated in AML cells compared with normal hematopoietic progenitor cells. ddC treatment inhibited mtDNA replication, oxidative phosphorylation, and induced cytotoxicity in a panel of AML cell lines. Furthermore, ddC preferentially inhibited mtDNA replication in a subset of primary human leukemia cells and selectively targeted leukemia cells while sparing normal progenitor cells. In animal models of human AML, treatment with ddC decreased mtDNA, electron transport chain proteins, and induced tumor regression without toxicity. ddC also targeted leukemic stem cells in secondary AML xenotransplantation assays. Thus, AML cells have increased cytidine nucleoside kinase activity that regulates mtDNA biogenesis and can be leveraged to selectively target oxidative phosphorylation in AML. PMID:28283480

Studies of ATM Kinase Activity Using Engineered ATM Sensitive to ATP Analogues (ATM-AS).

PubMed

Enari, Masato; Matsushima-Hibiya, Yuko; Miyazaki, Makoto; Otomo, Ryo

2017-01-01

Ataxia-telangiectasia mutated (ATM) protein is a member of the phosphatidylinositol 3-phosphate kinase (PI3-K)-related protein kinase (PIKK) family and is implicated in the initiation of signaling pathways following DNA double strand breaks (DSBs) elicited by exposure to ionizing irradiation (IR) or radiomimetic compounds. Loss of function of the ATM gene product results in the human genetic disorder ataxia-telangiectasia (A-T) characterized by neurodegeneration, immunodeficiency, genomic instability, and cancer predisposition. In response to DSBs, ATM is activated and phosphorylates Ser/Thr-Gln (S/T-Q) sequences on numerous proteins participating in DNA-damage responses. Among these proteins, phosphorylation of the tumor suppressor p53 at Ser15 is known as a target for ATM, which leads to the dissociation of MDM2, an E3 ubiquitin ligase, from p53 to prevent MDM2-dependent p53 degradation. Ser46 on p53 is phosphorylated in response to DSBs and contributes to the preferential transactivation of pro-apoptotic genes, such as p53AIP1, Noxa, and PUMA, to prevent tumor formation. Our group have shown that not only ATM preferentially phosphorylates S/T-Q sequences, but also Ser46, which is a noncanonical site with an S-P sequence for ATM. Ser46 on p53 is directly phosphorylated by ATM in a p53 conformation-dependent manner using the ATP analogue-accepting ATM mutant (ATM-AS) system. This protocol summarizes an approach to identify direct numerous targets for ATM kinase and is used to elucidate ATM signaling pathways in the DNA damage responses.

A Synergistic Antiobesity Effect by a Combination of Capsinoids and Cold Temperature Through Promoting Beige Adipocyte Biogenesis

PubMed Central

Ohyama, Kana; Nogusa, Yoshihito; Shinoda, Kosaku; Suzuki, Katsuya

2016-01-01

Beige adipocytes emerge postnatally within the white adipose tissue in response to certain environmental cues, such as chronic cold exposure. Because of its highly recruitable nature and relevance to adult humans, beige adipocytes have gained much attention as an attractive cellular target for antiobesity therapy. However, molecular circuits that preferentially promote beige adipocyte biogenesis remain poorly understood. We report that a combination of mild cold exposure at 17°C and capsinoids, a nonpungent analog of capsaicin, synergistically and preferentially promotes beige adipocyte biogenesis and ameliorates diet-induced obesity. Gain- and loss-of-function studies show that the combination of capsinoids and cold exposure synergistically promotes beige adipocyte development through the β2-adrenoceptor signaling pathway. This synergistic effect on beige adipocyte biogenesis occurs through an increased half-life of PRDM16, a dominant transcriptional regulator of brown/beige adipocyte development. We document a previously unappreciated molecular circuit that controls beige adipocyte biogenesis and suggest a plausible approach to increase whole-body energy expenditure by combining dietary components and environmental cues. PMID:26936964

Preferential melting of secondary structures during protein unfolding in different solvents: Competition between hydrophobic solvation and hydrogen bonding

NASA Astrophysics Data System (ADS)

Bagchi, Biman; Roy, Susmita; Ghosh, Rikhia

2014-03-01

Aqueous binary mixtures such as water-DMSO, water-urea, and water-ethanol are known to serve as denaturants of a host of proteins, although the detailed mechanism is often not known. Here we combine studies on several proteins in multiple binary mixtures to obtain a unified understanding of the phenomenon. We compare with experiments to support the simulation findings. The proteins considered include (i) chicken villin head piece (HP-36), (ii) immunoglobulin binding protein G (GB1), (iii) myoglobin and (iv) lysozyme. We find that for amphiphilic solvents like DMSO, the hydrophobic groups and the strong hydrogen bonding ability of the >S =O oxygen atom act together to facilitate the unfolding. However, the hydrophilic solvents like urea, due to the presence of more hydrophilic ends (C =O and two NH2) has a high propensity of forming hydrogen bonds with the side-chain residues and backbone of beta-sheet than the same of alpha helix. Such diversity among the unfolding pathways of a given protein in different chemical environments is especially characterized by the preferential solvation of a particular secondary structure.

Water movement and isoproturon behaviour in a drained heavy clay soil: 1. Preferential flow processes

NASA Astrophysics Data System (ADS)

Haria, A. H.; Johnson, A. C.; Bell, J. P.; Batchelor, C. H.

1994-12-01

The processes and mechanisms that control pesticide transport from drained heavy clay catchments are being studied at Wytham Farm (Oxford University) in southern England. In the first field season field-drain water contained high concentrations of pesticide. Soil studies demonstrated that the main mechanism for pesticide translocation was by preferential flow processes, both over the soil surface and through the soil profile via a macropore system that effectively by-passed the soil matrix. This macropore system included worm holes, shrinkage cracks and cracks resulting from ploughing. Rainfall events in early winter rapidly created a layer of saturation in the A horizon perched above a B horizon of very low hydraulic conductivity. Drain flow was initiated when the saturated layer in the A horizon extended into the upper 0.06m of the soil profile; thereafter water moved down slope via horizontal macropores possibly through a band of incorporated straw residues. These horizontal pathways for water movement connected with the fracture system of the mole drains, thus feeding the drains. Overland flow occurred infrequently during the season.

ESCRT-II/Vps25 constrains digit number by endosome-mediated selective modulation of FGF-SHH signaling.

PubMed

Handschuh, Karen; Feenstra, Jennifer; Koss, Matthew; Ferretti, Elisabetta; Risolino, Maurizio; Zewdu, Rediet; Sahai, Michelle A; Bénazet, Jean-Denis; Peng, Xiao P; Depew, Michael J; Quintana, Laura; Sharpe, James; Wang, Baolin; Alcorn, Heather; Rivi, Roberta; Butcher, Stephen; Manak, J Robert; Vaccari, Thomas; Weinstein, Harel; Anderson, Kathryn V; Lacy, Elizabeth; Selleri, Licia

2014-10-23

Sorting and degradation of receptors and associated signaling molecules maintain homeostasis of conserved signaling pathways during cell specification and tissue development. Yet, whether machineries that sort signaling proteins act preferentially on different receptors and ligands in different contexts remains mysterious. Here, we show that Vacuolar protein sorting 25, Vps25, a component of ESCRT-II (Endosomal Sorting Complex Required for Transport II), directs preferential endosome-mediated modulation of FGF signaling in limbs. By ENU-induced mutagenesis, we isolated a polydactylous mouse line carrying a hypomorphic mutation of Vps25 (Vps25(ENU)). Unlike Vps25-null embryos we generated, Vps25(ENU/ENU) mutants survive until late gestation. Their limbs display FGF signaling enhancement and consequent hyperactivation of the FGF-SHH feedback loop causing polydactyly, whereas WNT and BMP signaling remain unperturbed. Notably, Vps25(ENU/ENU) Mouse Embryonic Fibroblasts exhibit aberrant FGFR trafficking and degradation; however, SHH signaling is unperturbed. These studies establish that the ESCRT-II machinery selectively limits FGF signaling in vertebrate skeletal patterning.

Preferential Flow and Transport of Cryptosporidium Parvum Oocysts Through Vadose Zone: Experiments and Modeling

NASA Astrophysics Data System (ADS)

Darnault, C. J.; Darnault, C. J.; Garnier, P.; Kim, Y.; Oveson, K.; Jenkins, M.; Ghiorse, W.; Baveye, P.; Parlange, J.; Steenhuis, T.

2001-12-01

Oocysts of the protozoan Cryptosporidium parvum, when they contaminate drinking water supplies, can cause outbreaks of Cryptosporidiosis, a common waterborne disease. Of the different pathways by which oocysts can wind up in drinking water, one has received very little attention to date; because soils are often considered to be perfect filters, the transport of oocysts through the subsoil to groundwater by preferential flow is generally ignored. To evaluate its significance, three set of laboratory experiments investigated transport of oocysts through vadose zone. Experiment set I was carried out in a vertical 50 cm-long column filled with silica sand, under conditions known to foster fingered flow. Experiment set II investigates the effect of gas-water interfaces by modifying the hydrodynamical conditions in the sand columns with water-repellent sand barriers. Experiment III involved undisturbed soil columns subjected to macropores flow. The sand and soil columns were subjected to artificial rainfall and were allowed to reach steady-state. At that point, feces of contaminated calves were applied at the surface, along with a known amount of KCl to serve as tracer, and rainfall was continued at the same rate. The breakthrough of oocysts and Cl-, monitored in the effluent, demonstrate the importance of preferential flow - fingered flow and macropore flow - on the transport of oocysts through vadose zone. Peak oocyst concentrations were not appreciably delayed, compared to Cl-, and in some cases, occurred even before the Cl- peak. However, the numbers of oocysts present in the effluents were still orders of magnitude higher than the 5 to 10 oocysts per liter that are considerable sufficient to cause cryptosporidiosis in healthy adults. The transport of oocysts was simulated based on a partitioning the soil profile in both a distribution zone and a preferential zone, In particular, the model simulates accurately the markedly asymmetric breakthrough patterns, and the long exponential tailing. The spatial distribution of oocysts suggest a close relationship between oocyst retention and the extent of gas-water interfaces; sharp increases in oocyst numbers are consistently observed in regions of the sand where the water content has steep gradients, and therefore where one expects capillary meniscii to have maximal extent. These observations imply that oocyst transport in the vadose zone is likely to be very limited in the absence of preferential flow. However, experimental results suggest that the transport of oocysts in the subsurface via preferential flow may create a significant risk of groundwater contamination in some situations.

Inter-area correlations in the ventral visual pathway reflect feature integration

PubMed Central

Freeman, Jeremy; Donner, Tobias H.; Heeger, David J.

2011-01-01

During object perception, the brain integrates simple features into representations of complex objects. A perceptual phenomenon known as visual crowding selectively interferes with this process. Here, we use crowding to characterize a neural correlate of feature integration. Cortical activity was measured with functional magnetic resonance imaging, simultaneously in multiple areas of the ventral visual pathway (V1–V4 and the visual word form area, VWFA, which responds preferentially to familiar letters), while human subjects viewed crowded and uncrowded letters. Temporal correlations between cortical areas were lower for crowded letters than for uncrowded letters, especially between V1 and VWFA. These differences in correlation were retinotopically specific, and persisted when attention was diverted from the letters. But correlation differences were not evident when we substituted the letters with grating patches that were not crowded under our stimulus conditions. We conclude that inter-area correlations reflect feature integration and are disrupted by crowding. We propose that crowding may perturb the transformations between neural representations along the ventral pathway that underlie the integration of features into objects. PMID:21521832

Sterol partitioning by HMGR and DXR for routing intermediates toward withanolide biosynthesis.

PubMed

Singh, Shefali; Pal, Shaifali; Shanker, Karuna; Chanotiya, Chandan Singh; Gupta, Madan Mohan; Dwivedi, Upendra Nath; Shasany, Ajit Kumar

2014-12-01

Withanolides biosynthesis in the plant Withania somnifera (L.) Dunal is hypothesized to be diverged from sterol pathway at the level of 24-methylene cholesterol. The conversion and translocation of intermediates for sterols and withanolides are yet to be characterized in this plant. To understand the influence of mevalonate (MVA) and 2-C-methyl-d-erythritol-4-phosphate (MEP) pathways on sterols and withanolides biosynthesis in planta, we overexpressed the WsHMGR2 and WsDXR2 in tobacco, analyzed the effect of transient suppression through RNAi, inhibited MVA and MEP pathways and fed the leaf tissue with different sterols. Overexpression of WsHMGR2 increased cycloartenol, sitosterol, stigmasterol and campesterol compared to WsDXR2 transgene lines. Increase in cholesterol was, however, marginally higher in WsDXR2 transgenic lines. This was further validated through transient suppression analysis, and pathway inhibition where cholesterol reduction was found higher due to WsDXR2 suppression and all other sterols were affected predominantly by WsHMGR2 suppression in leaf. The transcript abundance and enzyme analysis data also correlate with sterol accumulation. Cholesterol feeding did not increase the withanolide content compared to cycloartenol, sitosterol, stigmasterol and campesterol. Hence, a preferential translocation of carbon from MVA and MEP pathways was found differentiating the sterols types. Overall results suggested that MVA pathway was predominant in contributing intermediates for withanolides synthesis mainly through the campesterol/stigmasterol route in planta. © 2014 Scandinavian Plant Physiology Society.

Secondary migration and leakage of methane from a major tight-gas system

NASA Astrophysics Data System (ADS)

Wood, James M.; Sanei, Hamed

2016-11-01

Tight-gas and shale-gas systems can undergo significant depressurization during basin uplift and erosion of overburden due primarily to the natural leakage of hydrocarbon fluids. To date, geologic factors governing hydrocarbon leakage from such systems are poorly documented and understood. Here we show, in a study of produced natural gas from 1,907 petroleum wells drilled into a Triassic tight-gas system in western Canada, that hydrocarbon fluid loss is focused along distinct curvilinear pathways controlled by stratigraphic trends with superior matrix permeability and likely also structural trends with enhanced fracture permeability. Natural gas along these pathways is preferentially enriched in methane because of selective secondary migration and phase separation processes. The leakage and secondary migration of thermogenic methane to surficial strata is part of an ongoing carbon cycle in which organic carbon in the deep sedimentary basin transforms into methane, and ultimately reaches the near-surface groundwater and atmosphere.

Immunogenicity is preferentially induced in sparse dendritic cell cultures.

PubMed

Nasi, Aikaterini; Bollampalli, Vishnu Priya; Sun, Meng; Chen, Yang; Amu, Sylvie; Nylén, Susanne; Eidsmo, Liv; Rothfuchs, Antonio Gigliotti; Réthi, Bence

2017-03-09

We have previously shown that human monocyte-derived dendritic cells (DCs) acquired different characteristics in dense or sparse cell cultures. Sparsity promoted the development of IL-12 producing migratory DCs, whereas dense cultures increased IL-10 production. Here we analysed whether the density-dependent endogenous breaks could modulate DC-based vaccines. Using murine bone marrow-derived DC models we show that sparse cultures were essential to achieve several key functions required for immunogenic DC vaccines, including mobility to draining lymph nodes, recruitment and massive proliferation of antigen-specific CD4+ T cells, in addition to their TH1 polarization. Transcription analyses confirmed higher commitment in sparse cultures towards T cell activation, whereas DCs obtained from dense cultures up-regulated immunosuppressive pathway components and genes suggesting higher differentiation plasticity towards osteoclasts. Interestingly, we detected a striking up-regulation of fatty acid and cholesterol biosynthesis pathways in sparse cultures, suggesting an important link between DC immunogenicity and lipid homeostasis regulation.

Secondary migration and leakage of methane from a major tight-gas system

PubMed Central

Wood, James M.; Sanei, Hamed

2016-01-01

Tight-gas and shale-gas systems can undergo significant depressurization during basin uplift and erosion of overburden due primarily to the natural leakage of hydrocarbon fluids. To date, geologic factors governing hydrocarbon leakage from such systems are poorly documented and understood. Here we show, in a study of produced natural gas from 1,907 petroleum wells drilled into a Triassic tight-gas system in western Canada, that hydrocarbon fluid loss is focused along distinct curvilinear pathways controlled by stratigraphic trends with superior matrix permeability and likely also structural trends with enhanced fracture permeability. Natural gas along these pathways is preferentially enriched in methane because of selective secondary migration and phase separation processes. The leakage and secondary migration of thermogenic methane to surficial strata is part of an ongoing carbon cycle in which organic carbon in the deep sedimentary basin transforms into methane, and ultimately reaches the near-surface groundwater and atmosphere. PMID:27874012

Dynamic Integration of Task-Relevant Visual Features in Posterior Parietal Cortex

PubMed Central

Freedman, David J.

2014-01-01

Summary The primate visual system consists of multiple hierarchically organized cortical areas, each specialized for processing distinct aspects of the visual scene. For example, color and form are encoded in ventral pathway areas such as V4 and inferior temporal cortex, while motion is preferentially processed in dorsal pathway areas such as the middle temporal area. Such representations often need to be integrated perceptually to solve tasks which depend on multiple features. We tested the hypothesis that the lateral intraparietal area (LIP) integrates disparate task-relevant visual features by recording from LIP neurons in monkeys trained to identify target stimuli composed of conjunctions of color and motion features. We show that LIP neurons exhibit integrative representations of both color and motion features when they are task relevant, and task-dependent shifts of both direction and color tuning. This suggests that LIP plays a role in flexibly integrating task-relevant sensory signals. PMID:25199703

Allosteric Pathways in the PPARγ-RXRα nuclear receptor complex

NASA Astrophysics Data System (ADS)

Ricci, Clarisse G.; Silveira, Rodrigo L.; Rivalta, Ivan; Batista, Victor S.; Skaf, Munir S.

2016-01-01

Understanding the nature of allostery in DNA-nuclear receptor (NR) complexes is of fundamental importance for drug development since NRs regulate the transcription of a myriad of genes in humans and other metazoans. Here, we investigate allostery in the peroxisome proliferator-activated/retinoid X receptor heterodimer. This important NR complex is a target for antidiabetic drugs since it binds to DNA and functions as a transcription factor essential for insulin sensitization and lipid metabolism. We find evidence of interdependent motions of Ω-loops and PPARγ-DNA binding domain with contacts susceptible to conformational changes and mutations, critical for regulating transcriptional functions in response to sequence-dependent DNA dynamics. Statistical network analysis of the correlated motions, observed in molecular dynamics simulations, shows preferential allosteric pathways with convergence centers comprised of polar amino acid residues. These findings are particularly relevant for the design of allosteric modulators of ligand-dependent transcription factors.

Origin of chemoselectivity in N-heterocyclic carbene catalyzed cross-benzoin reactions: DFT and experimental insights.

PubMed

Langdon, Steven M; Legault, Claude Y; Gravel, Michel

2015-04-03

An exploration into the origin of chemoselectivity in the NHC-catalyzed cross-benzoin reaction reveals several key factors governing the preferred pathway. In the first computational study to explore the cross-benzoin reaction, a piperidinone-derived triazolium catalyst produces kinetically controlled chemoselectivity. This is supported by (1)H NMR studies as well as a series of crossover experiments. Major contributors include the rapid and preferential formation of an NHC adduct with alkyl aldehydes, a rate-limiting carbon-carbon bond formation step benefiting from a stabilizing π-stacking/π-cation interaction, and steric penalties paid by competing pathways. The energy profile for the analogous pyrrolidinone-derived catalyst was found to be remarkably similar, despite experimental data showing that it is less chemoselective. The chemoselectivity could not be improved through kinetic control; however, equilibrating conditions show substantial preference for the same cross-benzoin product kinetically favored by the piperidinone-derived catalyst.

Inactivation of the Parietal Reach Region Causes Optic Ataxia, Impairing Reaches but Not Saccades

PubMed Central

Hwang, Eun Jung; Hauschild, Markus; Wilke, Melanie; Andersen, Richard A.

2013-01-01

SUMMARY Lesions in human posterior parietal cortex can cause optic ataxia (OA), in which reaches but not saccades to visual objects are impaired, suggesting separate visuomotor pathways for the two effectors. In monkeys, one potentially crucial area for reach control is the parietal reach region (PRR), in which neurons respond preferentially during reach planning as compared to saccade planning. However, direct causal evidence linking the monkey PRR to the deficits observed in OA is missing. We thus inactivated part of the macaque PRR, in the medial wall of the intraparietal sulcus, and produced the hallmarks of OA, misreaching for peripheral targets but unimpaired saccades. Furthermore, reach errors were larger for the targets preferred by the neural population local to the injection site. These results demonstrate that PRR is causally involved in reach-specific visuomotor pathways, and reach goal disruption in PRR can be a neural basis of OA. PMID:23217749

Tracking the Growth Transitions of A Solvent-Charged Model Globular Protein

NASA Astrophysics Data System (ADS)

Babcock, Jeremiah; Friday, Jacob; Brancaleon, Lorenzo

2011-03-01

Biophysical studies have shown that solutes like proteins undergo aggregation through specific pathways that often lead to long polymeric structures called fibrils. The knowledge of the size of early-stage protein aggregates (oligomers) has an important bearing on the elucidation of the dynamics of the process of protein unit combinations. In this study, bovine serum albumin, a well-characterized model protein known to polymerize in alkaline and acidic conditions in the normal (N) to basic (B) or (N) to (E) transition, was incubated at pH 9.0 and pH 3.1 for longer than eight days. Particle growth in solution was monitored by absorption, fluorescence and circular dichroism spectroscopy and concurrently measured by atomic force microscopy (AFM) methods to yield BSA oligomer size distributions. Results show that the BSA aggregation pathway is concentration-dependent and rapidly forms spherical aggregates, which preferentially come together to form flexible polymers.

Ab initio genotype–phenotype association reveals intrinsic modularity in genetic networks

PubMed Central

Slonim, Noam; Elemento, Olivier; Tavazoie, Saeed

2006-01-01

Microbial species express an astonishing diversity of phenotypic traits, behaviors, and metabolic capacities. However, our molecular understanding of these phenotypes is based almost entirely on studies in a handful of model organisms that together represent only a small fraction of this phenotypic diversity. Furthermore, many microbial species are not amenable to traditional laboratory analysis because of their exotic lifestyles and/or lack of suitable molecular genetic techniques. As an adjunct to experimental analysis, we have developed a computational information-theoretic framework that produces high-confidence gene–phenotype predictions using cross-species distributions of genes and phenotypes across 202 fully sequenced archaea and eubacteria. In addition to identifying the genetic basis of complex traits, our approach reveals the organization of these genes into generic preferentially co-inherited modules, many of which correspond directly to known enzymatic pathways, molecular complexes, signaling pathways, and molecular machines. PMID:16732191

Taste cell-expressed α-glucosidase enzymes contribute to gustatory responses to disaccharides

PubMed Central

Sukumaran, Sunil K.; Yee, Karen K.; Iwata, Shusuke; Kotha, Ramana; Quezada-Calvillo, Roberto; Nichols, Buford L.; Mohan, Sankar; Pinto, B. Mario; Shigemura, Noriatsu; Ninomiya, Yuzo; Margolskee, Robert F.

2016-01-01

The primary sweet sensor in mammalian taste cells for sugars and noncaloric sweeteners is the heteromeric combination of type 1 taste receptors 2 and 3 (T1R2+T1R3, encoded by Tas1r2 and Tas1r3 genes). However, in the absence of T1R2+T1R3 (e.g., in Tas1r3 KO mice), animals still respond to sugars, arguing for the presence of T1R-independent detection mechanism(s). Our previous findings that several glucose transporters (GLUTs), sodium glucose cotransporter 1 (SGLT1), and the ATP-gated K+ (KATP) metabolic sensor are preferentially expressed in the same taste cells with T1R3 provides a potential explanation for the T1R-independent detection of sugars: sweet-responsive taste cells that respond to sugars and sweeteners may contain a T1R-dependent (T1R2+T1R3) sweet-sensing pathway for detecting sugars and noncaloric sweeteners, as well as a T1R-independent (GLUTs, SGLT1, KATP) pathway for detecting monosaccharides. However, the T1R-independent pathway would not explain responses to disaccharide and oligomeric sugars, such as sucrose, maltose, and maltotriose, which are not substrates for GLUTs or SGLT1. Using RT-PCR, quantitative PCR, in situ hybridization, and immunohistochemistry, we found that taste cells express multiple α-glycosidases (e.g., amylase and neutral α glucosidase C) and so-called intestinal “brush border” disaccharide-hydrolyzing enzymes (e.g., maltase-glucoamylase and sucrase-isomaltase). Treating the tongue with inhibitors of disaccharidases specifically decreased gustatory nerve responses to disaccharides, but not to monosaccharides or noncaloric sweeteners, indicating that lingual disaccharidases are functional. These taste cell-expressed enzymes may locally break down dietary disaccharides and starch hydrolysis products into monosaccharides that could serve as substrates for the T1R-independent sugar sensing pathways. PMID:27162343

The ever-evolving role of mTOR in translation.

PubMed

Fonseca, Bruno D; Smith, Ewan M; Yelle, Nicolas; Alain, Tommy; Bushell, Martin; Pause, Arnim

2014-12-01

Control of translation allows for the production of stoichiometric levels of each protein in the cell. Attaining such a level of fine-tuned regulation of protein production requires the coordinated temporal and spatial control of numerous cellular signalling cascades impinging on the various components of the translational machinery. Foremost among these is the mTOR signalling pathway. The mTOR pathway regulates both the initiation and elongation steps of protein synthesis through the phosphorylation of numerous translation factors, while simultaneously ensuring adequate folding of nascent polypeptides through co-translational degradation of misfolded proteins. Perhaps most remarkably, mTOR is also a key regulator of the synthesis of ribosomal proteins and translation factors themselves. Two seminal studies have recently shown in translatome analysis that the mTOR pathway preferentially regulates the translation of mRNAs encoding ribosomal proteins and translation factors. Therefore, the role of the mTOR pathway in the control of protein synthesis extends far beyond immediate translational control. By controlling ribosome production (and ultimately ribosome availability), mTOR is a master long-term controller of protein synthesis. Herein, we review the literature spanning the early discoveries of mTOR on translation to the latest advances in our understanding of how the mTOR pathway controls the synthesis of ribosomal proteins. Crown Copyright © 2014. Published by Elsevier Ltd. All rights reserved.

MiR529a modulates panicle architecture through regulating SQUAMOSA PROMOTER BINDING-LIKE genes in rice (Oryza sativa).

PubMed

Yue, Erkui; Li, Chao; Li, Yu; Liu, Zhen; Xu, Jian-Hong

2017-07-01

MiR529a affects rice panicle architecture by targeting OsSPL2,OsSPL14 and OsSPL17 genes that could regulate their downstream panicle related genes. The panicle architecture determines the grain yield and quality of rice, which could be regulated by many transcriptional factors. The SQUAMOSA PROMOTER BINDING-LIKE (SPL) transcription factors are involved in the regulation of panicle development, which are targeted by miR156 and miR529. The expression profile demonstrated that miR529a is preferentially expressed in the early panicle of rice and it might regulate panicle development in rice. However, the regulation mechanism of miR529-SPL is still not clear. In this study, we predicted five miR529a putative target genes, OsSPL2, OsSPL14, OsSPL16, OsSPL17 and OsSPL18, while only the expression of OsSPL2, OsSPL14, and OsSPL17 was regulated by miR529a in the rice panicle. Overexpression of miR529a dramatically affected panicle architecture, which was regulated by OsSPL2, OsSPL14, and OsSPL17. Furthermore, the 117, 35, and 25 pathway genes associated with OsSPL2, OsSPL14 and OsSPL17, respectively, were predicted, and they shared 20 putative pathway genes. Our results revealed that miR529a could play a vital role in the regulation of panicle architecture through regulating OsSPL2, OsSPL14, OsSPL17 and the complex networks formed by their pathway and downstream genes. These findings will provide new genetic resources for reshaping ideal plant architecture and breeding high yield rice varieties.

Identification of the Dimer Exchange Interface of the Bacterial DNA Damage Response Protein UmuD.

PubMed

Murison, David A; Timson, Rebecca C; Koleva, Bilyana N; Ordazzo, Michael; Beuning, Penny J

2017-09-12

The Escherichia coli SOS response, an induced DNA damage response pathway, confers survival on bacterial cells by providing accurate repair mechanisms as well as the potentially mutagenic pathway translesion synthesis (TLS). The umuD gene products are upregulated after DNA damage and play roles in both nonmutagenic and mutagenic aspects of the SOS response. Full-length UmuD is expressed as a homodimer of 139-amino-acid subunits, which eventually cleaves its N-terminal 24 amino acids to form UmuD'. The cleavage product UmuD' and UmuC form the Y-family polymerase DNA Pol V (UmuD' 2 C) capable of performing TLS. UmuD and UmuD' exist as homodimers, but their subunits can readily exchange to form UmuDD' heterodimers preferentially. Heterodimer formation is an essential step in the degradation pathway of UmuD'. The recognition sequence for ClpXP protease is located within the first 24 amino acids of full-length UmuD, and the partner of full-length UmuD, whether UmuD or UmuD', is degraded by ClpXP. To better understand the mechanism by which UmuD subunits exchange, we measured the kinetics of exchange of a number of fluorescently labeled single-cysteine UmuD variants as detected by Förster resonance energy transfer. Labeling sites near the dimer interface correlate with increased rates of exchange, indicating that weakening the dimer interface facilitates exchange, whereas labeling sites on the exterior decrease the rate of exchange. In most but not all cases, homodimer and heterodimer exchange exhibit similar rates, indicating that somewhat different molecular surfaces mediate homodimer exchange and heterodimer formation.

Involvement of an ent-copalyl diphosphate synthase in tissue-specific accumulation of specialized diterpenes in Andrographis paniculata.

PubMed

Misra, Rajesh Chandra; Garg, Anchal; Roy, Sudeep; Chanotiya, Chandan Singh; Vasudev, Prema G; Ghosh, Sumit

2015-11-01

Ent-labdane-related diterpene (ent-LRD) specialized (i.e. secondary) metabolites of the medicinal plant kalmegh (Andrographis paniculata) have long been known for several pharmacological activities. However, our understanding of the ent-LRD biosynthetic pathway has remained largely incomplete. Since ent-LRDs accumulate in leaves, we carried out a comparative transcriptional analysis using leaf and root tissues, and identified 389 differentially expressed transcripts, including 223 transcripts that were preferentially expressed in leaf tissue. Analysis of the transcripts revealed various specialized metabolic pathways, including transcripts of the ent-LRD biosynthetic pathway. Two class II diterpene synthases (ApCPS1 and ApCPS2) along with one (ApCPS1') and two (ApCPS2' and ApCPS2″) transcriptional variants that were the outcomes of alternative splicing of the precursor mRNA and alternative transcriptional termination, respectively, were identified. ApCPS1 and ApCPS2 encode for 832- and 817-amino acids proteins, respectively, and are phylogenetically related to the dicotyledons ent-copalyl diphosphate synthases (ent-CPSs). The spatio-temporal patterns of ent-LRD metabolites accumulation and gene expression suggested a likely role for ApCPS1 in general (i.e. primary) metabolism, perhaps by providing precursor for the biosynthesis of phytohormone gibberellin (GA). However, ApCPS2 is potentially involved in tissue-specific accumulation of ent-LRD specialized metabolites. Bacterially expressed recombinant ApCPS2 catalyzed the conversion of (E,E,E)-geranylgeranyl diphosphate (GGPP), the general precursor of diterpenes to ent-copalyl diphosphate (ent-CPP), the precursor of ent-LRDs. Taken together, these results advance our understanding of the tissue-specific accumulation of specialized ent-LRDs of medicinal importance. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Assessing the Ability of Vegetation Indices to Identify Shallow Subsurface Water Flow Pathways from Hyperspectral Imagery Using Machine Learning: Application

NASA Astrophysics Data System (ADS)

Doctor, K.; Byers, J. M.

2017-12-01

Shallow underground water flow pathways expressed as slight depressions are common in the land surface. Under conditions of saturated overland flow, such as during heavy rain or snow melt, these areas of preferential flow might appear on the surface as very shallow flowing streams. When there is no water flowing in these ephemeral channels it can be difficult to identify them. It is especially difficult to discern the slight depressions above the subsurface water flow pathways (SWFP) when the area is covered by vegetation. Since the soil moisture content in these SWFP is often greater than the surrounding area, the vegetation growing on top of these channels shows different vigor and moisture content than the vegetation growing above the non-SWFP area. Vegetation indices (VI) are used in visible and near infrared (VNIR) hyperspectral imagery to enhance biophysical properties of vegetation, and so the brightness values between vegetation atop SWFP and the surrounding vegetation were highlighted. We performed supervised machine learning using ground-truth class labels to determine the conditional probability of a SWFP at a given pixel given either the spectral distribution or VI at that pixel. The training data estimates the probability distributions to a determined finite sampling accuracy for a binary Naïve Bayes classifier between SWFP and non-SWFP. The ground-truth data provides a test bed for understanding the ability to build SWFP classifiers using hyperspectral imagery. SWFP were distinguishable in the imagery within corn and grass fields and in areas with low-lying vegetation. However, the training data is limited to particular types of terrain and vegetation cover in the Shenandoah Valley, Virginia and this would limit the resulting classifier. Further training data could extend its use to other environments.

Visual Input to the Drosophila Central Complex by Developmentally and Functionally Distinct Neuronal Populations.

PubMed

Omoto, Jaison Jiro; Keleş, Mehmet Fatih; Nguyen, Bao-Chau Minh; Bolanos, Cheyenne; Lovick, Jennifer Kelly; Frye, Mark Arthur; Hartenstein, Volker

2017-04-24

The Drosophila central brain consists of stereotyped neural lineages, developmental-structural units of macrocircuitry formed by the sibling neurons of single progenitors called neuroblasts. We demonstrate that the lineage principle guides the connectivity and function of neurons, providing input to the central complex, a collection of neuropil compartments important for visually guided behaviors. One of these compartments is the ellipsoid body (EB), a structure formed largely by the axons of ring (R) neurons, all of which are generated by a single lineage, DALv2. Two further lineages, DALcl1 and DALcl2, produce neurons that connect the anterior optic tubercle, a central brain visual center, with R neurons. Finally, DALcl1/2 receive input from visual projection neurons of the optic lobe medulla, completing a three-legged circuit that we call the anterior visual pathway (AVP). The AVP bears a fundamental resemblance to the sky-compass pathway, a visual navigation circuit described in other insects. Neuroanatomical analysis and two-photon calcium imaging demonstrate that DALcl1 and DALcl2 form two parallel channels, establishing connections with R neurons located in the peripheral and central domains of the EB, respectively. Although neurons of both lineages preferentially respond to bright objects, DALcl1 neurons have small ipsilateral, retinotopically ordered receptive fields, whereas DALcl2 neurons share a large excitatory receptive field in the contralateral hemifield. DALcl2 neurons become inhibited when the object enters the ipsilateral hemifield and display an additional excitation after the object leaves the field of view. Thus, the spatial position of a bright feature, such as a celestial body, may be encoded within this pathway. Copyright © 2017 Elsevier Ltd. All rights reserved.

Atxn2 Knockout and CAG42-Knock-in Cerebellum Shows Similarly Dysregulated Expression in Calcium Homeostasis Pathway.

PubMed

Halbach, Melanie Vanessa; Gispert, Suzana; Stehning, Tanja; Damrath, Ewa; Walter, Michael; Auburger, Georg

2017-02-01

Spinocerebellar ataxia type 2 (SCA2) is an autosomal dominantly inherited neurodegenerative disorder with preferential affection of Purkinje neurons, which are known as integrators of calcium currents. The expansion of a polyglutamine (polyQ) domain in the RNA-binding protein ataxin-2 (ATXN2) is responsible for this disease, but the causal roles of deficient ATXN2 functions versus aggregation toxicity are still under debate. Here, we studied mouse mutants with Atxn2 knockout (KO) regarding their cerebellar global transcriptome by microarray and RT-qPCR, in comparison with data from Atxn2-CAG42-knock-in (KIN) mouse cerebellum. Global expression downregulations involved lipid and growth signaling pathways in good agreement with previous data. As a novel effect, downregulations of key factors in calcium homeostasis pathways (the transcription factor Rora, transporters Itpr1 and Atp2a2, as well as regulator Inpp5a) were observed in the KO cerebellum, and some of them also occurred subtly early in KIN cerebellum. The ITPR1 protein levels were depleted from soluble fractions of cerebellum in both mutants, but accumulated in its membrane-associated form only in the SCA2 model. Coimmunoprecipitation demonstrated no association of ITPR1 with Q42-expanded or with wild-type ATXN2. These findings provide evidence that the physiological functions and protein interactions of ATXN2 are relevant for calcium-mediated excitation of Purkinje cells as well as for ATXN2-triggered neurotoxicity. These insights may help to understand pathogenesis and tissue specificity in SCA2 and other polyQ ataxias like SCA1, where inositol regulation of calcium flux and RORalpha play a role.

Monitoring flux through the oxidative pentose phosphate pathway using [1-14C]gluconate.

PubMed

Garlick, Andrew P; Moore, Catherine; Kruger, Nicholas J

2002-12-01

The aim of this work was to examine the metabolism of exogenous gluconate by a 4-day-old cell suspension culture of Arabidopsis thaliana (L.) Heynh. Release of (14)CO(2) from [1-(14)C]gluconate was dependent on the concentration in the medium and could be resolved into a substrate-saturable component (apparent K(m) of approximately 0.4 mM) and an unsaturable component. At an external concentration of 0.3 mM, the rate of decarboxylation of applied gluconate was 0.2% of the rate of oxygen consumption by the cells. There was no effect of 0.3 mM gluconate on the rate of oxygen consumption, or on the rate of (14)CO(2) release from either [1-(14)C]glucose or [6-(14)C]glucose by the culture. The following observations argue that gluconate taken up by the cells is metabolised by direct phosphorylation to 6-phosphogluconate and subsequent decarboxylation through 6-phosphogluconate dehydrogenase. First, more than 95% of the label released from [1-(14)C]gluconate during metabolism by the cell culture was recovered as (14)CO(2). Secondly, inhibition of the oxidative pentose phosphate pathway (OPPP) by treatment with 6-aminonicotinamide preferentially inhibited release of (14)CO(2) from [1-(14)C]gluconate relative to that from [1-(14)C]glucose. Thirdly, perturbation of glucose metabolism by glucosamine did not affect (14)CO(2) from [1-(14)C]gluconate. Fourth, stimulation of the OPPP by phenazine methosulphate stimulated release of (14)CO(2) from [1-(14)C]gluconate to a far greater extent than that from [1-(14)C]glucose. It is proposed that measurement of (14)CO(2) from [1-(14)C]gluconate provides a simple and sensitive technique for monitoring flux through the OPPP pathway in plants.

Pinpointing retrovirus entry sites in cells expressing alternatively spliced receptor isoforms by single virus imaging.

PubMed

Padilla-Parra, Sergi; Marin, Mariana; Kondo, Naoyuki; Melikyan, Gregory B

2014-06-16

The majority of viruses enter host cells via endocytosis. Current knowledge of viral entry pathways is largely based upon infectivity measurements following genetic and/or pharmacological interventions that disrupt vesicular trafficking and maturation. Imaging of single virus entry in living cells provides a powerful means to delineate viral trafficking pathways and entry sites under physiological conditions. Here, we visualized single avian retrovirus co-trafficking with markers for early (Rab5) and late (Rab7) endosomes, acidification of endosomal lumen and the resulting viral fusion measured by the viral content release into the cytoplasm. Virus-carrying vesicles either merged with the existing Rab5-positive early endosomes or slowly accumulated Rab5. The Rab5 recruitment to virus-carrying endosomes correlated with acidification of their lumen. Viral fusion occurred either in early (Rab5-positive) or intermediate (Rab5- and Rab7-positive) compartments. Interestingly, different isoforms of the cognate receptor directed virus entry from distinct endosomes. In cells expressing the transmembrane receptor, viruses preferentially entered and fused with slowly maturing early endosomes prior to accumulation of Rab7. By comparison, in cells expressing the GPI-anchored receptor, viruses entered both slowly and quickly maturing endosomes and fused with early (Rab5-positive) and intermediate (Rab5- and Rab7-positive) compartments. Since the rate of low pH-triggered fusion was independent of the receptor isoform, we concluded that the sites of virus entry are determined by the kinetic competition between endosome maturation and viral fusion. Our findings demonstrate the ability of this retrovirus to enter cells via alternative endocytic pathways and establish infection by releasing its content from distinct endosomal compartments.

RNA-Sequencing Reveals Unique Transcriptional Signatures of Running and Running-Independent Environmental Enrichment in the Adult Mouse Dentate Gyrus.

PubMed

Grégoire, Catherine-Alexandra; Tobin, Stephanie; Goldenstein, Brianna L; Samarut, Éric; Leclerc, Andréanne; Aumont, Anne; Drapeau, Pierre; Fulton, Stephanie; Fernandes, Karl J L

2018-01-01

Environmental enrichment (EE) is a powerful stimulus of brain plasticity and is among the most accessible treatment options for brain disease. In rodents, EE is modeled using multi-factorial environments that include running, social interactions, and/or complex surroundings. Here, we show that running and running-independent EE differentially affect the hippocampal dentate gyrus (DG), a brain region critical for learning and memory. Outbred male CD1 mice housed individually with a voluntary running disk showed improved spatial memory in the radial arm maze compared to individually- or socially-housed mice with a locked disk. We therefore used RNA sequencing to perform an unbiased interrogation of DG gene expression in mice exposed to either a voluntary running disk (RUN), a locked disk (LD), or a locked disk plus social enrichment and tunnels [i.e., a running-independent complex environment (CE)]. RNA sequencing revealed that RUN and CE mice showed distinct, non-overlapping patterns of transcriptomic changes versus the LD control. Bio-informatics uncovered that the RUN and CE environments modulate separate transcriptional networks, biological processes, cellular compartments and molecular pathways, with RUN preferentially regulating synaptic and growth-related pathways and CE altering extracellular matrix-related functions. Within the RUN group, high-distance runners also showed selective stress pathway alterations that correlated with a drastic decline in overall transcriptional changes, suggesting that excess running causes a stress-induced suppression of running's genetic effects. Our findings reveal stimulus-dependent transcriptional signatures of EE on the DG, and provide a resource for generating unbiased, data-driven hypotheses for novel mediators of EE-induced cognitive changes.

Optimum bus headway for preemption : a simulation approach

DOT National Transportation Integrated Search

1997-01-01

Preemption techniques are designed to provide preferential treatment for buses at signalized intersections. A preemption strategy, if properly designed, can provide continuous green phases for buses at successive intersections, thereby reducing trave...

Physical-Chemical Properties of the Chiral Fungicide Fenamidone and Strategies for Enantioselective Crystallization.

PubMed

Kort, Anne-Kathleen; Lorenz, Heike; Seidel-Morgenstern, Andreas

2016-06-01

Thermodynamic and kinetic parameters are of prime importance for designing crystallization processes. In this article, Preferential Crystallization, as a special approach to carry out enantioselective crystallization, is described to resolve the enantiomers of the chiral fungicide fenamidone. In preliminary investigations the melting behavior and solid-liquid equilibria in the presence of solvents were quantified. The analyses revealed a stable solid phase behavior of fenamidone in the applied solvents. Based on the results obtained, a two-step crystallization route was designed and realized capable of providing highly pure enantiomers. An initial Preferential Crystallization of the racemate was performed prior to crystallizing the target enantiomer preferentially out of the enriched mother liquor. Chirality 28:514-520, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Infants use compression information to infer objects’ weights: Examining cognition, exploration, and prospective action in a preferential-reaching task

PubMed Central

Hauf, Petra; Paulus, Markus; Baillargeon, Renée

2012-01-01

The present research used a preferential-reaching task to examine whether 9- and 11-month-olds (n = 144) could infer the relative weights of two objects resting on a soft, compressible platform. Experiment 1 established that infants reached preferentially for the lighter of two boxes. In Experiments 2 to 4, infants saw two boxes identical except in weight resting on a cotton wool platform. Infants reached prospectively for the lighter box, but only when their initial exploratory activities provided critical information. At 11 months, infants succeeded as long as they first determined that the platform was compressible; at 9 months, infants succeeded only if they also explored the boxes and thus had advance knowledge that they differed in weight. PMID:22861050

Characterization of rapid intervascular transport of cadmium in rice stem by radioisotope imaging

PubMed Central

Tanoi, Keitaro

2013-01-01

Participation of the intervascular transport system within the rice stem during cadmium (Cd) partitioning was investigated by characterizing 109Cd behaviour in the shoot. In addition, 45Ca, 32P, and 35S partitioning patterns were analysed for comparison with that of 109Cd. Each tracer was applied to the seedling roots for 15min, and the shoots were harvested either at 15min (i.e. immediately after tracer application) or at 48h. Distribution patterns of each element at 15min were studied to identify the primary transport pathway before remobilization was initiated. 32P was preferentially transported to completely expanded leaf blades having the highest transpiration rate. The newest leaf received minimal amounts of 32P. In contrast, the amount of 35S transported to the newest leaf was similar to that transported to the other mature leaf blades. Preferential movement towards the newest leaf was evident for 109Cd and 45Ca. These results directly indicate that elemental transport is differentially regulated in the vegetative stem as early as 15min before the elements are transported to leaves. Cd behaviour in the stem was investigated in detail by obtaining serial section images from the bottom part of shoots after 109Cd was applied to a single crown root. At 30min, the maximum amount of 109Cd was distributed in the peripheral cylinder of the longitudinal vascular bundles (PV) and, interestingly, some amount of 109Cd was transported downwards along the PV. This transport manner of 109Cd provides evidence that Cd can be loaded on the phloem at the stem immediately after Cd is transported from the root. PMID:23202130

Cell Science and Cell Biology Research at MSFC: Summary

NASA Technical Reports Server (NTRS)

2003-01-01

The common theme of these research programs is that they investigate regulation of gene expression in cells, and ultimately gene expression is controlled by the macromolecular interactions between regulatory proteins and DNA. The NASA Critical Path Roadmap identifies Muscle Alterations and Atrophy and Radiation Effects as Very Serious Risks and Severe Risks, respectively, in long term space flights. The specific problem addressed by Dr. Young's research ("Skeletal Muscle Atrophy and Muscle Cell Signaling") is that skeletal muscle loss in space cannot be prevented by vigorous exercise. Aerobic skeletal muscles (i.e., red muscles) undergo the most extensive atrophy during long-term space flight. Of the many different potential avenues for preventing muscle atrophy, Dr. Young has chosen to study the beta-adrenergic receptor (betaAR) pathway. The reason for this choice is that a family of compounds called betaAR agonists will preferentially cause an increase in muscle mass of aerobic muscles (i.e., red muscle) in animals, potentially providing a specific pharmacological solution to muscle loss in microgravity. In addition, muscle atrophy is a widespread medical problem in neuromuscular diseases, spinal cord injury, lack of exercise, aging, and any disease requiring prolonged bedridden status. Skeletal muscle cells in cell culture are utilized as a model system to study this problem. Dr. Richmond's research ("Radiation & Cancer Biology of Mammary Cells in Culture") is directed toward developing a laboratory model for use in risk assessment of cancer caused by space radiation. This research is unique because a human model will be developed utilizing human mammary cells that are highly susceptible to tumor development. This approach is preferential over using animal cells because of problems in comparing radiation-induced cancers between humans and animals.

Urban nuisance flooding and topographic wetness index: does excess runoff collect where we think it should in urban landscapes?

NASA Astrophysics Data System (ADS)

Kelleher, C.; McPhillips, L. E.

2017-12-01

Urban landscapes translate water in a variety of ways that diverge from more natural systems. In particular, due to the presence of impervious surfaces and alteration of topography, they are prone to nuisance flooding when it rains. To track the locations of areas of minor flooding and other complaints, many cities are now facilitating nuisance reports from residents via information technology services like 311. These reports provide useful information for tracking where in the landscape water may collect during rain events; we sought to use this information to test potential geospatial indices for predictively identifying locations prone to nuisance flooding in urban areas. In this study, we utilized a tool commonly applied in natural systems, topographic indices, to create spatially contiguous estimates of topographic wetness index (TWI), a value that can be used to identify areas within a watershed expected to be preferentially wetter or drier based on topographic slope and surface flow pathways. For several watersheds across Baltimore and New York City (USA), we tested three different resolutions of LiDAR-derived topography and two different methods of flow routing to calculate continuous distributions of TWI. When comparing these values to nuisance flooding locations, we found that distributions of TWI values within a radius of reported nuisance floods were higher, on average, than the distribution of TWI values across each watershed. We also employed a spatial Monte Carlo sampling strategy, randomly selecting grid cells within each watershed to determine if these randomly selected grid cells have preferentially lower TWI values than those near nuisance flooding locations. Overall, we demonstrate that topographic indices may be useful predictors of localized flooding within urban environments.

Biogas upgrading by chemical absorption using ammonia rich absorbents derived from wastewater.

PubMed

McLeod, Andrew; Jefferson, Bruce; McAdam, Ewan J

2014-12-15

The use of ammonia (NH3) rich wastewaters as an ecological chemical absorption solvent for the selective extraction of carbon dioxide (CO2) during biogas upgrading to 'biomethane' has been studied. Aqueous ammonia absorbents of up to 10,000 gNH3 m(-3) demonstrated CO2 absorption rates higher than recorded in the literature for packed columns using 20,000-80,000 g NH3 m(-3) which can be ascribed to the process intensification provided by the hollow fibre membrane contactor used in this study to support absorption. Centrifuge return liquors (2325 g m(-3) ionised ammonium, NH4(+)) and a regenerant (477 gNH4(+) m(-3)) produced from a cationic ion exchanger used to harvest NH4(+) from crude wastewater were also tested. Carbon dioxide fluxes measured for both wastewaters compared reasonably with analogue ammonia absorption solvents of equivalent NH3 concentration. Importantly, this demonstrates that ammonia rich wastewaters can facilitate chemically enhanced CO2 separation which eliminates the need for costly exogenic chemicals or complex chemical handling which are critical barriers to implementation of chemical absorption. When testing NH3 analogues, the potential to recover the reaction product ammonium bicarbonate (NH4HCO3) in crystalline form was also illustrated. This is significant as it suggests a new pathway for ammonia separation which avoids biological nitrification and produces ammonia stabilised into a commercially viable fertiliser (NH4HCO3). However, in real ammonia rich wastewaters, sodium bicarbonate and calcium carbonate were preferentially formed over NH4HCO3 although it is proposed that NH4HCO3 can be preferentially formed by manipulating both ion exchange and absorbent chemistry. Copyright © 2014. Published by Elsevier Ltd.

Cobalt intercalation at the graphene/iridium(111) interface: Influence of rotational domains, wrinkles, and atomic steps

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vlaic, S.; Kimouche, A.; Coraux, J.

Using low-energy electron microscopy, we study Co intercalation under graphene grown on Ir(111). Depending on the rotational domain of graphene on which it is deposited, Co is found intercalated at different locations. While intercalated Co is observed preferentially at the substrate step edges below certain rotational domains, it is mostly found close to wrinkles below other domains. These results indicate that curved regions (near substrate atomic steps and wrinkles) of the graphene sheet facilitate Co intercalation and suggest that the strength of the graphene/Ir interaction determines which pathway is energetically more favorable.

Quantum Dot Distribution in the Olfactory Epithelium After Nasal Delivery

NASA Astrophysics Data System (ADS)

Garzotto, D.; De Marchis, S.

2010-10-01

Nanoparticles are used in a wide range of human applications from industrial to bio-medical fields. However, the unique characteristics of nanoparticles, such as the small size, large surface area per mass and high reactivity raises great concern on the adverse effects of these particles on ecological systems and human health. There are several pioneer studies reporting translocation of inhaled particulates to the brain through a potential neuronal uptake mediated by the olfactory nerve (1, 2, 3). However, no direct evidences have been presented up to now on the pathway followed by the nanoparticles from the nose to the brain. In addition to a neuronal pathway, nanoparticles could gain access to the central nervous system through extracellular pathways (perineuronal, perivascular and cerebrospinal fluid paths). In the present study we investigate the localization of intranasally delivered fluorescent nanoparticles in the olfactory epithelium. To this purpose we used quantum dots (QDs), a model of innovative fluorescent semiconductor nanocrystals commonly used in cell and animal biology (4). Intranasal treatments with QDs were performed acutely on adult CD1 mice. The olfactory epithelium was collected and analysed by confocal microscopy at different survival time after treatment. Data obtained indicate that the neuronal components of the olfactory epithelium are not preferentially involved in QDs uptake, thus suggesting nanoparticles can cross the olfactory epithelium through extracellular pathways.

Chromosome specific repetitive DNA sequences

DOEpatents

Moyzis, Robert K.; Meyne, Julianne

1991-01-01

A method is provided for determining specific nucleotide sequences useful in forming a probe which can identify specific chromosomes, preferably through in situ hybridization within the cell itself. In one embodiment, chromosome preferential nucleotide sequences are first determined from a library of recombinant DNA clones having families of repetitive sequences. Library clones are identified with a low homology with a sequence of repetitive DNA families to which the first clones respectively belong and variant sequences are then identified by selecting clones having a pattern of hybridization with genomic DNA dissimilar to the hybridization pattern shown by the respective families. In another embodiment, variant sequences are selected from a sequence of a known repetitive DNA family. The selected variant sequence is classified as chromosome specific, chromosome preferential, or chromosome nonspecific. Sequences which are classified as chromosome preferential are further sequenced and regions are identified having a low homology with other regions of the chromosome preferential sequence or with known sequences of other family me This invention is the result of a contract with the Department of Energy (Contract No. W-7405-ENG-36).

Post-learning hippocampal dynamics promote preferential retention of rewarding events

PubMed Central

Gruber, Matthias J.; Ritchey, Maureen; Wang, Shao-Fang; Doss, Manoj K.; Ranganath, Charan

2016-01-01

Reward motivation is known to modulate memory encoding, and this effect depends on interactions between the substantia nigra/ ventral tegmental area complex (SN/VTA) and the hippocampus. It is unknown, however, whether these interactions influence offline neural activity in the human brain that is thought to promote memory consolidation. Here, we used functional magnetic resonance imaging (fMRI) to test the effect of reward motivation on post-learning neural dynamics and subsequent memory for objects that were learned in high- or low-reward motivation contexts. We found that post-learning increases in resting-state functional connectivity between the SN/VTA and hippocampus predicted preferential retention of objects that were learned in high-reward contexts. In addition, multivariate pattern classification revealed that hippocampal representations of high-reward contexts were preferentially reactivated during post-learning rest, and the number of hippocampal reactivations was predictive of preferential retention of items learned in high-reward contexts. These findings indicate that reward motivation alters offline post-learning dynamics between the SN/VTA and hippocampus, providing novel evidence for a potential mechanism by which reward could influence memory consolidation. PMID:26875624

The effect of using cow genomic information on accuracy and bias of genomic breeding values in a simulated Holstein dairy cattle population.

PubMed

Dehnavi, E; Mahyari, S Ansari; Schenkel, F S; Sargolzaei, M

2018-06-01

Using cow data in the training population is attractive as a way to mitigate bias due to highly selected training bulls and to implement genomic selection for countries with no or limited proven bull data. However, one potential issue with cow data is a bias due to the preferential treatment. The objectives of this study were to (1) investigate the effect of including cow genotype and phenotype data into the training population on accuracy and bias of genomic predictions and (2) assess the effect of preferential treatment for different proportions of elite cows. First, a 4-pathway Holstein dairy cattle population was simulated for 2 traits with low (0.05) and moderate (0.3) heritability. Then different numbers of cows (0, 2,500, 5,000, 10,000, 15,000, or 20,000) were randomly selected and added to the training group composed of different numbers of top bulls (0, 2,500, 5,000, 10,000, or 15,000). Reliability levels of de-regressed estimated breeding values for training cows and bulls were 30 and 75% for traits with low heritability and were 60 and 90% for traits with moderate heritability, respectively. Preferential treatment was simulated by introducing upward bias equal to 35% of phenotypic variance to 5, 10, and 20% of elite bull dams in each scenario. Two different validation data sets were considered: (1) all animals in the last generation of both elite and commercial tiers (n = 42,000) and (2) only animals in the last generation of the elite tier (n = 12,000). Adding cow data into the training population led to an increase in accuracy (r) and decrease in bias of genomic predictions in all considered scenarios without preferential treatment. The gain in r was higher for the low heritable trait (from 0.004 to 0.166 r points) compared with the moderate heritable trait (from 0.004 to 0.116 r points). The gain in accuracy in scenarios with a lower number of training bulls was relatively higher (from 0.093 to 0.166 r points) than with a higher number of training bulls (from 0.004 to 0.09 r points). In this study, as expected, the bull-only reference population resulted in higher accuracy compared with the cow-only reference population of the same size. However, the cow reference population might be an option for countries with a small-scale progeny testing scheme or for minor breeds in large counties, and for traits measured only on a small fraction of the population. The inclusion of preferential treatment to 5 to 20% of the elite cows led to an adverse effect on both accuracy and bias of predictions. When preferential treatment was present, random selection of cows did not reduce the effect of preferential treatment. Copyright © 2018 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Quantitative framework for preferential flow initiation and partitioning

USGS Publications Warehouse

Nimmo, John R.

2016-01-01

A model for preferential flow in macropores is based on the short-range spatial distribution of soil matrix infiltrability. It uses elementary areas at two different scales. One is the traditional representative elementary area (REA), which includes a sufficient heterogeneity to typify larger areas, as for measuring field-scale infiltrability. The other, called an elementary matrix area (EMA), is smaller, but large enough to represent the local infiltrability of soil matrix material, between macropores. When water is applied to the land surface, each EMA absorbs water up to the rate of its matrix infiltrability. Excess water flows into a macropore, becoming preferential flow. The land surface then can be represented by a mesoscale (EMA-scale) distribution of matrix infiltrabilities. Total preferential flow at a given depth is the sum of contributions from all EMAs. Applying the model, one case study with multi-year field measurements of both preferential and diffuse fluxes at a specific depth was used to obtain parameter values by inverse calculation. The results quantify the preferential–diffuse partition of flow from individual storms that differed in rainfall amount, intensity, antecedent soil water, and other factors. Another case study provided measured values of matrix infiltrability to estimate parameter values for comparison and illustrative predictions. These examples give a self-consistent picture from the combination of parameter values, directions of sensitivities, and magnitudes of differences caused by different variables. One major practical use of this model is to calculate the dependence of preferential flow on climate-related factors, such as varying soil wetness and rainfall intensity.

Visualization of self-delivering hydrophobically modified siRNA cellular internalization

PubMed Central

Ly, Socheata; Navaroli, Deanna M.; Didiot, Marie-Cécile; Cardia, James; Pandarinathan, Lakshmipathi; Alterman, Julia F.; Fogarty, Kevin; Standley, Clive; Lifshitz, Lawrence M.; Bellve, Karl D.; Prot, Matthieu; Echeverria, Dimas; Corvera, Silvia; Khvorova, Anastasia

2017-01-01

siRNAs are a new class of therapeutic modalities with promising clinical efficacy that requires modification or formulation for delivery to the tissue and cell of interest. Conjugation of siRNAs to lipophilic groups supports efficient cellular uptake by a mechanism that is not well characterized. Here we study the mechanism of internalization of asymmetric, chemically stabilized, cholesterol-modified siRNAs (sd-rxRNAs®) that efficiently enter cells and tissues without the need for formulation. We demonstrate that uptake is rapid with significant membrane association within minutes of exposure followed by the formation of vesicular structures and internalization. Furthermore, sd-rxRNAs are internalized by a specific class of early endosomes and show preferential association with epidermal growth factor (EGF) but not transferrin (Tf) trafficking pathways as shown by live cell TIRF and structured illumination microscopy (SIM). In fixed cells, we observe ∼25% of sd-rxRNA co-localizing with EGF and <5% with Tf, which is indicative of selective endosomal sorting. Likewise, preferential sd-rxRNA co-localization was demonstrated with EEA1 but not RBSN-containing endosomes, consistent with preferential EGF-like trafficking through EEA1-containing endosomes. sd-rxRNA cellular uptake is a two-step process, with rapid membrane association followed by internalization through a selective, saturable subset of the endocytic process. However, the mechanistic role of EEA1 is not yet known. This method of visualization can be used to better understand the kinetics and mechanisms of hydrophobic siRNA cellular uptake and will assist in further optimization of these types of compounds for therapeutic intervention. PMID:27899655

Functional dissociation between PIKfyve-synthesized PtdIns5P and PtdIns(3,5)P2 by means of the PIKfyve inhibitor YM201636

PubMed Central

Sbrissa, Diego; Ikonomov, Ognian C.; Filios, Catherine; Delvecchio, Khortnal

2012-01-01

PIKfyve is an essential mammalian lipid kinase with pleiotropic cellular functions whose genetic knockout in mice leads to preimplantation lethality. Despite several reports for PIKfyve-catalyzed synthesis of phosphatidylinositol 5-phosphate (PtdIns5P) along with phosphatidylinositol-3,5-biphosphate [PtdIns(3,5)P2] in vitro and in vivo, the role of the PIKfyve pathway in intracellular PtdIns5P production remains underappreciated and the function of the PIKfyve-synthesized PtdIns5P pool poorly characterized. Hence, the recently discovered potent PIKfyve-selective inhibitor, the YM201636 compound, has been solely tested for inhibiting PtdIns(3,5)P2 synthesis. Here, we have compared the in vitro and in vivo inhibitory potency of YM201636 toward PtdIns5P and PtdIns(3,5)P2. Unexpectedly, we observed that at low doses (10–25 nM), YM201636 inhibited preferentially PtdIns5P rather than PtdIns(3,5)P2 production in vitro, whereas at higher doses, the two products were similarly inhibited. In cellular contexts, YM201636 at 160 nM inhibited PtdIns5P synthesis twice more effectively compared with PtdIns(3,5)P2 synthesis. In 3T3L1 adipocytes, human embryonic kidney 293 and Chinese hamster ovary (CHO-T) cells, levels of PtdIns5P dropped by 62–71% of the corresponding untreated controls, whereas those of PtdIns(3,5)P2 fell by only 28–46%. The preferential inhibition of PtdIns5P versus PtdIns(3,5)P2 at low doses of YM201636 was explored to probe contributions of the PIKfyve-catalyzed PtdIns5P pool to insulin-induced actin stress fiber disassembly in CHO-T cells, GLUT4 translocation in 3T3L1 adipocytes, and induction of aberrant cellular vacuolation in these or other cell types. The results provide the first experimental evidence that the principal pathway for PtdIns5P intracellular production is through PIKfyve and that insulin effect on actin stress fiber disassembly is mediated entirely by the PIKfyve-produced PtdIns5P pool. PMID:22621786

Dynamic synchronization of ongoing neuronal activity across spinal segments regulates sensory information flow

PubMed Central

Contreras-Hernández, E; Chávez, D; Rudomin, P

2015-01-01

Previous studies on the correlation between spontaneous cord dorsum potentials recorded in the lumbar spinal segments of anaesthetized cats suggested the operation of a population of dorsal horn neurones that modulates, in a differential manner, transmission along pathways mediating Ib non-reciprocal postsynaptic inhibition and pathways mediating primary afferent depolarization and presynaptic inhibition. In order to gain further insight into the possible neuronal mechanisms that underlie this process, we have measured changes in the correlation between the spontaneous activity of individual dorsal horn neurones and the cord dorsum potentials associated with intermittent activation of these inhibitory pathways. We found that high levels of neuronal synchronization within the dorsal horn are associated with states of incremented activity along the pathways mediating presynaptic inhibition relative to pathways mediating Ib postsynaptic inhibition. It is suggested that ongoing changes in the patterns of functional connectivity within a distributed ensemble of dorsal horn neurones play a relevant role in the state-dependent modulation of impulse transmission along inhibitory pathways, among them those involved in the central control of sensory information. This feature would allow the same neuronal network to be involved in different functional tasks. Key points We have examined, in the spinal cord of the anaesthetized cat, the relationship between ongoing correlated fluctuations of dorsal horn neuronal activity and state-dependent activation of inhibitory reflex pathways. We found that high levels of synchronization between the spontaneous activity of dorsal horn neurones occur in association with the preferential activation of spinal pathways leading to primary afferent depolarization and presynaptic inhibition relative to activation of pathways mediating Ib postsynaptic inhibition. It is suggested that changes in synchronization of ongoing activity within a distributed network of dorsal horn neurones play a relevant role in the configuration of structured (non-random) patterns of functional connectivity that shape the interaction of sensory inputs with spinal reflex pathways subserving different functional tasks. PMID:25653206

Centromere strength provides the cell biological basis for meiotic drive and karyotype evolution in mice.

PubMed

Chmátal, Lukáš; Gabriel, Sofia I; Mitsainas, George P; Martínez-Vargas, Jessica; Ventura, Jacint; Searle, Jeremy B; Schultz, Richard M; Lampson, Michael A

2014-10-06

Mammalian karyotypes (number and structure of chromosomes) can vary dramatically over short evolutionary time frames. There are examples of massive karyotype conversion, from mostly telocentric (centromere terminal) to mostly metacentric (centromere internal), in 10(2)-10(5) years. These changes typically reflect rapid fixation of Robertsonian (Rb) fusions, a common chromosomal rearrangement that joins two telocentric chromosomes at their centromeres to create one metacentric. Fixation of Rb fusions can be explained by meiotic drive: biased chromosome segregation during female meiosis in violation of Mendel's first law. However, there is no mechanistic explanation of why fusions would preferentially segregate to the egg in some populations, leading to fixation and karyotype change, while other populations preferentially eliminate the fusions and maintain a telocentric karyotype. Here we show, using both laboratory models and wild mice, that differences in centromere strength predict the direction of drive. Stronger centromeres, manifested by increased kinetochore protein levels and altered interactions with spindle microtubules, are preferentially retained in the egg. We find that fusions preferentially segregate to the polar body in laboratory mouse strains when the fusion centromeres are weaker than those of telocentrics. Conversely, fusion centromeres are stronger relative to telocentrics in natural house mouse populations that have changed karyotype by accumulating metacentric fusions. Our findings suggest that natural variation in centromere strength explains how the direction of drive can switch between populations. They also provide a cell biological basis of centromere drive and karyotype evolution. Copyright © 2014 Elsevier Ltd. All rights reserved.

The Effect of Initial Irrigation Conditions on Heap Leaching Efficiency

NASA Astrophysics Data System (ADS)

Briseño Arellano, A. D.; Milczarek, M.; Yao, M.; Brusseau, M. L. L.

2017-12-01

Heap leaching is an unsaturated flow metal recovery process, in which mined ore is irrigated with a lixiviant to dissolve metal contained in the ore. The metal is then extracted from solution. Large scale operations involve stacking ore to depths of 6 to 18 meters on pads that may be hundreds of hectares in area. Heterogeneities within the stacked ore can lead to uneven wetting and the formation of preferential flow pathways, which reduces solution contact and lowers metal recovery. Furthermore, mineral dissolution can cause alteration of the porous media structure and loss of ore permeability. Many mine operators believe that slow initial irrigation rates help minimize permeability loss and increase metal recovery rates. However, this phenomenon has not been studied in detail. Experiments were conducted to investigate the effect of varying initial irrigation rates on leach ore stability. These were conducted with large columns (1.5 m high, 0.5 m in diameter) packed with crushed ore samples that are known to have permeability constraints. The columns were highly instrumented to assess potential changes in material properties both spatially and temporally. Water content was measured with three different methods: capacitance soil moisture sensors placed at 20-cm intervals; a neutron probe to periodically log every 30 cm from four different directions; and electrical resistivity sensors to create a 2-dimensional tomography profile of water content over time. Tensiometers were paired with the soil moisture sensors to measure matric suction and characterize moisture retention characteristics. A non-reactive tracer was used to characterize advective-dispersive transport under unsaturated conditions. A dye solution was introduced at the end of each experiment to map preferential pathways. Continuous monitoring of settling at the surface assisted in measuring consolidation and loss in permeability.

Direct inhibition of interleukin-2 receptor alpha-mediated signaling pathway induces G1 arrest and apoptosis in human head-and-neck cancer cells.

PubMed

Kuhn, Deborah J; Dou, Q Ping

2005-05-15

Overexpression of the interleukin-2 receptor (IL-2R) alpha chain in tumor cells is associated with tumor progression and a poor patient prognosis. IL-2Ralpha is responsible for the high affinity binding of the receptor to IL-2, leading to activation of several proliferative and anti-apoptotic intracellular signaling pathways. We have previously shown that human squamous cell carcinoma of a head-and-neck line (PCI-13) genetically engineered to overexpress IL-2Ralpha exhibit increased transforming activity, proliferation, and drug resistance, compared to the vector control cells (J Cell Biochem 2003;89:824-836). In this study, we report that IL-2Ralpha(+) cells express high levels of total and phosphorylated Jak3 protein and are more resistant to apoptosis induced by a Jak3 inhibitor than the control LacZ cells. Furthermore, we used daclizumab, a monoclonal antibody specific to IL-2Ralpha, and determined the effects of IL-2Ralpha inhibition on cell cycle and apoptosis as well as the involvement of potential cell cycle and apoptosis regulatory proteins. We found that daclizumab induces G(1) arrest, associated with down-regulation of cyclin A protein, preferentially in IL-2Ralpha(+) cells, but not in LacZ cells. In addition, daclizumab activates apoptotic death program via Bcl-2 down-regulation preferentially in IL-2Ralpha(+) cells. Finally, daclizumab also sensitizes IL-2Ralpha(+) cells to other apoptotic stimuli, although the effect is moderate. These results indicate that daclizumab inhibits the proliferative potential of IL-2Ralpha(+) cells via inhibition of cell cycle progression and induction of apoptosis.

ß3 integrin modulates transforming growth factor beta induced (TGFBI) function and paclitaxel response in ovarian cancer cells.

PubMed

Tumbarello, David A; Temple, Jillian; Brenton, James D

2012-05-28

The extracellular matrix (ECM) has a key role in facilitating the progression of ovarian cancer and we have shown recently that the secreted ECM protein TGFBI modulates the response of ovarian cancer to paclitaxel-induced cell death. We have determined TGFBI signaling from the extracellular environment is preferential for the cell surface αvß3 integrin heterodimer, in contrast to periostin, a TGFBI paralogue, which signals primarily via a ß1 integrin-mediated pathway. We demonstrate that suppression of ß1 integrin expression, in ß3 integrin-expressing ovarian cancer cells, increases adhesion to rTGFBI. In addition, Syndecan-1 and -4 expression is dispensable for adhesion to rTGFBI and loss of Syndecan-1 cooperates with the loss of ß1 integrin to further enhance adhesion to rTGFBI. The RGD motif present in the carboxy-terminus of TGFBI is necessary, but not sufficient, for SKOV3 cell adhesion and is dispensable for adhesion of ovarian cancer cells lacking ß3 integrin expression. In contrast to TGFBI, the carboxy-terminus of periostin, lacking a RGD motif, is unable to support adhesion of ovarian cancer cells. Suppression of ß3 integrin in SKOV3 cells increases resistance to paclitaxel-induced cell death while suppression of ß1 integrin has no effect. Furthermore, suppression of TGFBI expression stimulates a paclitaxel resistant phenotype while suppression of fibronectin expression, which primarily signals through a ß1 integrin-mediated pathway, increases paclitaxel sensitivity. Therefore, different ECM components use distinct signaling mechanisms in ovarian cancer cells and in particular, TGFBI preferentially interacts through a ß3 integrin receptor mediated mechanism to regulate the response of cells to paclitaxel-induced cell death.

Dispersion Analysis Using Particle Tracking Simulations Through Heterogeneity Based on Outcrop Lidar Imagery

NASA Astrophysics Data System (ADS)

Klise, K. A.; Weissmann, G. S.; McKenna, S. A.; Tidwell, V. C.; Frechette, J. D.; Wawrzyniec, T. F.

2007-12-01

Solute plumes are believed to disperse in a non-Fickian manner due to small-scale heterogeneity and variable velocities that create preferential pathways. In order to accurately predict dispersion in naturally complex geologic media, the connection between heterogeneity and dispersion must be better understood. Since aquifer properties can not be measured at every location, it is common to simulate small-scale heterogeneity with random field generators based on a two-point covariance (e.g., through use of sequential simulation algorithms). While these random fields can produce preferential flow pathways, it is unknown how well the results simulate solute dispersion through natural heterogeneous media. To evaluate the influence that complex heterogeneity has on dispersion, we utilize high-resolution terrestrial lidar to identify and model lithofacies from outcrop for application in particle tracking solute transport simulations using RWHet. The lidar scan data are used to produce a lab (meter) scale two-dimensional model that captures 2-8 mm scale natural heterogeneity. Numerical simulations utilize various methods to populate the outcrop structure captured by the lidar-based image with reasonable hydraulic conductivity values. The particle tracking simulations result in residence time distributions used to evaluate the nature of dispersion through complex media. Particle tracking simulations through conductivity fields produced from the lidar images are then compared to particle tracking simulations through hydraulic conductivity fields produced from sequential simulation algorithms. Based on this comparison, the study aims to quantify the difference in dispersion when using realistic and simplified representations of aquifer heterogeneity. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Diagenetic susceptibility of carbonate archives - an experimental approach

NASA Astrophysics Data System (ADS)

Pederson, C.; Purgstaller, B.; Mavromatis, V.; Dietzel, M.; Jöns, N.; Buhl, D.; Neuser, R. D.; Breitenbach, S. F. M.; Hoffmann, R.; Kwiecien, O.; Riechelmann, S.; Immenhauser, A.

2017-12-01

Carbonate sediments and biominerals can record environmental conditions during both deposition and subsequent diagenesis, making them important archives of within the geologic record. Therefore, the alteration processes of these paleoenvironmental proxies are important to understand if one is to deduce environmental conditions based on their petrographic and geochemical signature. This study uses an experimental approach in order to best indicate the controls and effects of the diagenesis of various carbonate archives. Samples are hydrothermally altered at known conditions including pore water chemistry (meteoric and brine fluids), and temperature (100-200°C), and are directly compared to an unaltered subsample (same specimen) for petrographic and geochemical alteration, allowing for reduced heterogeneity, and a quantitative and systematic approach to determine the type, extent, and controls of diagenesis. Initial results indicate little-no alteration at the lower temperature experiments (100°C), and almost complete alteration observed at higher temperatures (175-200°C), while intermediate temperature ranges (130-160°C) prove promising for the evaluation of both diagenetic mechanisms, as well as rate limiting factors controlling alteration. Initial results indicate partial recrystallization of the bivalve A. Islandica, as well as other carbonates (corals, bivalves, gastropods, ammonites, and speleothems), with a visually distinct recrystallization front for select specimens. Results indicate that the diagenetic pathway preferentially follows organic distribution, and internal structures within the organo-sediments and minerals, possibly formed during initial formation. Alteration also suggests preferential movement of intercrystalline organics in some sample types, where they appear to be pushed away from the diagenetic front, causing concentration of the water insoluble organics, and the production of visually darker areas surrounding diagenetic fluid pathways.

Peripheral Sensory Neurons Expressing Melanopsin Respond to Light

PubMed Central

Matynia, Anna; Nguyen, Eileen; Sun, Xiaoping; Blixt, Frank W.; Parikh, Sachin; Kessler, Jason; Pérez de Sevilla Müller, Luis; Habib, Samer; Kim, Paul; Wang, Zhe Z.; Rodriguez, Allen; Charles, Andrew; Nusinowitz, Steven; Edvinsson, Lars; Barnes, Steven; Brecha, Nicholas C.; Gorin, Michael B.

2016-01-01

The ability of light to cause pain is paradoxical. The retina detects light but is devoid of nociceptors while the trigeminal sensory ganglia (TG) contain nociceptors but not photoreceptors. Melanopsin-expressing intrinsically photosensitive retinal ganglion cells (ipRGCs) are thought to mediate light-induced pain but recent evidence raises the possibility of an alternative light responsive pathway independent of the retina and optic nerve. Here, we show that melanopsin is expressed in both human and mouse TG neurons. In mice, they represent 3% of small TG neurons that are preferentially localized in the ophthalmic branch of the trigeminal nerve and are likely nociceptive C fibers and high-threshold mechanoreceptor Aδ fibers based on a strong size-function association. These isolated neurons respond to blue light stimuli with a delayed onset and sustained firing, similar to the melanopsin-dependent intrinsic photosensitivity observed in ipRGCs. Mice with severe bilateral optic nerve crush exhibit no light-induced responses including behavioral light aversion until treated with nitroglycerin, an inducer of migraine in people and migraine-like symptoms in mice. With nitroglycerin, these same mice with optic nerve crush exhibit significant light aversion. Furthermore, this retained light aversion remains dependent on melanopsin-expressing neurons. Our results demonstrate a novel light-responsive neural function independent of the optic nerve that may originate in the peripheral nervous system to provide the first direct mechanism for an alternative light detection pathway that influences motivated behavior. PMID:27559310

In TCR-Stimulated T-cells, N-ras Regulates Specific Genes and Signal Transduction Pathways

PubMed Central

Lynch, Stephen J.; Zavadil, Jiri; Pellicer, Angel

2013-01-01

It has been recently shown that N-ras plays a preferential role in immune cell development and function; specifically: N-ras, but not H-ras or K-ras, could be activated at and signal from the Golgi membrane of immune cells following a low level T-cell receptor stimulus. The goal of our studies was to test the hypothesis that N-ras and H-ras played distinct roles in immune cells at the level of the transcriptome. First, we showed via mRNA expression profiling that there were over four hundred genes that were uniquely differentially regulated either by N-ras or H-ras, which provided strong evidence in favor of the hypothesis that N-ras and H-ras have distinct functions in immune cells. We next characterized the genes that were differentially regulated by N-ras in T cells following a low-level T-cell receptor stimulus. Of the large pool of candidate genes that were differentially regulated by N-ras downstream of TCR ligation, four genes were verified in qRT-PCR-based validation experiments (Dntt, Slc9a6, Chst1, and Lars2). Finally, although there was little overlap between individual genes that were regulated by N-ras in unstimulated thymocytes and stimulated CD4+ T-cells, there was a nearly complete correspondence between the signaling pathways that were regulated by N-ras in these two immune cell types. PMID:23755101

Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors.

PubMed

Martin-Malpartida, Pau; Batet, Marta; Kaczmarska, Zuzanna; Freier, Regina; Gomes, Tiago; Aragón, Eric; Zou, Yilong; Wang, Qiong; Xi, Qiaoran; Ruiz, Lidia; Vea, Angela; Márquez, José A; Massagué, Joan; Macias, Maria J

2017-12-12

Smad transcription factors activated by TGF-β or by BMP receptors form trimeric complexes with Smad4 to target specific genes for cell fate regulation. The CAGAC motif has been considered as the main binding element for Smad2/3/4, whereas Smad1/5/8 have been thought to preferentially bind GC-rich elements. However, chromatin immunoprecipitation analysis in embryonic stem cells showed extensive binding of Smad2/3/4 to GC-rich cis-regulatory elements. Here, we present the structural basis for specific binding of Smad3 and Smad4 to GC-rich motifs in the goosecoid promoter, a nodal-regulated differentiation gene. The structures revealed a 5-bp consensus sequence GGC(GC)|(CG) as the binding site for both TGF-β and BMP-activated Smads and for Smad4. These 5GC motifs are highly represented as clusters in Smad-bound regions genome-wide. Our results provide a basis for understanding the functional adaptability of Smads in different cellular contexts, and their dependence on lineage-determining transcription factors to target specific genes in TGF-β and BMP pathways.

Aversive Learning and Appetitive Motivation Toggle Feed-Forward Inhibition in the Drosophila Mushroom Body.

PubMed

Perisse, Emmanuel; Owald, David; Barnstedt, Oliver; Talbot, Clifford B; Huetteroth, Wolf; Waddell, Scott

2016-06-01

In Drosophila, negatively reinforcing dopaminergic neurons also provide the inhibitory control of satiety over appetitive memory expression. Here we show that aversive learning causes a persistent depression of the conditioned odor drive to two downstream feed-forward inhibitory GABAergic interneurons of the mushroom body, called MVP2, or mushroom body output neuron (MBON)-γ1pedc>α/β. However, MVP2 neuron output is only essential for expression of short-term aversive memory. Stimulating MVP2 neurons preferentially inhibits the odor-evoked activity of avoidance-directing MBONs and odor-driven avoidance behavior, whereas their inhibition enhances odor avoidance. In contrast, odor-evoked activity of MVP2 neurons is elevated in hungry flies, and their feed-forward inhibition is required for expression of appetitive memory at all times. Moreover, imposing MVP2 activity promotes inappropriate appetitive memory expression in food-satiated flies. Aversive learning and appetitive motivation therefore toggle alternate modes of a common feed-forward inhibitory MVP2 pathway to promote conditioned odor avoidance or approach. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Nanostructural evolution and behavior of H and Li in ion-implanted γ-LiAlO 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, Weilin; Zhang, Jiandong; Edwards, Danny J.

In-situ He+ ion irradiation is performed under a helium ion microscope to study nanostructural evolution in polycrystalline gamma-LiAlO2 pellets. Various locations within a grain, across grain boundaries and at a cavity are selected. The results exhibit He bubble formation, grain-boundary cracking, nanoparticle agglomeration, increasing surface brightness with dose, and material loss from the surface. Similar brightening effects at grain boundaries are also observed under a scanning electron microscope. Li diffusion and loss from polycrystalline gamma-LiAlO2 is faster than its monocrystalline counterpart during H2+ ion implantation at elevated temperatures. There is also more significant H diffusion and release from polycrystalline pelletsmore » during thermal annealing of 300 K implanted samples. Grain boundaries and cavities could provide a faster pathway for H and Li diffusion. H release is slightly faster from the 573 K implanted monocrystalline gamma-LiAlO2 during annealing at 773 K. Metal hydrides could be formed preferentially along the grain boundaries to immobilize hydrogen.« less

Assessing the Risks to Human Health in Heterogeneous Aquifers under Uncertainty

NASA Astrophysics Data System (ADS)

de Barros, Felipe

2015-04-01

Reliable quantification of human health risk from toxic chemicals present in groundwater is a challenging task. The main difficulty relies on the fact that many of the components that constitute human health risk assessment are uncertain and requires interdisciplinary knowledge. Understanding the impact from each of these components in risk estimation can provide guidance for decision makers to manage contaminated sites and best allocate resources towards minimal prediction uncertainty. This presentation will focus on the impact of aquifer heterogeneity in human health risk. Spatial heterogeneity of the hydrogeological properties can lead to the formation of preferential flow channels which control the plume spreading rates and travel time statistics, both which are critical in assessing the risk level. By making use of an integrated hydrogeological-health stochastic framework, the significance of characteristic length scales (e.g. characterizing flow, transport and sampling devices) in both controlling the uncertainty of health risk and determining data needs is highlighted. Through a series of examples, we show how fundamental knowledge on the main physical mechanisms affecting solute pathways are necessary to understand the human health response to varying drivers.

Ca cycling and isotopic fluxes in forested ecosystems in Hawaii

USGS Publications Warehouse

Wiegand, B.A.; Chadwick, O.A.; Vitousek, P.M.; Wooden, J.L.

2005-01-01

Biogeochemical processes fractionate Ca isotopes in plants and soils along a 4 million year developmental sequence in the Hawaiian Islands. We observed that plants preferentially take up 40Ca relative to 44Ca, and that biological fractionation and changes in the relative contributions from volcanic and marine sources produce a significant increase in 44Ca in soil exchangeable pools. Our results imply moderate fluxes enriched in 44Ca from strongly nutrient-depleted old soils, in contrast with high 40Ca fluxes in young and little weathered environments. In addition, biological fractionation controls divergent geochemical pathways of Ca and Sr in the plant-soil system. While Ca depletes progressively with increasing soil age, Sr/Ca ratios increase systematically. Sr isotope ratios provide a valuable tracer for provenance studies of alkaline earth elements in forested ecosystems, but its usefulness is limited when deciphering biogeochemical processes involved in the terrestrial Ca cycle. Ca isotopes in combination with Sr/ Ca ratios reveal more complex processes involved in the biogeochemistry of Ca and Sr. Copyright 2005 by the American Geophysical Union.

C9orf72 BAC Mouse Model with Motor Deficits and Neurodegenerative Features of ALS/FTD.

PubMed

Liu, Yuanjing; Pattamatta, Amrutha; Zu, Tao; Reid, Tammy; Bardhi, Olgert; Borchelt, David R; Yachnis, Anthony T; Ranum, Laura P W

2016-05-04

To define how the C9orf72 GGGGCC expansion mutation causes ALS/FTD and to facilitate therapy development, a mouse model that recapitulates the molecular and phenotypic features of the disease is urgently needed. Two groups recently reported BAC mouse models that produce RNA foci and RAN proteins but, surprisingly, do not develop the neurodegenerative or behavioral features of ALS/FTD. We now report a BAC mouse model of C9orf72 ALS/FTD that shows decreased survival, paralysis, muscle denervation, motor neuron loss, anxiety-like behavior, and cortical and hippocampal neurodegeneration. These mice express C9orf72 sense transcripts and upregulated antisense transcripts. In contrast to sense RNA foci, antisense foci preferentially accumulate in ALS/FTD-vulnerable cell populations. RAN protein accumulation increases with age and disease, and TDP-43 inclusions are found in degenerating brain regions in end-stage animals. The ALS/FTD phenotypes in our mice provide a unique tool that will facilitate developing therapies targeting pathways that prevent neurodegeneration and increase survival. Copyright © 2016 Elsevier Inc. All rights reserved.

Seasonal GPR Signal Changes in Two Contrasting Soils in the Shale Hills Catchment

NASA Astrophysics Data System (ADS)

Lin, H.; Zhang, J.; Doolittle, J. A.

2011-12-01

Repeated GPR surveys in different seasons, combined with real-time soil water monitoring, provide a useful methodology to reveal subsurface hydrologic processes and their underlying mechanisms in different soils and hillslopes. This was demonstrated in the Shale Hills Critical Zone Observatory using two contrasting soils over several dry and wet seasons. Our results showed that 1) the radar reflection in the BC-C horizon interface in the deep Rushtown soil became clearer as soil became wetter, which was linked to lateral flow above this horizon interface that increased the contrast, and 2) the reflection in the soil-bedrock interface and the weathered-unweathered rock interface in the shallow Weikert soil become intermittent as soil became wetter, which was attributed to non-uniform distribution of water in bedrock fractures that created locally strong contrast, leading to point scatter of GPR reflection. This study shows the optimal time for using GPR to detect soil horizon interfaces, the value of nondestructive mapping of soil-rock moisture distribution patterns, and the possibility of identifying preferential flow pathways in the subsurface.

Gene expression profiling at early organogenesis reveals both common and diverse mechanisms in foregut patterning

PubMed Central

Fagman, Henrik; Amendola, Elena; Parrillo, Luca; Zoppoli, Pietro; Marotta, Pina; Scarfò, Marzia; De Luca, Pasquale; de Carvalho, Denise Pires; Ceccarelli, Michele; De Felice, Mario; Di Lauro, Roberto

2011-01-01

The thyroid and lungs originate as neighboring bud shaped outgrowths from the midline of the embryonic foregut. When and how organ specific programs regulate development into structures of distinct shapes, positions and functions is incompletely understood. To characterize, at least in part, the genetic basis of these events, we have employed laser capture microdissection and microarray analysis to define gene expression in the mouse thyroid and lung primordia at E10.5. By comparing the transcriptome of each bud to that of the whole embryo as well as to each other, we broadly describe the genes that are preferentially expressed in each developing organ as well as those with an enriched expression common to both. The results thus obtained provide a valuable resource for further analysis of genes previously unrecognized to participate in thyroid and lung morphogenesis and to discover organ specific as well as common developmental mechanisms. As an initial step in this direction we describe a regulatory pathway involving the anti-apoptotic gene Bcl2 that controls cell survival in early thyroid development. PMID:21924257

Brain Mechanisms Supporting Discrimination of Sensory Features of Pain: A New Model

PubMed Central

Oshiro, Yoshitetsu; Quevedo, Alexandre S.; McHaffie, John G.; Kraft, Robert A.; Coghill, Robert C.

2010-01-01

Pain can be very intense or only mild, and can be well localized or diffuse. To date, little is known as to how such distinct sensory aspects of noxious stimuli are processed by the human brain. Using functional magnetic resonance imaging and a delayed match-to-sample task, we show that discrimination of pain intensity, a non-spatial aspect of pain, activates a ventrally directed pathway extending bilaterally from the insular cortex to the prefrontal cortex. This activation is distinct from the dorsally-directed activation of the posterior parietal cortex and right dorsolateral prefrontal cortex that occurs during spatial discrimination of pain. Both intensity and spatial discrimination tasks activate highly similar aspects of the anterior cingulate cortex, suggesting that this structure contributes to common elements of the discrimination task such as the monitoring of sensory comparisons and response selection. Taken together, these results provide the foundation for a new model of pain in which bidirectional dorsal and ventral streams preferentially amplify and process distinct sensory features of noxious stimuli according to top-down task demands. PMID:19940188

RBPJ maintains brain tumor–initiating cells through CDK9-mediated transcriptional elongation

PubMed Central

Xie, Qi; Wu, Qiulian; Kim, Leo; Miller, Tyler E.; Liau, Brian B.; Mack, Stephen C.; Yang, Kailin; Factor, Daniel C.; Fang, Xiaoguang; Huang, Zhi; Zhou, Wenchao; Alazem, Kareem; Wang, Xiuxing; Bernstein, Bradley E.; Bao, Shideng; Rich, Jeremy N.

2016-01-01

Glioblastomas co-opt stem cell regulatory pathways to maintain brain tumor–initiating cells (BTICs), also known as cancer stem cells. NOTCH signaling has been a molecular target in BTICs, but NOTCH antagonists have demonstrated limited efficacy in clinical trials. Recombining binding protein suppressor of hairless (RBPJ) is considered a central transcriptional mediator of NOTCH activity. Here, we report that pharmacologic NOTCH inhibitors were less effective than targeting RBPJ in suppressing tumor growth. While NOTCH inhibitors decreased canonical NOTCH gene expression, RBPJ regulated a distinct profile of genes critical to BTIC stemness and cell cycle progression. RBPJ was preferentially expressed by BTICs and required for BTIC self-renewal and tumor growth. MYC, a key BTIC regulator, bound the RBPJ promoter and treatment with a bromodomain and extraterminal domain (BET) family bromodomain inhibitor decreased MYC and RBPJ expression. Proteomic studies demonstrated that RBPJ binds CDK9, a component of positive transcription elongation factor b (P-TEFb), to target gene promoters, enhancing transcriptional elongation. Collectively, RBPJ links MYC and transcriptional control through CDK9, providing potential nodes of fragility for therapeutic intervention, potentially distinct from NOTCH. PMID:27322055

Human brain regions involved in recognizing environmental sounds.

PubMed

Lewis, James W; Wightman, Frederic L; Brefczynski, Julie A; Phinney, Raymond E; Binder, Jeffrey R; DeYoe, Edgar A

2004-09-01

To identify the brain regions preferentially involved in environmental sound recognition (comprising portions of a putative auditory 'what' pathway), we collected functional imaging data while listeners attended to a wide range of sounds, including those produced by tools, animals, liquids and dropped objects. These recognizable sounds, in contrast to unrecognizable, temporally reversed control sounds, evoked activity in a distributed network of brain regions previously associated with semantic processing, located predominantly in the left hemisphere, but also included strong bilateral activity in posterior portions of the middle temporal gyri (pMTG). Comparisons with earlier studies suggest that these bilateral pMTG foci partially overlap cortex implicated in high-level visual processing of complex biological motion and recognition of tools and other artifacts. We propose that the pMTG foci process multimodal (or supramodal) information about objects and object-associated motion, and that this may represent 'action' knowledge that can be recruited for purposes of recognition of familiar environmental sound-sources. These data also provide a functional and anatomical explanation for the symptoms of pure auditory agnosia for environmental sounds reported in human lesion studies.

Alcohol-abuse drug disulfiram targets cancer via p97 segregase adaptor NPL4.

PubMed

Skrott, Zdenek; Mistrik, Martin; Andersen, Klaus Kaae; Friis, Søren; Majera, Dusana; Gursky, Jan; Ozdian, Tomas; Bartkova, Jirina; Turi, Zsofia; Moudry, Pavel; Kraus, Marianne; Michalova, Martina; Vaclavkova, Jana; Dzubak, Petr; Vrobel, Ivo; Pouckova, Pavla; Sedlacek, Jindrich; Miklovicova, Andrea; Kutt, Anne; Li, Jing; Mattova, Jana; Driessen, Christoph; Dou, Q Ping; Olsen, Jørgen; Hajduch, Marian; Cvek, Boris; Deshaies, Raymond J; Bartek, Jiri

2017-12-14

Cancer incidence is rising and this global challenge is further exacerbated by tumour resistance to available medicines. A promising approach to meet the need for improved cancer treatment is drug repurposing. Here we highlight the potential for repurposing disulfiram (also known by the trade name Antabuse), an old alcohol-aversion drug that has been shown to be effective against diverse cancer types in preclinical studies. Our nationwide epidemiological study reveals that patients who continuously used disulfiram have a lower risk of death from cancer compared to those who stopped using the drug at their diagnosis. Moreover, we identify the ditiocarb-copper complex as the metabolite of disulfiram that is responsible for its anti-cancer effects, and provide methods to detect preferential accumulation of the complex in tumours and candidate biomarkers to analyse its effect on cells and tissues. Finally, our functional and biophysical analyses reveal the molecular target of disulfiram's tumour-suppressing effects as NPL4, an adaptor of p97 (also known as VCP) segregase, which is essential for the turnover of proteins involved in multiple regulatory and stress-response pathways in cells.

β-catenin contributes to lung tumor development induced by EGFR mutations

PubMed Central

Nakayama, Sohei; Sng, Natasha; Carretero, Julian; Welner, Robert; Hayashi, Yuichiro; Yamamoto, Mihoko; Tan, Alistair J.; Yamaguchi, Norihiro; Yasuda, Hiroyuki; Li, Danan; Soejima, Kenzo; Soo, Ross A.; Costa, Daniel B.; Wong, Kwok-Kin; Kobayashi, Susumu S.

2014-01-01

The discovery of somatic mutations in epidermal growth factor receptor (EGFR) and development of EGFR tyrosine kinase inhibitors (TKIs) have revolutionized treatment for lung cancer. However, resistance to TKIs emerges in almost all patients and currently no effective treatment is available. Here we show that β-catenin is essential for development of EGFR mutated lung cancers. β-catenin was upregulated and activated in EGFR mutated cells. Mutant EGFR preferentially bound to and tyrosine-phosphorylated β-catenin, leading to increase in β-catenin-mediated transactivation, particularly in cells harboring the gefitinib/erlotinib-resistant gatekeeper EGFR-T790M mutation. Pharmacological inhibition of β-catenin suppressed EGFR-L858R-T790M mutated lung tumor growth and genetic deletion of the β-catenin gene dramatically reduced lung tumor formation in EGFR-L858R-T790M transgenic mice. These data suggest that β-catenin plays an essential role in lung tumorigenesis and that targeting the β-catenin pathway may provide novel strategies to prevent lung cancer development or overcome resistance to EGFR TKIs. PMID:25164010

Thermally induced texture flip in semiconducting polymer stabilized by epitaxial relationship

NASA Astrophysics Data System (ADS)

O'Hara, Kathryn A.; Pokuri, Balaji S. S.; Takacs, Christopher J.; Beaujuge, Pierre M.; Ganapathysubramanian, Baskar; Chabinyc, Michael L.

The morphology of semiconducting polymer films has a large effect on the charge transport properties. Charges can move easily along the conjugated backbone and in the pi-pi stacking direction. However, transport through the film is determined by the connectivity between domains, which is not well understood. We previously observed quadrites in the polymer, PSBTBT, and proposed that the preferential overlap between lamellae may improve connectivity and provide an additional conduction pathway. Now, the presence of quadrites is revealed in another successful donor polymer, PBDTTPD, using high resolution transmission electron microscopy (HRTEM). A study of how side-chain substitution affects the epitaxial crossing is conducted by examining several PBDTTPD derivatives. The stability of the film texture with annealing is also examined as a function of quadrite formation. It has been shown that heating some semicrystalline polymers above the melting temperature and slow cooling can flip the lamellar texture from face-on to edge-on. We hypothesize that the orientation of lamellar crystallites in PBDTTPD films is stabilized by the epitaxial overlap between adjacent crystalline domains. This may have important implications for the electronic transport properties.

Inscuteable Regulates the Pins-Mud Spindle Orientation Pathway

PubMed Central

Mauser, Jonathon F.; Prehoda, Kenneth E.

2012-01-01

During asymmetric cell division, alignment of the mitotic spindle with the cell polarity axis ensures that the cleavage furrow separates fate determinants into distinct daughter cells. The protein Inscuteable (Insc) is thought to link cell polarity and spindle positioning in diverse systems by binding the polarity protein Bazooka (Baz; aka Par-3) and the spindle orienting protein Partner of Inscuteable (Pins; mPins or LGN in mammals). Here we investigate the mechanism of spindle orientation by the Insc-Pins complex. Previously, we defined two Pins spindle orientation pathways: a complex with Mushroom body defect (Mud; NuMA in mammals) is required for full activity, whereas binding to Discs large (Dlg) is sufficient for partial activity. In the current study, we have examined the role of Inscuteable in mediating downstream Pins-mediated spindle orientation pathways. We find that the Insc-Pins complex requires Gαi for partial activity and that the complex specifically recruits Dlg but not Mud. In vitro competition experiments revealed that Insc and Mud compete for binding to the Pins TPR motifs, while Dlg can form a ternary complex with Insc-Pins. Our results suggest that Insc does not passively couple polarity and spindle orientation but preferentially inhibits the Mud pathway, while allowing the Dlg pathway to remain active. Insc-regulated complex assembly may ensure that the spindle is attached to the cortex (via Dlg) before activation of spindle pulling forces by Dynein/Dynactin (via Mud). PMID:22253744

CaM kinase signaling induces cardiac hypertrophy and activates the MEF2 transcription factor in vivo

PubMed Central

Passier, Robert; Zeng, Hong; Frey, Norbert; Naya, Francisco J.; Nicol, Rebekka L.; McKinsey, Timothy A.; Overbeek, Paul; Richardson, James A.; Grant, Stephen R.; Olson, Eric N.

2000-01-01

Hypertrophic growth is an adaptive response of the heart to diverse pathological stimuli and is characterized by cardiomyocyte enlargement, sarcomere assembly, and activation of a fetal program of cardiac gene expression. A variety of Ca2+-dependent signal transduction pathways have been implicated in cardiac hypertrophy, but whether these pathways are independent or interdependent and whether there is specificity among them are unclear. Previously, we showed that activation of the Ca2+/calmodulin-dependent protein phosphatase calcineurin or its target transcription factor NFAT3 was sufficient to evoke myocardial hypertrophy in vivo. Here, we show that activated Ca2+/calmodulin-dependent protein kinases-I and -IV (CaMKI and CaMKIV) also induce hypertrophic responses in cardiomyocytes in vitro and that CaMKIV overexpressing mice develop cardiac hypertrophy with increased left ventricular end-diastolic diameter and decreased fractional shortening. Crossing this transgenic line with mice expressing a constitutively activated form of NFAT3 revealed synergy between these signaling pathways. We further show that CaMKIV activates the transcription factor MEF2 through a posttranslational mechanism in the hypertrophic heart in vivo. Activated calcineurin is a less efficient activator of MEF2-dependent transcription, suggesting that the calcineurin/NFAT and CaMK/MEF2 pathways act in parallel. These findings identify MEF2 as a downstream target for CaMK signaling in the hypertrophic heart and suggest that the CaMK and calcineurin pathways preferentially target different transcription factors to induce cardiac hypertrophy. PMID:10811847

Evidence of a sewer vapor transport pathway at the USEPA ...

EPA Pesticide Factsheets

The role of sewer lines as preferential pathways for vapor intrusion is poorly understood. Although the importance of sewer lines for volatile organic compound (VOC) transport has been documented at a small number of sites with vapor intrusion, sewer lines are not routinely sampled during most vapor intrusion investigations. We have used a tracer study and VOC concentration measurements to evaluate the role of the combined sanitary/storm sewer line in VOC transport at the USEPA vapor intrusion research duplex in Indianapolis, Indiana. The results from the tracer study demonstrated gas migration from the sewer main line into the duplex. The migration pathway appears to be complex and may include leakage from the sewer lateral at a location below the building foundation. Vapor samples collected from the sewer line demonstrated the presence of tetrachloroethene (PCE) and chloroform in the sewer main in front of the duplex and at multiple sample locations within the sewer line upstream of the duplex. These test results combined with results from the prior multi-year study of the duplex indicate that the sewer line plays an important role in transport of VOCs from the subsurface source to the immediate vicinity of the duplex building envelope. Highlights • The sewer line is an important pathway for VOC transport at the USEPA duplex. • The importance of this pathway was not identified during prior study of the duplex. • Sewer lines should be routinely evaluated

Reactive transport simulations of alternative flow pathways in the ambient unsaturated zone at Yucca Mountain, Nevada

NASA Astrophysics Data System (ADS)

Browning, L.; Murphy, W.; Manepally, C.; Fedors, R.

2003-04-01

Uncertainties in simulated ambient system unsaturated zone flow could have a significant impact on performance evaluations of the proposed nuclear waste repository at Yucca Mountain, Nevada. In addition to determining variations in the quantity of water available to corrode engineered materials and transport radionuclides, model assumptions regarding flow pathways may significantly affect estimates of groundwater chemistry. The manner and extent to which groundwater compositions evolve along a flow pathway are determined mainly by thermohydrologic conditions, the types of reactive materials encountered, and the interaction times with those materials. Simulated groundwater compositions can thus vary significantly depending on whether or not the flow model includes lateral diversion of infiltrating waters, or preferential flow pathways in variably-saturated materials. To assist a regulatory review of a potential license application for a geologic repository for high-level waste, we developed a reactive transport model for the ambient hydrogeochemical system at Yucca Mountain. The model simulates two phase, nonisothermal, advective and diffusive flow and transport through a one dimensional, matrix and fracture continua (dual permeability) containing ten kinetically reactive hydrostatigraphic layers in the vicinity of the SD-9 borehole at Yucca Mountain. In this presentation, we describe how the model was used to evaluate alternative ambient unsaturated zone flow pathways proposed by the U.S. Department of Energy. This abstract is an independent product of the CNWRA and does not necessarily reflect the views or regulatory position of the NRC.

An inhibitory interaction of human cortical responses to stimuli preferentially exciting Aδ or C fibers

PubMed Central

Tran, Tuan D.; Matre, Dagfinn; Casey, Kenneth L.

2008-01-01

Finely myelinated (type Aδ) and unmyelinated (type C) fibers are the major afferent inputs to spinothalamic tract neurons mediating sensory and reflex responses to noxious and thermal stimuli. These two fiber types differ in their sensory and biophysical properties, raising questions about the interaction of their supraspinal responses. Therefore, we investigated the interaction of cortical responses to stimuli that preferentially excite these fibers in human subjects using evoked potential recordings in a paired conditioning stimulation (CS) and test stimulation (TS) paradigm. There were two experiments, one with Aδ as CS and C as TS (Aδ-C) and another with these stimuli reversed (C-Aδ). We used intra-epidermal electrical pulses applied to the dorsal left hand at 2 and 1 × pinprick threshold (pp) for the preferential stimulation of Aδ fibers and 37 – 50°C contact heat pulses applied to the left or right thenar and left hypothenar eminences for the preferential stimulation of C fibers. We found that the cortical response to preferential Aδ or C fiber stimulation was attenuated whenever either cortical response preceded the other. Standardized values of peak and integrated amplitudes were < 1 in all paring conditions and in all subjects in both experiments. The suppressive effect varied in magnitude with the intensity of the conditioning stimulus in both Aδ-C and C-Aδ experiments. Furthermore, intra-segmental interaction was differentially effective for Aδ conditioning, (peak amplitude, p < 0.008; ANOVA). Our experiments provide the first neurophysiological evidence for a somatotopically distributed, mutually suppressive interaction between cortical responses to preferentially activated Aδ and C afferents in humans. This suppressive interaction of cortical responses suggests contrasting and possibly mutually exclusive sensori-motor functions mediated through the Aδ and C fiber afferent channels. PMID:18308475

Preferential induction of Th17 cells in vitro and in vivo by Fucogalactan from Ganoderma lucidum (Reishi).

PubMed

Yoshida, Hideyuki; Suzuki, Mayu; Sakaguchi, Ryota; Tani, Ito; Kotani, Hitoshi; Shudo, Norimasa; Yoshimura, Akihiko

2012-05-25

The mushroom known as Reishi (Ganoderma lucidum) has been used as an herbal medicine for tumor treatment and immune system activation. Because its effects on the differentiation of effector T helper cells have not yet been fully understood, we investigated the effects of Reishi and those of its principal ingredient, β-glucan, on the activation of dendritic cells and the differentiation of Th17 cells. Reishi extracts as well as purified β-glucan (Curdran) activated DCs and caused them to produce large amounts of IL-23. β-glucan also enhanced and sustained the transcription of IL-23p19. The MEK-ERK signaling pathway positively regulates IL-23p19 transcription in β-glucan-stimulated DCs. In a mixed leukocyte reaction, Reishi-stimulated DCs preferentially induced Th17 cells. Furthermore, orally-administrated Reishi increased the percentages of Th17 cells and the transcription levels of antimicrobial peptides. Our results show that Reishi and β-glucan activate DCs to produce large amounts of IL-23, which induces Th17 differentiation both in vitro and in vivo. Copyright © 2012 Elsevier Inc. All rights reserved.

Isoflurane Impairs Low-Frequency Feedback but Leaves High-Frequency Feedforward Connectivity Intact in the Fly Brain.

PubMed

Cohen, Dror; van Swinderen, Bruno; Tsuchiya, Naotsugu

2018-01-01

Hierarchically organized brains communicate through feedforward (FF) and feedback (FB) pathways. In mammals, FF and FB are mediated by higher and lower frequencies during wakefulness. FB is preferentially impaired by general anesthetics in multiple mammalian species. This suggests FB serves critical functions in waking brains. The brain of Drosophila melanogaster (fruit fly) is also hierarchically organized, but the presence of FB in these brains is not established. Here, we studied FB in the fly brain, by simultaneously recording local field potentials (LFPs) from low-order peripheral structures and higher-order central structures. We analyzed the data using Granger causality (GC), the first application of this analysis technique to recordings from the insect brain. Our analysis revealed that low frequencies (0.1-5 Hz) mediated FB from the center to the periphery, while higher frequencies (10-45 Hz) mediated FF in the opposite direction. Further, isoflurane anesthesia preferentially reduced FB. Our results imply that the spectral characteristics of FF and FB may be a signature of hierarchically organized brains that is conserved from insects to mammals. We speculate that general anesthetics may induce unresponsiveness across species by targeting the mechanisms that support FB.

Isoflurane Impairs Low-Frequency Feedback but Leaves High-Frequency Feedforward Connectivity Intact in the Fly Brain

PubMed Central

2018-01-01

Abstract Hierarchically organized brains communicate through feedforward (FF) and feedback (FB) pathways. In mammals, FF and FB are mediated by higher and lower frequencies during wakefulness. FB is preferentially impaired by general anesthetics in multiple mammalian species. This suggests FB serves critical functions in waking brains. The brain of Drosophila melanogaster (fruit fly) is also hierarchically organized, but the presence of FB in these brains is not established. Here, we studied FB in the fly brain, by simultaneously recording local field potentials (LFPs) from low-order peripheral structures and higher-order central structures. We analyzed the data using Granger causality (GC), the first application of this analysis technique to recordings from the insect brain. Our analysis revealed that low frequencies (0.1–5 Hz) mediated FB from the center to the periphery, while higher frequencies (10–45 Hz) mediated FF in the opposite direction. Further, isoflurane anesthesia preferentially reduced FB. Our results imply that the spectral characteristics of FF and FB may be a signature of hierarchically organized brains that is conserved from insects to mammals. We speculate that general anesthetics may induce unresponsiveness across species by targeting the mechanisms that support FB. PMID:29541686

Human Th17 Cells Lack HIV-Inhibitory RNases and Are Highly Permissive to Productive HIV Infection

PubMed Central

Christensen-Quick, Aaron; Lafferty, Mark; Sun, Lingling; Marchionni, Luigi; DeVico, Anthony

2016-01-01

ABSTRACT Human immunodeficiency virus (HIV) infects and depletes CD4+ T cells, but subsets of CD4+ T cells vary in their susceptibility and permissiveness to infection. For example, HIV preferentially depletes interleukin-17 (IL-17)-producing T helper 17 (Th17) cells and T follicular helper (Tfh) cells. The preferential loss of Th17 cells during the acute phase of infection impairs the integrity of the gut mucosal barrier, which drives chronic immune activation—a key determinant of disease progression. The preferential loss of Th17 cells has been attributed to high CD4, CCR5, and CXCR4 expression. Here, we show that Th17 cells also exhibit heightened permissiveness to productive HIV infection. Primary human CD4+ T cells were sorted, activated under Th17- or Th0-polarizing conditions and infected, and then analyzed by flow cytometry. Th17-polarizing cytokines increased HIV infection, and HIV infection was disproportionately higher among Th17 cells than among IL-17− or gamma interferon-positive (IFN-γ+) cells, even upon infection with a replication-defective HIV vector with a pseudotype envelope. Further, Th17-polarized cells produced more viral capsid protein. Our data also reveal that Th17-polarized cells have diminished expression of RNase A superfamily proteins, and we report for the first time that RNase 6 inhibits HIV. Thus, our findings link Th17 polarization to increased HIV replication. IMPORTANCE Our study compares the intracellular replicative capacities of several different HIV isolates among different T cell subsets, providing a link between the differentiation of Th17 cells and HIV replication. Th17 cells are of key importance in mucosal integrity and in the immune response to certain pathogens. Based on our findings and the work of others, we propose a model in which HIV replication is favored by the intracellular environment of two CD4+ T cell subsets that share several requirements for their differentiation: Th17 and Tfh cells. Characterizing cells that support high levels of viral replication (rather than becoming latently infected or undergoing cell death) informs the search for new therapeutics aimed at manipulating intracellular signaling pathways and/or transcriptional factors that affect HIV replication. PMID:27334595

Geo-Hydro Statistical Characterization of Preferential Flow and Transport Processes in Karst Groundwater Systems

NASA Astrophysics Data System (ADS)

Anaya, A. A.; Padilla, I. Y.; Macchiavelli, R. E.

2011-12-01

Karst groundwater systems are highly productive and provide an important fresh water resource for human development and ecological integrity. Their high productivity is often associated with conduit flow and high matrix permeability. The same characteristics that make these aquifers productive also make them highly vulnerable to contamination and a likely for contaminant exposure. Of particular interest are chlorinated organic contaminants and phthalates derived from industrial solvents and plastic by-products. These chemicals have been identified as potential precursors of pre-term birth, a leading cause of neonatal complications with a significant health and societal cost. The general objectives of this work are to: (1) develop fundamental knowledge and determine the processes controlling the release, mobility, persistence, and possible pathways of contaminants in karst groundwater systems, and (2) characterize transport processes in conduit and diffusion-dominated flow under base flow and storm flow conditions. The work presented herein focuses on the development of geo-hydro statistical tools to characterize flow and transport processes under different flow regimes. Multidimensional, laboratory-scale Geo-Hydrobed models were developed and tested for this purpose. The models consist of stainless-steel tanks containing karstified limestone blocks collected from the karst aquifer formation of northern Puerto Rico. The models a network of sampling wells to monitor flow, pressure, and solute concentrations temporally and spatially. Experimental work entailed making a series of point injections in wells while monitoring the hydraulic response in other wells. Statistical mixed models were applied to spatial probabilities of hydraulic response and weighted injected volume data, and were used to determinate the best spatial correlation structure to represent paths of preferential flow in the limestone units under different groundwater flow regimes. Preliminary testing of the karstified models show that the system can be used to represent the variable transport regime characterized by conduit and diffuses flow in the karst systems. Initial hydraulic characterization indicates a highly heterogeneous system resulting in large preferential flow components. Future works involve characterization of dual porosity system using conservative tracers, fate and transport experiments using phthalates and chlorinated solvents, geo-temporal statistical modeling, and the testing of "green" remediation technologies in karst groundwater. This work is supported by the U.S. Department of Energy, Savannah River (Grant Award No. DE-FG09-07SR22571), and the National Institute of Environmental Health Sciences (NIEHS, Grant Award No. P42ES017198).

Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels

DOE PAGES

Petit, Elsa; Coppi, Maddalena V.; Hayes, James C.; ...

2015-06-02

Clostridium phytofermentans was isolated from forest soil and is distinguished by its capacity to directly ferment plant cell wall polysaccharides into ethanol as the primary product, suggesting that it possesses unusual catabolic pathways. The objective of our present study was to understand the molecular mechanisms of biomass conversion to ethanol in a single organism, Clostridium phytofermentans, by analyzing its complete genome and transcriptome during growth on plant carbohydrates. The saccharolytic versatility of C. phytofermentans is reflected in a diversity of genes encoding ATP-binding cassette sugar transporters and glycoside hydrolases, many of which may have been acquired through horizontal gene transfer.more » These genes are frequently organized as operons that may be controlled individually by the many transcriptional regulators identified in the genome. Preferential ethanol production may be due to high levels of expression of multiple ethanol dehydrogenases and additional pathways maximizing ethanol yield. The genome also encodes three different proteinaceous bacterial microcompartments with the capacity to compartmentalize pathways that divert fermentation intermediates to various products. Lastly, these characteristics make C. phytofermentans an attractive resource for improving the efficiency and speed of biomass conversion to biofuels.« less

Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels.

PubMed

Petit, Elsa; Coppi, Maddalena V; Hayes, James C; Tolonen, Andrew C; Warnick, Thomas; Latouf, William G; Amisano, Danielle; Biddle, Amy; Mukherjee, Supratim; Ivanova, Natalia; Lykidis, Athanassios; Land, Miriam; Hauser, Loren; Kyrpides, Nikos; Henrissat, Bernard; Lau, Joanne; Schnell, Danny J; Church, George M; Leschine, Susan B; Blanchard, Jeffrey L

2015-01-01

Clostridium phytofermentans was isolated from forest soil and is distinguished by its capacity to directly ferment plant cell wall polysaccharides into ethanol as the primary product, suggesting that it possesses unusual catabolic pathways. The objective of the present study was to understand the molecular mechanisms of biomass conversion to ethanol in a single organism, Clostridium phytofermentans, by analyzing its complete genome and transcriptome during growth on plant carbohydrates. The saccharolytic versatility of C. phytofermentans is reflected in a diversity of genes encoding ATP-binding cassette sugar transporters and glycoside hydrolases, many of which may have been acquired through horizontal gene transfer. These genes are frequently organized as operons that may be controlled individually by the many transcriptional regulators identified in the genome. Preferential ethanol production may be due to high levels of expression of multiple ethanol dehydrogenases and additional pathways maximizing ethanol yield. The genome also encodes three different proteinaceous bacterial microcompartments with the capacity to compartmentalize pathways that divert fermentation intermediates to various products. These characteristics make C. phytofermentans an attractive resource for improving the efficiency and speed of biomass conversion to biofuels.

A role for the CAMKK pathway in visual object recognition memory.

PubMed

Tinsley, Chris J; Narduzzo, Katherine E; Brown, Malcolm W; Warburton, E Clea

2012-03-01

The role of the CAMKK pathway in object recognition memory was investigated. Rats' performance in a preferential object recognition test was examined after local infusion into the perirhinal cortex of the CAMKK inhibitor STO-609. STO-609 infused either before or immediately after acquisition impaired memory tested after a 24 h but not a 20-min delay. Memory was not impaired when STO-609 was infused 20 min after acquisition. The expression of a downstream reaction product of CAMKK was measured by immunohistochemical staining for phospho-CAMKI(Thr177) at 10, 40, 70, and 100 min following the viewing of novel and familiar images of objects. Processing familiar images resulted in more pCAMKI stained neurons in the perirhinal cortex than processing novel images at the 10- and 40-min delays. Prior infusion of STO-609 caused a reduction in pCAMKI stained neurons in response to viewing either novel or familiar images, consistent with its role as an inhibitor of CAMKK. The results establish that the CAMKK pathway within the perirhinal cortex is important for the consolidation of object recognition memory. The activation of pCAMKI after acquisition is earlier than previously reported for pCAMKII. Copyright © 2011 Wiley Periodicals, Inc.

Chiral pathways in DNA dinucleotides using gradient optimized refinement along metastable borders

NASA Astrophysics Data System (ADS)

Romano, Pablo; Guenza, Marina

We present a study of DNA breathing fluctuations using Markov state models (MSM) with our novel refinement procedure. MSM have become a favored method of building kinetic models, however their accuracy has always depended on using a significant number of microstates, making the method costly. We present a method which optimizes macrostates by refining borders with respect to the gradient along the free energy surface. As the separation between macrostates contains highest discretization errors, this method corrects for any errors produced by limited microstate sampling. Using our refined MSM methods, we investigate DNA breathing fluctuations, thermally induced conformational changes in native B-form DNA. Running several microsecond MD simulations of DNA dinucleotides of varying sequences, to include sequence and polarity effects, we've analyzed using our refined MSM to investigate conformational pathways inherent in the unstacking of DNA bases. Our kinetic analysis has shown preferential chirality in unstacking pathways that may be critical in how proteins interact with single stranded regions of DNA. These breathing dynamics can help elucidate the connection between conformational changes and key mechanisms within protein-DNA recognition. NSF Chemistry Division (Theoretical Chemistry), the Division of Physics (Condensed Matter: Material Theory), XSEDE.

Demonstration of Laser Induced Acoustic Desoprtion - Chemical Ionization Mass Spectrometry (LIAD-CIMS) for Fragment-Free Measurements of Organic Aerosol Molecular Composition

NASA Astrophysics Data System (ADS)

Browne, E. C.; Abdelhamid, A.; Berry, J.; Alton, M.

2017-12-01

Organic compounds account for a significant portion of fine atmospheric aerosol. Current analytical techniques have provided insights on organic aerosol (OA) sources, composition, and chemical modification pathways. Despite this knowledge, large uncertainties remain and hinder our understanding of aerosol impacts on climate, air quality, and health. Measuring OA composition is challenging due to the complex chemical composition and the wide variation in the properties (e.g., vapor pressure, solubility, reactivity) of organic compounds. In many current measurement techniques, the ability to chemically resolve and quantify OA components is complicated by molecular decomposition, matrix effects, and/or preferential ionization mechanisms. Here, we utilize a novel desorption technique, laser induced acoustic desorption (LIAD), that generates fragment-free, neutral gas-phase molecules. We couple LIAD with a high-resolution chemical ionization mass spectrometer (CIMS) to provide molecular composition OA measurements. Through a series of laboratory experiments, we demonstrate the ability of this technique to measure large, thermally labile species without fragmentation/thermal decomposition. We discuss quantification and detection limits of this technique. We compare LIAD-CIMS measurements with thermal desorption-CIMS measurements using off-line measurements of ambient aerosol collected in Boulder, CO. Lastly, we discuss future development for on-line measurements of OA using LIAD-CIMS.

Genetic Causes of Microcephaly and Lessons for Neuronal Development

PubMed Central

Gilmore, Edward C.; Walsh, Christopher A.

2012-01-01

The study of human developmental microcephaly is providing important insights into brain development. It has become clear that developmental microcephalies are associated with abnormalities in cellular production, and that the pathophysiology of microcephaly provides remarkable insights into how the brain generates the proper number of neurons that determine brain size. Most of the genetic causes of ‘primary’ developmental microcephaly (i.e., not associated with other syndromic features) are associated with centrosomal abnormalities. In addition to other functions, centrosomal proteins control the mitotic spindle, which is essential for normal cell proliferation during mitosis. However, the brain is often uniquely affected when microcephaly genes are mutated implying special centrosomal related functions in neuronal production. Although models explaining how this could occur have some compelling data, they are not without controversy. Interestingly, some of the microcephaly genes show evidence that they were targets of evolutionary selection in primates and human ancestors, suggesting potential evolutionary roles in controlling neuronal number and brain volume across species. Mutations in DNA repair pathway genes also lead to microcephaly. Double stranded DNA breaks appear to be a prominent type of damage that needs to be repaired during brain development, yet why defects in DNA repair affect the brain preferentially and if DNA repair relates to centrosome function, are not clearly understood. PMID:24014418

Non-invasive water-table imaging with joint DC-resistivity/microgravity/hydrologic-model inversion

NASA Astrophysics Data System (ADS)

Kennedy, J.; Macy, J. P.

2017-12-01

The depth of the water table, and fluctuations thereof, is a primary concern in hydrology. In riparian areas, the water table controls when and where vegetation grows. Fluctuations in the water table depth indicate changes in aquifer storage and variation in ET, and may also be responsible for the transport and degradation of contaminants. In the latter case, installation of monitoring wells is problematic because of the potential to create preferential flow pathways. We present a novel method for non-invasive water table monitoring using combined DC resistivity and repeat microgravity data. Resistivity profiles provide spatial resolution, but a quantifiable relation between resistivity changes and aquifer-storage changes depends on a petrophysical relation (typically, Archie's Law), with additional parameters and therefore uncertainty. Conversely, repeat microgravity data provide a direct, quantifiable measurement of aquifer-storage change but lack depth resolution. We show how these two geophysical measurements, together with an unsaturated-zone flow model (Hydrogeosphere), effectively constrain the water table position and help identify groundwater-flow model parameters. A demonstration of the method is made using field data collected during the historic 2014 pulse flow in the Colorado River Delta, which shows that geophysical data can effectively constrain a coupled surface-water/groundwater model used to simulate the potential for riparian vegetation germination and recruitment.

Effects of preferential concentration on direct radiation transmission in a turbulent duct flow

NASA Astrophysics Data System (ADS)

Villafane, Laura; Banko, Andrew; Kim, Ji Hoon; Elkins, Chris; Eaton, John

2017-11-01

Inertial particles in turbulent flows preferentially concentrate, giving rise to spatial and temporal fluctuations of particle number density that affect radiation transmission through the medium. Positive particle correlations enhance direct transmission when compared to the exponential attenuation predicted by the Beer's Law for randomly distributed particles. In the context of a particle based solar receiver, this work studies the effects of preferential concentration and optical depth on direct transmission through a particle laden turbulent duct flow. Time resolved measurements of transmission through the mixture were performed for various particle loadings and Reynolds numbers, thus varying particle correlation lengths, optical depth and concentration fluctuations. These measurements were made using a photodiode to record the transmission of a collimated laser beam along the wall bisector of the duct. A synchronized high-speed camera provided particle positions along most of the beam path. Average and fluctuating radiation transmission results are compared to predictions derived from the imaged number density fields and to simplified analytical models. Simplified models are able to capture the correct trends with varying loading and preferential concentration. This work is funded by the Department of Energy's National Nuclear Security Administration, Grant #DE-NA0002373-1.

Exploring the surface reactivity of 3d metal endofullerenes: a density-functional theory study.

PubMed

Estrada-Salas, Rubén E; Valladares, Ariel A

2009-09-24

Changes in the preferential sites of electrophilic, nucleophilic, and radical attacks on the pristine C60 surface with endohedral doping using 3d transition metal atoms were studied via two useful reactivity indices, namely the Fukui functions and the molecular electrostatic potential. Both of these were calculated at the density functional BPW91 level of theory with the DNP basis set. Our results clearly show changes in the preferential reactivity sites on the fullerene surface when it is doped with Mn, Fe, Co, or Ni atoms, whereas there are no significant changes in the preferential reactivity sites on the C60 surface upon endohedral doping with Cu and Zn atoms. Electron affinities (EA), ionization potentials (IP), and HOMO-LUMO gaps (Eg) were also calculated to complete the study of the endofullerene's surface reactivity. These findings provide insight into endofullerene functionalization, an important issue in their application.

Selection of Two-Phase Flow Patterns at a Simple Junction in Microfluidic Devices

NASA Astrophysics Data System (ADS)

Engl, W.; Ohata, K.; Guillot, P.; Colin, A.; Panizza, P.

2006-04-01

We study the behavior of a confined stream made of two immiscible fluids when it reaches a T junction. Two flow patterns are witnessed: the stream is either directed in only one sidearm, yielding a preferential flow pathway for the dispersed phase, or splits between both. We show that the selection of these patterns is not triggered by the shape of the junction nor by capillary effects, but results from confinement. It can be anticipated in terms of the hydrodynamic properties of the flow. A simple model yielding universal behavior in terms of the relevant adimensional parameters of the problem is presented and discussed.

Ideological pathways to policy and practice.

PubMed

Levy, C S

1983-01-01

Social policy is a reflection of changing ideological stances; and ideological stances are influenced by social conditions and events. Policy-makers and social welfare administrators need to be acutely aware of the existing ideologies and the subtle or dramatic shifts as they occur and affect perceptions of clients, programmatic components, and the nature of social service delivery. The author offers a dichotomy of ideological positions as they are applied to the issues of social problems vs sub-populations, societal vs individual responsibility, residual vs institutional welfare, enforceable rights vs revocable privilege, existential vs preferential attention to social needs, government regulation vs deregulation, and governmental aid vs voluntary philanthropy.

The thrifty lipids: Endocannabinoids and the neural control of energy conservation

PubMed Central

DiPatrizio, Nicholas V.; Piomelli, Daniele

2013-01-01

The “thrifty gene hypothesis” posits that evolution preferentially selects physiological mechanisms that optimize energy storage to increase survival under alternating conditions of abundance and scarcity of food. Recent experiments suggest that endocannabinoids – a class of lipid-derived mediators that activate cannabinoid receptors in many cells of the body – are key agents of energy conservation. The new evidence indicates that these compounds increase energy intake and decrease energy expenditure by controlling the activity of peripheral and central neural pathways involved in the sensing and hedonic processing of sweet and fatty foods, as well as in the storage of their energy content for future use. PMID:22622030

Access to Housing in Urban China

PubMed Central

Logan, John R.; Fang, Yiping; Zhang, Zhanxin

2013-01-01

Like income inequality, housing inequality in urban China is strongly affected by state policies that give preferential treatment to insiders. In this case, the key policies are related to their residence status, which involves not only their migration history but also their legal position. Using data from the Chinese census of 2000 for eight large cities, this study shows how residence status affects access to various pathways to housing. In addition to the well-known marginal housing situation of the recent ‘floating population’, it documents surprising advantages for migrants with urban registration status and persistent disadvantages for rural migrants regardless of how long they have lived in the city. PMID:23976818

Carbon Source-Dependent Inducible Metabolism of Veratryl Alcohol and Ferulic Acid in Pseudomonas putida CSV86

PubMed Central

Mohan, Karishma

2017-01-01

ABSTRACT Pseudomonas putida CSV86 degrades lignin-derived metabolic intermediates, viz., veratryl alcohol, ferulic acid, vanillin, and vanillic acid, as the sole sources of carbon and energy. Strain CSV86 also degraded lignin sulfonate. Cell respiration, enzyme activity, biotransformation, and high-pressure liquid chromatography (HPLC) analyses suggest that veratryl alcohol and ferulic acid are metabolized to vanillic acid by two distinct carbon source-dependent inducible pathways. Vanillic acid was further metabolized to protocatechuic acid and entered the central carbon pathway via the β-ketoadipate route after ortho ring cleavage. Genes encoding putative enzymes involved in the degradation were found to be present at fer, ver, and van loci. The transcriptional analysis suggests a carbon source-dependent cotranscription of these loci, substantiating the metabolic studies. Biochemical and quantitative real-time (qRT)-PCR studies revealed the presence of two distinct O-demethylases, viz., VerAB and VanAB, involved in the oxidative demethylation of veratric acid and vanillic acid, respectively. This report describes the various steps involved in metabolizing lignin-derived aromatic compounds at the biochemical level and identifies the genes involved in degrading veratric acid and the arrangement of phenylpropanoid metabolic genes as three distinct inducible transcription units/operons. This study provides insight into the bacterial degradation of lignin-derived aromatics and the potential of P. putida CSV86 as a suitable candidate for producing valuable products. IMPORTANCE Pseudomonas putida CSV86 metabolizes lignin and its metabolic intermediates as a carbon source. Strain CSV86 displays a unique property of preferential utilization of aromatics, including for phenylpropanoids over glucose. This report unravels veratryl alcohol metabolism and genes encoding veratric acid O-demethylase, hitherto unknown in pseudomonads, thereby providing new insight into the metabolic pathway and gene pool for lignin degradation in bacteria. The biochemical and genetic characterization of phenylpropanoid metabolism makes it a prospective system for its application in producing valuable products, such as vanillin and vanillic acid, from lignocellulose. This study supports the immense potential of P. putida CSV86 as a suitable candidate for bioremediation and biorefinery. PMID:28188206

BAM 1 and RECEPTOR-LIKE PROTEIN KINASE 2 constitute a signaling pathway and modulate CLE peptide-triggered growth inhibition in Arabidopsis root.

PubMed

Shimizu, Noriko; Ishida, Takashi; Yamada, Masashi; Shigenobu, Shuji; Tabata, Ryo; Kinoshita, Atsuko; Yamaguchi, Katsushi; Hasebe, Mitsuyasu; Mitsumasu, Kanako; Sawa, Shinichiro

2015-12-01

Ligand receptor-based signaling is a means of cell-to-cell communication for coordinating developmental and physiological processes in multicellular organisms. In plants, cell-producing meristems utilize this signaling to regulate their activities and ensure for proper development. Shoot and root systems share common requirements for carrying out this process; however, its molecular basis is largely unclear. It has been suggested that synthetic CLV3/EMBRYO SURROUNDING REGION (CLE) peptide shrinks the root meristem through the actions of CLAVATA2 (CLV2) and the RECEPTOR-LIKE PROTEIN KINASE 2 (RPK2) pathway in Arabidopsis thaliana. Our genetic screening for mutations that resist CLE peptide signaling in roots determined that BAM1, which is a member of the leucine-rich repeat receptor-like kinase (LRR-RLK) family, is also involved in this pathway. BAM1 is preferentially expressed in the root tip, including the quiescent center and its surrounding stem cells. Our genetic analysis revealed that BAM1 functions together with RPK2. Using coimmunoprecipitation assay, we showed that BAM1 is capable of forming heteromeric complexes with RPK2. These findings suggest that the BAM1 and RPK2 receptors constitute a signaling pathway that modulates cell proliferation in the root meristem and that related molecules are employed in root and shoot meristems. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Axon guidance pathways served as common targets for human speech/language evolution and related disorders.

PubMed

Lei, Huimeng; Yan, Zhangming; Sun, Xiaohong; Zhang, Yue; Wang, Jianhong; Ma, Caihong; Xu, Qunyuan; Wang, Rui; Jarvis, Erich D; Sun, Zhirong

2017-11-01

Human and several nonhuman species share the rare ability of modifying acoustic and/or syntactic features of sounds produced, i.e. vocal learning, which is the important neurobiological and behavioral substrate of human speech/language. This convergent trait was suggested to be associated with significant genomic convergence and best manifested at the ROBO-SLIT axon guidance pathway. Here we verified the significance of such genomic convergence and assessed its functional relevance to human speech/language using human genetic variation data. In normal human populations, we found the affected amino acid sites were well fixed and accompanied with significantly more associated protein-coding SNPs in the same genes than the rest genes. Diseased individuals with speech/language disorders have significant more low frequency protein coding SNPs but they preferentially occurred outside the affected genes. Such patients' SNPs were enriched in several functional categories including two axon guidance pathways (mediated by netrin and semaphorin) that interact with ROBO-SLITs. Four of the six patients have homozygous missense SNPs on PRAME gene family, one youngest gene family in human lineage, which possibly acts upon retinoic acid receptor signaling, similarly as FOXP2, to modulate axon guidance. Taken together, we suggest the axon guidance pathways (e.g. ROBO-SLIT, PRAME gene family) served as common targets for human speech/language evolution and related disorders. Copyright © 2017 Elsevier Inc. All rights reserved.

Classical autophagy proteins LC3B and ATG4B facilitate melanosome movement on cytoskeletal tracks.

PubMed

Ramkumar, Amrita; Murthy, Divya; Raja, Desingu Ayyappa; Singh, Archana; Krishnan, Anusha; Khanna, Sangeeta; Vats, Archana; Thukral, Lipi; Sharma, Pushkar; Sivasubbu, Sridhar; Rani, Rajni; Natarajan, Vivek T; Gokhale, Rajesh S

2017-08-03

Macroautophagy/autophagy is a dynamic and inducible catabolic process that responds to a variety of hormonal and environmental cues. Recent studies highlight the interplay of this central pathway in a variety of pathophysiological diseases. Although defective autophagy is implicated in melanocyte proliferation and pigmentary disorders, the mechanistic relationship between the 2 pathways has not been elucidated. In this study, we show that autophagic proteins LC3B and ATG4B mediate melanosome trafficking on cytoskeletal tracks. While studying melanogenesis, we observed spatial segregation of LC3B-labeled melanosomes with preferential absence at the dendritic ends of melanocytes. This LC3B labeling of melanosomes did not impact the steady-state levels of these organelles but instead facilitated their intracellular positioning. Melanosomes primarily traverse on microtubule and actin cytoskeletal tracks and our studies reveal that LC3B enables the assembly of microtubule translocon complex. At the microtubule-actin crossover junction, ATG4B detaches LC3B from melanosomal membranes by enzymatic delipidation. Further, by live-imaging we show that melanosomes transferred to keratinocytes lack melanocyte-specific LC3B. Our study thus elucidates a new role for autophagy proteins in directing melanosome movement and reveal the unconventional use of these proteins in cellular trafficking pathways. Such crosstalk between the central cellular function and housekeeping pathway may be a crucial mechanism to balance melanocyte bioenergetics and homeostasis.

Neuroimaging reveals dual routes to reading in simultaneous proficient readers of two orthographies

PubMed Central

Das, T.; Padakannaya, P.; Pugh, K. R.; Singh, N. C.

2012-01-01

Orthographic differences across languages impose differential weighting on distinct component processes, and consequently on different pathways during word-reading tasks. Readers of transparent orthographies such as Italian and Hindi are thought to rely on spelling-to-sound assembly and show increased activation in phonologically-tuned areas along the dorsal pathway, whereas reading an opaque orthography such as English is thought to rely more on lexically-mediated processing associated with increased activation of semantically-tuned regions along the ventral pathway. To test if biliterate Hindi/English readers exhibit orthography-specific reading pathways, we used behavioural measures and functional neuroimaging. Reaction times and activation patterns of monolingual English and Hindi readers were compared to two groups of adult biliterates; 14 simultaneous readers who learnt to read both languages at age 5 and 10 sequential readers who learnt Hindi at 5 and English at 10. Simultaneous, but not sequential readers demonstrated relative activation differences of dorsal and ventral areas in the two languages. Similar to native counterparts, simultaneous readers preferentially activated the left inferior temporal gyrus for English and left inferior parietal lobule (L-IPL) for Hindi, whereas, sequential readers showed higher activation along the L-IPL for reading both languages. We suggest that early simultaneous exposure to reading distinct orthographies results in orthography-specific plasticity that persists through adulthood. PMID:20854914

The adsorption of preferential binding peptides to apatite-based materials

PubMed Central

Segvich, Sharon J.; Smith, Hayes C.; Kohn, David H.

2009-01-01

The objective of this work was to identify peptide sequences with high affinity to bone-like mineral (BLM) to provide alternative design methods for functional bone regeneration peptides. Adsorption of preferential binding peptide sequences on four apatite-based substrates [BLM and three sintered apatite disks pressed from powders containing 0% CO32− (HA), 5.6% CO32− (CA5), 10.5% CO32− (CA10)] with varied compositions and morphologies was investigated. A combination of phage display, ELISA, and computational modeling was used to elucidate three 12-mer peptide sequences APWHLSSQYSRT (A), STLPI-PHEFSRE (S), and VTKHLNQISQSY (V), from 243 candidates with preferential adsorption on BLM and HA. Overall, peptides S and V have a significantly higher adsorption to the apatite-based materials in comparison to peptide A (for S vs. A, BLM p = 0.001, CA5 p < 0.001, CA10 p < 0.001, HA p = 0.038; for V vs. A, BLM p = 0.006, CA5 p = 0.033, CA10 p = 0.029). FT-IR analysis displayed carbonate levels in CA5 and CA10 dropped to approximately 1.1–2.2% after sintering, whereas SEM imaging displayed CA5 and CA10 possess distinct morphologies. Adsorption results normalized to surface area indicate that small changes in carbonate percentage at a similar morphological scale did not provide enough carbonate incorporation to show statistical differences in peptide adsorption. Because the identified peptides (S and V) have preferential binding to apatite, their use can now be investigated in bone and dentin tissue engineering, tendon and ligament repair, and enamel formation. PMID:19095299

Immunogenicity is preferentially induced in sparse dendritic cell cultures

PubMed Central

Nasi, Aikaterini; Bollampalli, Vishnu Priya; Sun, Meng; Chen, Yang; Amu, Sylvie; Nylén, Susanne; Eidsmo, Liv; Rothfuchs, Antonio Gigliotti; Réthi, Bence

2017-01-01

We have previously shown that human monocyte-derived dendritic cells (DCs) acquired different characteristics in dense or sparse cell cultures. Sparsity promoted the development of IL-12 producing migratory DCs, whereas dense cultures increased IL-10 production. Here we analysed whether the density-dependent endogenous breaks could modulate DC-based vaccines. Using murine bone marrow-derived DC models we show that sparse cultures were essential to achieve several key functions required for immunogenic DC vaccines, including mobility to draining lymph nodes, recruitment and massive proliferation of antigen-specific CD4+ T cells, in addition to their TH1 polarization. Transcription analyses confirmed higher commitment in sparse cultures towards T cell activation, whereas DCs obtained from dense cultures up-regulated immunosuppressive pathway components and genes suggesting higher differentiation plasticity towards osteoclasts. Interestingly, we detected a striking up-regulation of fatty acid and cholesterol biosynthesis pathways in sparse cultures, suggesting an important link between DC immunogenicity and lipid homeostasis regulation. PMID:28276533

A decade of understanding spatio-temporal regulation of DNA repair by the nuclear architecture.

PubMed

Saad, Hicham; Cobb, Jennifer A

2016-10-01

The nucleus is a hub for gene expression and is a highly organized entity. The nucleoplasm is heterogeneous, owing to the preferential localization of specific metabolic factors, which lead to the definition of nuclear compartments or bodies. The genome is organized into chromosome territories, as well as heterochromatin and euchromatin domains. Recent observations have indicated that nuclear organization is important for maintaining genomic stability. For example, nuclear organization has been implicated in stabilizing damaged DNA, repair-pathway choice, and in preventing chromosomal rearrangements. Over the past decade, several studies have revealed that dynamic changes in the nuclear architecture are important during double-strand break repair. Stemming from work in yeast, relocation of a damaged site prior to repair appears to be at least partially conserved in multicellular eukaryotes. In this review, we will discuss genome and nucleoplasm architecture, particularly the importance of the nuclear periphery in genome stability. We will also discuss how the site of relocation regulates repair-pathway choice.

Opposing activities of Notch and Wnt signaling regulate intestinal stem cells and gut homeostasis

PubMed Central

Tian, Hua; Biehs, Brian; Chiu, Cecilia; Siebel, Chris; Wu, Yan; Costa, Mike; de Sauvage, Frederic J.; Klein, Ophir D.

2015-01-01

Summary Proper organ homeostasis requires tight control of adult stem cells and differentiation through integration of multiple inputs. In the mouse small intestine, Notch and Wnt signaling are required both for stem cell maintenance and for a proper balance of differentiation between secretory and absorptive cell lineages. In the absence of Notch signaling, stem cells preferentially generate secretory cells at the expense of absorptive cells. Here, we use function-blocking antibodies against Notch receptors to demonstrate that Notch blockade perturbs intestinal stem cell function by causing a de-repression of the Wnt signaling pathway, leading to mis-expression of prosecretory genes. Importantly, attenuation of the Wnt pathway rescued the phenotype associated with Notch blockade. These studies bring to light a negative regulatory mechanism that maintains stem cell activity and balanced differentiation, and we propose that the interaction between Wnt and Notch signaling described here represents a common theme in adult stem cell biology. PMID:25818302

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aratani, Satoko; Oishi, Takayuki; Fujita, Hidetoshi

RNA helicase A (RHA), an ATPase/helicase, regulates the gene expression at various steps including transcriptional activation and RNA processing. RHA is known to shuttle between the nucleus and cytoplasm. We identified the nuclear localization signal (NLS) of RHA and analyzed the nuclear import mechanisms. The NLS of RHA (RHA-NLS) consisting of 19 amino acid residues is highly conserved through species and does not have the consensus classical NLS. In vitro nuclear import assays revealed that the nuclear import of RHA was Ran-dependent and mediated with the classical importin-{alpha}/{beta}-dependent pathway. The binding assay indicated that the basic residues in RHA-NLS weremore » used for interaction with importin-{alpha}. Furthermore, the nuclear import of RHA-NLS was supported by importin-{alpha}1 and preferentially importin-{alpha}3. Our results indicate that the nuclear import of RHA is mediated by the importin-{alpha}3/importin-{beta}-dependent pathway and suggest that the specificity for importin may regulate the functions of cargo proteins.« less

Tracer Tests in the Fractured Rock to Investigate Preferential Groundwater Flow

NASA Astrophysics Data System (ADS)

Chan, W.; Chung, L.; Lee, T.; Liu, C.; Chia, Y.; Teng, M.

2012-12-01

Hydraulic tests are often used to obtain hydraulic conductivity in the aquifer. Test results usually reflect the average hydraulic conductivity in the surrounding strat. However, in fractured rock, groundwater flows primarily through a few fractures. Saltwater tracer test can be used to detect the direction of groundwater flow, but it was difficult to know the hydraulic connectivity between fractures. In this study, we use a variety of field tests, including tracer test, hydraulic test, and heat-pulse flowmeter test, to locate the permeable fractures and detect the hydraulic connections between boreholes. There are eight test wells and two observation wells on field experimental site in central Taiwan. Geological survey results show that there are at least three sets of joint planes. In order to realize the location of the preferential pathway of groundwater flow, heat-pulse flowmeter measurement was adopted to identify the depth of permeable fractures. Multi-well pumping test was also performed to investigate the hydraulic connectivity between these wells. Tracer tests were then used to detect the hydraulic connectivity of permeable fractures between two wells. Injection of nano zero valent iron in one well and and collection of iron tracer with a magnet array in the other well can specifically locate the permeable fracture and determine the connectivity. Saltwater tracer test result can be used to support that of nano-iron tracer test, and verify the relationship between well water conductivity increases and rock fracture location. The results show that tracer test is a useful tool to investigate the preferential groundwater flow in the fractured rock, but it is essential to flush the mud in fractures prior to the test.

A detailed gene expression study of the Miscanthus genus reveals changes in the transcriptome associated with the rejuvenation of spring rhizomes.

PubMed

Barling, Adam; Swaminathan, Kankshita; Mitros, Therese; James, Brandon T; Morris, Juliette; Ngamboma, Ornella; Hall, Megan C; Kirkpatrick, Jessica; Alabady, Magdy; Spence, Ashley K; Hudson, Matthew E; Rokhsar, Daniel S; Moose, Stephen P

2013-12-09

The Miscanthus genus of perennial C4 grasses contains promising biofuel crops for temperate climates. However, few genomic resources exist for Miscanthus, which limits understanding of its interesting biology and future genetic improvement. A comprehensive catalog of expressed sequences were generated from a variety of Miscanthus species and tissue types, with an emphasis on characterizing gene expression changes in spring compared to fall rhizomes. Illumina short read sequencing technology was used to produce transcriptome sequences from different tissues and organs during distinct developmental stages for multiple Miscanthus species, including Miscanthus sinensis, Miscanthus sacchariflorus, and their interspecific hybrid Miscanthus × giganteus. More than fifty billion base-pairs of Miscanthus transcript sequence were produced. Overall, 26,230 Sorghum gene models (i.e., ~ 96% of predicted Sorghum genes) had at least five Miscanthus reads mapped to them, suggesting that a large portion of the Miscanthus transcriptome is represented in this dataset. The Miscanthus × giganteus data was used to identify genes preferentially expressed in a single tissue, such as the spring rhizome, using Sorghum bicolor as a reference. Quantitative real-time PCR was used to verify examples of preferential expression predicted via RNA-Seq. Contiguous consensus transcript sequences were assembled for each species and annotated using InterProScan. Sequences from the assembled transcriptome were used to amplify genomic segments from a doubled haploid Miscanthus sinensis and from Miscanthus × giganteus to further disentangle the allelic and paralogous variations in genes. This large expressed sequence tag collection creates a valuable resource for the study of Miscanthus biology by providing detailed gene sequence information and tissue preferred expression patterns. We have successfully generated a database of transcriptome assemblies and demonstrated its use in the study of genes of interest. Analysis of gene expression profiles revealed biological pathways that exhibit altered regulation in spring compared to fall rhizomes, which are consistent with their different physiological functions. The expression profiles of the subterranean rhizome provides a better understanding of the biological activities of the underground stem structures that are essentials for perenniality and the storage or remobilization of carbon and nutrient resources.

Brain Networks Shaping Religious Belief

PubMed Central

Deshpande, Gopikrishna; Krueger, Frank; Thornburg, Matthew P.; Grafman, Jordan Henry

2014-01-01

Abstract We previously demonstrated with functional magnetic resonance imaging (fMRI) that religious belief depends upon three cognitive dimensions, which can be mapped to specific brain regions. In the present study, we considered these co-activated regions as nodes of three networks each one corresponding to a particular dimension, corresponding to each dimension and examined the causal flow within and between these networks to address two important hypotheses that remained untested in our previous work. First, we hypothesized that regions involved in theory of mind (ToM) are located upstream the causal flow and drive non-ToM regions, in line with theories attributing religion to the evolution of ToM. Second, we hypothesized that differences in directional connectivity are associated with differences in religiosity. To test these hypotheses, we performed a multivariate Granger causality-based directional connectivity analysis of fMRI data to demonstrate the causal flow within religious belief-related networks. Our results supported both hypotheses. Religious subjects preferentially activated a pathway from inferolateral to dorsomedial frontal cortex to monitor the intent and involvement of supernatural agents (SAs; intent-related ToM). Perception of SAs engaged pathways involved in fear regulation and affective ToM. Religious beliefs are founded both on propositional statements for doctrine, but also on episodic memory and imagery. Beliefs based on doctrine engaged a pathway from Broca's to Wernicke's language areas. Beliefs related to everyday life experiences engaged pathways involved in imagery. Beliefs implying less involved SAs and evoking imagery activated a pathway from right lateral temporal to occipital regions. This pathway was more active in non-religious compared to religious subjects, suggesting greater difficulty and procedural demands for imagining and processing the intent of SAs. Insights gained by Granger connectivity analysis inform us about the causal binding of individual regions activated during religious belief processing. PMID:24279687

Brain networks shaping religious belief.

PubMed

Kapogiannis, Dimitrios; Deshpande, Gopikrishna; Krueger, Frank; Thornburg, Matthew P; Grafman, Jordan Henry

2014-02-01

We previously demonstrated with functional magnetic resonance imaging (fMRI) that religious belief depends upon three cognitive dimensions, which can be mapped to specific brain regions. In the present study, we considered these co-activated regions as nodes of three networks each one corresponding to a particular dimension, corresponding to each dimension and examined the causal flow within and between these networks to address two important hypotheses that remained untested in our previous work. First, we hypothesized that regions involved in theory of mind (ToM) are located upstream the causal flow and drive non-ToM regions, in line with theories attributing religion to the evolution of ToM. Second, we hypothesized that differences in directional connectivity are associated with differences in religiosity. To test these hypotheses, we performed a multivariate Granger causality-based directional connectivity analysis of fMRI data to demonstrate the causal flow within religious belief-related networks. Our results supported both hypotheses. Religious subjects preferentially activated a pathway from inferolateral to dorsomedial frontal cortex to monitor the intent and involvement of supernatural agents (SAs; intent-related ToM). Perception of SAs engaged pathways involved in fear regulation and affective ToM. Religious beliefs are founded both on propositional statements for doctrine, but also on episodic memory and imagery. Beliefs based on doctrine engaged a pathway from Broca's to Wernicke's language areas. Beliefs related to everyday life experiences engaged pathways involved in imagery. Beliefs implying less involved SAs and evoking imagery activated a pathway from right lateral temporal to occipital regions. This pathway was more active in non-religious compared to religious subjects, suggesting greater difficulty and procedural demands for imagining and processing the intent of SAs. Insights gained by Granger connectivity analysis inform us about the causal binding of individual regions activated during religious belief processing.

Identifying pathways and processes affecting nitrate and orthophosphate inputs to streams in agricultural watersheds

USGS Publications Warehouse

Tesoriero, A.J.; Duff, J.H.; Wolock, D.M.; Spahr, N.E.; Almendinger, J.E.

2009-01-01

Understanding nutrient pathways to streams will improve nutrient management strategies and estimates of the time lag between when changes in land use practices occur and when water quality effects that result from these changes are observed. Nitrate and orthophosphate (OP) concentrations in several environmental compartments were examined in watersheds having a range of base flow index (BFI) values across the continental United States to determine the dominant pathways for water and nutrient inputs to streams. Estimates of the proportion of stream nitrate that was derived from groundwater increased as BFI increased. Nitrate concentration gradients between groundwater and surface water further supported the groundwater source of nitrate in these high BFI streams. However, nitrate concentrations in stream-bed pore water in all settings were typically lower than stream or upland groundwater concentrations, suggesting that nitrate discharge to streams was not uniform through the bed. Rather, preferential pathways (e.g., springs, seeps) may allow high nitrate groundwater to bypass sites of high biogeochemical transformation. Rapid pathway compartments (e.g., overland flow, tile drains) had OP concentrations that were typically higher than in streams and were important OP conveyers in most of these watersheds. In contrast to nitrate, the proportion of stream OP that is derived from ground water did not systematically increase as BFI increased. While typically not the dominant source of OP, groundwater discharge was an important pathway of OP transport to streams when BFI values were very high and when geochemical conditions favored OP mobility in groundwater. Copyright ?? 2009 by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. All rights reserved.

CH4 and CO2 production below two contrasting peatland micro-relief forms: An inhibitor and δ13C study.

PubMed

Krohn, Johannes; Lozanovska, Ivana; Kuzyakov, Yakov; Parvin, Shahnaj; Dorodnikov, Maxim

2017-05-15

Two peatland micro-relief forms (microforms) - hummocks and hollows - differ by their hydrological characteristics (water table level, i.e. oxic-anoxic conditions) and vegetation communities. We studied the CH 4 and CO 2 production potential and the localization of methanogenic pathways in both hummocks and hollows at depths of 15, 50, 100, 150 and 200cm in a laboratory incubation experiment. For this purpose, we measured CH 4 and CO 2 production rates, peat elemental composition, as well as δ 13 C values of gases and solids; the specific inhibitor of methanogenesis BES (2-bromo-ethane sulfonate, 1mM) was aimed to preferentially block the acetoclastic pathway. The cumulative CH 4 production of all depths was almost one fold higher in hollows than in hummocks, with no differences in CO 2 . With depth, CO 2 and CH 4 production decreased, and the relative contribution of the hydrogenotrophic pathway of methanogenesis increased. The highest methanogenic activity among all depths and both microforms was measured at 15cm of hollows (91%) at which the highest relative contribution of acetoclastic vs. hydrogenotrophic pathway (92 and 8%, respectively) was detected. For hummocks, the CH 4 production was the highest at 50cm (82%), where relative contribution of acetoclastic methanogenesis comprised 89%. The addition of 1mM BES was not selective and inhibited both methanogenic pathways in the soil. Thus, BES was less efficient in partitioning the pathways compared with the δ 13 C signature. We conclude that the peat microforms - dry hummocks and wet hollows - play an important role for CH 4 but not for CO 2 production when the effects of living vegetation are excluded. Copyright © 2017 Elsevier B.V. All rights reserved.

Insight into bacterial virulence mechanisms against host immune response via the Yersinia pestis-human protein-protein interaction network.

PubMed

Yang, Huiying; Ke, Yuehua; Wang, Jian; Tan, Yafang; Myeni, Sebenzile K; Li, Dong; Shi, Qinghai; Yan, Yanfeng; Chen, Hui; Guo, Zhaobiao; Yuan, Yanzhi; Yang, Xiaoming; Yang, Ruifu; Du, Zongmin

2011-11-01

A Yersinia pestis-human protein interaction network is reported here to improve our understanding of its pathogenesis. Up to 204 interactions between 66 Y. pestis bait proteins and 109 human proteins were identified by yeast two-hybrid assay and then combined with 23 previously published interactions to construct a protein-protein interaction network. Topological analysis of the interaction network revealed that human proteins targeted by Y. pestis were significantly enriched in the proteins that are central in the human protein-protein interaction network. Analysis of this network showed that signaling pathways important for host immune responses were preferentially targeted by Y. pestis, including the pathways involved in focal adhesion, regulation of cytoskeleton, leukocyte transendoepithelial migration, and Toll-like receptor (TLR) and mitogen-activated protein kinase (MAPK) signaling. Cellular pathways targeted by Y. pestis are highly relevant to its pathogenesis. Interactions with host proteins involved in focal adhesion and cytoskeketon regulation pathways could account for resistance of Y. pestis to phagocytosis. Interference with TLR and MAPK signaling pathways by Y. pestis reflects common characteristics of pathogen-host interaction that bacterial pathogens have evolved to evade host innate immune response by interacting with proteins in those signaling pathways. Interestingly, a large portion of human proteins interacting with Y. pestis (16/109) also interacted with viral proteins (Epstein-Barr virus [EBV] and hepatitis C virus [HCV]), suggesting that viral and bacterial pathogens attack common cellular functions to facilitate infections. In addition, we identified vasodilator-stimulated phosphoprotein (VASP) as a novel interaction partner of YpkA and showed that YpkA could inhibit in vitro actin assembly mediated by VASP.

Temporal and Spatial Patterns of Preferential Flow Occurrence in the Shale Hills Catchment: From the Hillslope to the Catchment Scales

NASA Astrophysics Data System (ADS)

Liu, H.; Lin, H.

2013-12-01

Understanding temporal and spatial patterns of preferential flow (PF) occurrence is important in revealing hillslope and catchment hydrologic and biogeochemical processes. Quantitative assessment of the frequency and control of PF occurrence in the field, however, has been limited, especially at the landscape scale of hillslope and catchment. By using 5.5-years' (2007-2012) real-time soil moisture at 10 sites response to 323 precipitation events, we tested the temporal consistency of PF occurrence at the hillslope scale in the forested Shale Hills Catchment; and by using 25 additional sites with at least 1-year data (2011-2012), we evaluated the spatial patterns of PF occurrence across the catchment. To explore the potential effects of PF occurrence on catchment hydrology, wavelet analysis was performed on the recorded time series of hydrological signals (i.e., precipitation, soil moisture, catchment discharge). Considerable temporal consistence was observed in both the frequency and the main controls of PF occurrence at the hillslope scale, which was attributed largely to the statistical stability of precipitation pattern over the monitoring period and the relatively stable subsurface preferential pathways. Preferential flow tended to occur more often in response to intense rainfall events, and favored the conditions at dry hilltop or wet valley floor sites. When upscaling to the entire catchment, topographic control on the PF occurrence was amplified remarkably, leading to the identification of a subsurface PF network in the catchment. Higher frequency of PF occurrence was observed at the valley floor (average 48%), hilltop (average 46%), and swales/hillslopes near the stream (average 40%), while the hillslopes in the eastern part of the catchment were least likely to experience PF (0-20%). No clear relationship, however, was observed between terrain attributes and PF occurrence, because the initiation and persistency of PF in this catchment was controlled jointly by complex interactions among landform units, soil types, initial soil moisture, precipitation features, and season. Through the wavelet method (coherence spectrum and phase differences), dual-pore filtering effects of soil system were proven, rendering it possible to further infer characteristic properties of the underlying hydrological processes in the subsurface. We found that preferential flow dominates the catchment discharge response at short-time periods (< 3 days), while the matrix flow may dominate the discharge response at the time scales of around 10-12 days. The temporal and spatial patterns of PF occurrence revealed in this study can help advance the modeling and prediction of complex PF dynamics in this and other similar landscapes.

CO2 Reduction Catalyzed by Nitrogenase: Pathways to Formate, Carbon Monoxide, and Methane.

PubMed

Khadka, Nimesh; Dean, Dennis R; Smith, Dayle; Hoffman, Brian M; Raugei, Simone; Seefeldt, Lance C

2016-09-06

The reduction of N2 to NH3 by Mo-dependent nitrogenase at its active-site metal cluster FeMo-cofactor utilizes reductive elimination of Fe-bound hydrides with obligatory loss of H2 to activate the enzyme for binding/reduction of N2. Earlier work showed that wild-type nitrogenase and a nitrogenase with amino acid substitutions in the MoFe protein near FeMo-cofactor can catalytically reduce CO2 by two or eight electrons/protons to carbon monoxide (CO) and methane (CH4) at low rates. Here, it is demonstrated that nitrogenase preferentially reduces CO2 by two electrons/protons to formate (HCOO(-)) at rates >10 times higher than rates of CO2 reduction to CO and CH4. Quantum mechanical calculations on the doubly reduced FeMo-cofactor with a Fe-bound hydride and S-bound proton (E2(2H) state) favor a direct reaction of CO2 with the hydride ("direct hydride transfer" reaction pathway), with facile hydride transfer to CO2 yielding formate. In contrast, a significant barrier is observed for reaction of Fe-bound CO2 with the hydride ("associative" reaction pathway), which leads to CO and CH4. Remarkably, in the direct hydride transfer pathway, the Fe-H behaves as a hydridic hydrogen, whereas in the associative pathway it acts as a protic hydrogen. MoFe proteins with amino acid substitutions near FeMo-cofactor (α-70(Val→Ala), α-195(His→Gln)) are found to significantly alter the distribution of products between formate and CO/CH4.

MicroRNA regulation of bovine monocyte inflammatory and metabolic networks in an in vivo infection model.

PubMed

Lawless, Nathan; Reinhardt, Timothy A; Bryan, Kenneth; Baker, Mike; Pesch, Bruce; Zimmerman, Duane; Zuelke, Kurt; Sonstegard, Tad; O'Farrelly, Cliona; Lippolis, John D; Lynn, David J

2014-01-27

Bovine mastitis is an inflammation-driven disease of the bovine mammary gland that costs the global dairy industry several billion dollars per year. Because disease susceptibility is a multifactorial complex phenotype, an integrative biology approach is required to dissect the molecular networks involved. Here, we report such an approach using next-generation sequencing combined with advanced network and pathway biology methods to simultaneously profile mRNA and miRNA expression at multiple time points (0, 12, 24, 36 and 48 hr) in milk and blood FACS-isolated CD14(+) monocytes from animals infected in vivo with Streptococcus uberis. More than 3700 differentially expressed (DE) genes were identified in milk-isolated monocytes (MIMs), a key immune cell recruited to the site of infection during mastitis. Upregulated genes were significantly enriched for inflammatory pathways, whereas downregulated genes were enriched for nonglycolytic metabolic pathways. Monocyte transcriptional changes in the blood, however, were more subtle but highlighted the impact of this infection systemically. Genes upregulated in blood-isolated monocytes (BIMs) showed a significant association with interferon and chemokine signaling. Furthermore, 26 miRNAs were DE in MIMs and three were DE in BIMs. Pathway analysis revealed that predicted targets of downregulated miRNAs were highly enriched for roles in innate immunity (FDR < 3.4E-8), particularly TLR signaling, whereas upregulated miRNAs preferentially targeted genes involved in metabolism. We conclude that during S. uberis infection miRNAs are key amplifiers of monocyte inflammatory response networks and repressors of several metabolic pathways. Copyright © 2014 Lawless et al.

Thixotropic gel for vadose zone remediation

DOEpatents

Riha, Brian D.

2012-07-03

A thixotropic gel suitable for use in subsurface bioremediation is provided along with a process of using the gel. The thixotropic gel provides a non-migrating injectable substrate that can provide below ground barrier properties. In addition, the gel components provide for a favorable environment in which certain contaminants are preferentially sequestered in the gel and subsequently remediated by either indigenous or introduced microorganisms.

Thixotropic gel for vadose zone remediation

DOEpatents

Rhia, Brian D [Augusta, GA

2011-03-01

A thixotropic gel suitable for use in subsurface bioremediation is provided along with a process of using the gel. The thixotropic gel provides a non-migrating injectable substrate that can provide below ground barrier properties. In addition, the gel components provide for a favorable environment in which certain contaminants are preferentially sequestered in the gel and subsequently remediated by either indigenous or introduced microorganisms.

Thixotropic gel for vadose zone remediation

DOEpatents

Riha, Brian D.; Looney, Brian B.

2015-10-27

A thixotropic gel suitable for use in subsurface bioremediation is provided along with a process of using the gel. The thixotropic gel provides a non-migrating injectable substrate that can provide below ground barrier properties. In addition, the gel components provide for a favorable environment in which certain contaminants are preferentially sequestered in the gel and subsequently remediated by either indigenous or introduced microorganisms.

Oxidatively denatured proteins are degraded by an ATP-independent proteolytic pathway in Escherichia coli.

PubMed

Davies, K J; Lin, S W

1988-01-01

E. coli contains a soluble proteolytic pathway which can recognize and degrade oxidatively denatured proteins and protein fragments, and which may act as a "secondary antioxidant defense." We now provide evidence that this proteolytic pathway is distinct from the previously described ATP-dependent, and protease "La"-dependent, pathway which may degrade other abnormal proteins. Cells (K12) which were depleted of ATP, by arsenate treatment or anaerobic incubation (after growth on succinate), exhibited proteolytic responses to oxidative stress which were indistinguishable from those observed in cells with normal ATP levels. Furthermore, the proteolytic responses to oxidative damage by menadione or H2O2 were almost identical in the isogenic strains RM312 (a K12 derivative) and RM1385 (a lon deletion mutant of RM312). Since the lon (or capR) gene codes for the ATP-dependent protease "La," these results indicate that neither ATP nor protease "La" are required for the degradation of oxidatively denatured proteins. We next prepared cell-free extracts of K12, RM312, and RM1385 and tested the activity of their soluble proteases against proteins (albumin, hemoglobin, superoxide dismutase, catalase) which had been oxidatively denatured (in vitro) by exposure to .OH, .OH + O2- (+O2), H2O2, or ascorbate plus iron. The breakdown of oxidatively denatured proteins was several-fold higher than that of untreated proteins in extracts from all three strains, and ATP did not stimulate degradation. Incubation of extracts at 45 degrees C, which inactivates protease "La," actually stimulated the degradation of oxidatively denatured proteins. Although Ca2+ had little effect on proteolysis, serine reagents, transition metal chelators, and hemin effectively inhibited the degradation of oxidatively denatured proteins in both intact cells and cell-free extracts. Degradation of oxidatively denatured proteins in cell-free extracts was maximal at pH 7.8, and was unaffected by dialysis of the extracts against membranes with molecular weight cutoffs as high as 50,000. Our results indicate the presence of a neutral, ATP- and calcium- independent proteolytic pathway in the E. coli cytosol, which contains serine- and metallo- proteases (with molecular weights greater than 50,000), and which preferentially degrades oxidatively denatured proteins.

Targeted cellular ablation based on the morphology of malignant cells

NASA Astrophysics Data System (ADS)

Ivey, Jill W.; Latouche, Eduardo L.; Sano, Michael B.; Rossmeisl, John H.; Davalos, Rafael V.; Verbridge, Scott S.

2015-11-01

Treatment of glioblastoma multiforme (GBM) is especially challenging due to a shortage of methods to preferentially target diffuse infiltrative cells, and therapy-resistant glioma stem cell populations. Here we report a physical treatment method based on electrical disruption of cells, whose action depends strongly on cellular morphology. Interestingly, numerical modeling suggests that while outer lipid bilayer disruption induced by long pulses (~100 μs) is enhanced for larger cells, short pulses (~1 μs) preferentially result in high fields within the cell interior, which scale in magnitude with nucleus size. Because enlarged nuclei represent a reliable indicator of malignancy, this suggested a means of preferentially targeting malignant cells. While we demonstrate killing of both normal and malignant cells using pulsed electric fields (PEFs) to treat spontaneous canine GBM, we proposed that properly tuned PEFs might provide targeted ablation based on nuclear size. Using 3D hydrogel models of normal and malignant brain tissues, which permit high-resolution interrogation during treatment testing, we confirmed that PEFs could be tuned to preferentially kill cancerous cells. Finally, we estimated the nuclear envelope electric potential disruption needed for cell death from PEFs. Our results may be useful in safely targeting the therapy-resistant cell niches that cause recurrence of GBM tumors.

Preferential solvation and solvation shell composition of free base and protonated 5, 10, 15, 20-tetrakis(4-sulfonatophenyl)porphyrin in aqueous organic mixed solvents

NASA Astrophysics Data System (ADS)

Farajtabar, Ali; Jaberi, Fatemeh; Gharib, Farrokh

2011-12-01

The solvatochromic properties of the free base and the protonated 5, 10, 15, 20-tetrakis(4-sulfonatophenyl)porphyrin (TPPS) were studied in pure water, methanol, ethanol (protic solvents), dimethylsulfoxide, DMSO, (non-protic solvent), and their corresponding aqueous-organic binary mixed solvents. The correlation of the empirical solvent polarity scale ( ET) values of TPPS with composition of the solvents was analyzed by the solvent exchange model of Bosch and Roses to clarify the preferential solvation of the probe dyes in the binary mixed solvents. The solvation shell composition and the synergistic effects in preferential solvation of the solute dyes were investigated in terms of both solvent-solvent and solute-solvent interactions and also, the local mole fraction of each solvent composition was calculated in cybotactic region of the probe. The effective mole fraction variation may provide significant physico-chemical insights in the microscopic and molecular level of interactions between TPPS species and the solvent components and therefore, can be used to interpret the solvent effect on kinetics and thermodynamics of TPPS. The obtained results from the preferential solvation and solvent-solvent interactions have been successfully applied to explain the variation of equilibrium behavior of protonation of TPPS occurring in aqueous organic mixed solvents of methanol, ethanol and DMSO.

Targeted cellular ablation based on the morphology of malignant cells

PubMed Central

Ivey, Jill W.; Latouche, Eduardo L.; Sano, Michael B.; Rossmeisl, John H.; Davalos, Rafael V.; Verbridge, Scott S.

2015-01-01

Treatment of glioblastoma multiforme (GBM) is especially challenging due to a shortage of methods to preferentially target diffuse infiltrative cells, and therapy-resistant glioma stem cell populations. Here we report a physical treatment method based on electrical disruption of cells, whose action depends strongly on cellular morphology. Interestingly, numerical modeling suggests that while outer lipid bilayer disruption induced by long pulses (~100 μs) is enhanced for larger cells, short pulses (~1 μs) preferentially result in high fields within the cell interior, which scale in magnitude with nucleus size. Because enlarged nuclei represent a reliable indicator of malignancy, this suggested a means of preferentially targeting malignant cells. While we demonstrate killing of both normal and malignant cells using pulsed electric fields (PEFs) to treat spontaneous canine GBM, we proposed that properly tuned PEFs might provide targeted ablation based on nuclear size. Using 3D hydrogel models of normal and malignant brain tissues, which permit high-resolution interrogation during treatment testing, we confirmed that PEFs could be tuned to preferentially kill cancerous cells. Finally, we estimated the nuclear envelope electric potential disruption needed for cell death from PEFs. Our results may be useful in safely targeting the therapy-resistant cell niches that cause recurrence of GBM tumors. PMID:26596248

How people make friends in social networking sites—A microscopic perspective

NASA Astrophysics Data System (ADS)

Hu, Haibo; Wang, Xiaofan

2012-02-01

We study the detailed growth of a social networking site with full temporal information by examining the creation process of each friendship relation that can collectively lead to the macroscopic properties of the network. We first study the reciprocal behavior of users, and find that link requests are quickly responded to and that the distribution of reciprocation intervals decays in an exponential form. The degrees of inviters/accepters are slightly negatively correlative with reciprocation time. In addition, the temporal feature of the online community shows that the distributions of intervals of user behaviors, such as sending or accepting link requests, follow a power law with a universal exponent, and peaks emerge for intervals of an integral day. We finally study the preferential selection and linking phenomena of the social networking site and find that, for the former, a linear preference holds for preferential sending and reception, and for the latter, a linear preference also holds for preferential acceptance, creation, and attachment. Based on the linearly preferential linking, we put forward an analyzable network model which can reproduce the degree distribution of the network. The research framework presented in the paper could provide a potential insight into how the micro-motives of users lead to the global structure of online social networks.

Investigation of Preferential Flow in Low Impact Development Practice

NASA Astrophysics Data System (ADS)

Liu, L.; Cao, R.; Wang, C.; Jiang, W.; Wang, J.; Xia, Z.

2016-12-01

The characteristics of preferential flow in soil affect Low Impact Development (LID) practices in two aspects. On the one hand, preferential flow may facilitate drainage of stormwater by causing non-uniform movement of water through a small portion of media (such as cracks and holes), and thus leading to much faster transport of water and solutes in one specific direction than others. On the other hand, within a certain ranges, preferential flow may weaken the subgrade capacity of pressure and/or shear stress resistance. Therefore, for the purpose of improving LID practices, there may exist an optimum scenario with a high allowable flowrate and least negative impact of resistance capacity for a soil layer. This project aims to assist the LID design by exploring the features of preferential flow in different soil compositions, studying how different flow paths affect the stability of subgrade, preliminarily analyzing the sensitivity of preferential flow impacting on drainage capacity and subgrade stability in the LID, and further optimizing LID practices. Accordingly, the concepts of Essential Direction Path, Unessential Direction Path and the Sensitivity Coefficient are defined and analyzed to simulate a hypothetical funneling scenario in LID practice. Both irrigation apparatus experiments and numerical models are utilized in this research to investigate the features of preferential flow, effective strength and overall shear strength. The main conclusions include: (1) Investigation of preferential flow characteristics in essential direction path and unessential direction path, respectively; (2) Optimum design of preferential flow in LID practice; (3) Transport capacity determination of preferential flow path in different soils; (4) Study of preferential flow impact on roadbed stability. KEY WORDS: Preferential Flow, Subgrade stability, LID, Sensitivity Coefficient, Funneling Preferential Flow Path

Simulating adverse event spontaneous reporting systems as preferential attachment networks: application to the Vaccine Adverse Event Reporting System.

PubMed

Scott, J; Botsis, T; Ball, R

2014-01-01

Spontaneous Reporting Systems [SRS] are critical tools in the post-licensure evaluation of medical product safety. Regulatory authorities use a variety of data mining techniques to detect potential safety signals in SRS databases. Assessing the performance of such signal detection procedures requires simulated SRS databases, but simulation strategies proposed to date each have limitations. We sought to develop a novel SRS simulation strategy based on plausible mechanisms for the growth of databases over time. We developed a simulation strategy based on the network principle of preferential attachment. We demonstrated how this strategy can be used to create simulations based on specific databases of interest, and provided an example of using such simulations to compare signal detection thresholds for a popular data mining algorithm. The preferential attachment simulations were generally structurally similar to our targeted SRS database, although they had fewer nodes of very high degree. The approach was able to generate signal-free SRS simulations, as well as mimicking specific known true signals. Explorations of different reporting thresholds for the FDA Vaccine Adverse Event Reporting System suggested that using proportional reporting ratio [PRR] > 3.0 may yield better signal detection operating characteristics than the more commonly used PRR > 2.0 threshold. The network analytic approach to SRS simulation based on the principle of preferential attachment provides an attractive framework for exploring the performance of safety signal detection algorithms. This approach is potentially more principled and versatile than existing simulation approaches. The utility of network-based SRS simulations needs to be further explored by evaluating other types of simulated signals with a broader range of data mining approaches, and comparing network-based simulations with other simulation strategies where applicable.

Designed cellulose nanocrystal surface properties for improving barrier properties in polylactide nanocomposites.

PubMed

Espino-Pérez, Etzael; Bras, Julien; Almeida, Giana; Plessis, Cédric; Belgacem, Naceur; Perré, Patrick; Domenek, Sandra

2018-03-01

Nanocomposites are an opportunity to increase the performance of polymer membranes by fine-tuning their morphology. In particular, the understanding of the contribution of the polymer matrix/nanofiller interface to the overall transport properties is key to design membranes with tailored selective and adsorptive properties. In that aim, cellulose nanocrystals (CNC)/polylactide (PLA) nanocomposites were fabricated with chemically designed interfaces, which were ensuring the compatibility between the constituents and impacting the mass transport mechanism. A detailed analysis of the mass transport behaviour of different permeants in CNC/PLA nanocomposites was carried out as a function of their chemical affinity to grafted CNC surfaces. Penetrants (O 2 and cyclohexane), which were found to slightly interact with the constituents of the nanocomposites, provided information on the small tortuosity effect of CNC on diffusive mass transport. The mass transport of water (highly interacting with CNC) and anisole (interacting only with designed CNC surfaces) exhibited non-Fickian, Case II behaviour. The water vapour caused significant swelling of the CNC, which created a preferential pathway for mass transport. CNC surface grafting could attenuate this phenomenon and decrease the water transport rate. Anisole, an aromatic organic vapour, became reversibly trapped at the specifically designed CNC/PLA interface, but without any swelling or creation of an accelerated pathway. This caused the decrease of the overall mass transport rate. The latter finding could open a way to the creation of materials with specifically designed barrier properties by designing nanocomposites interfaces with specific interactions towards permeants. Copyright © 2017 Elsevier Ltd. All rights reserved.

Carbon nanotubes as gene carriers: Focus on internalization pathways related to functionalization and properties.

PubMed

Caoduro, Cécile; Hervouet, Eric; Girard-Thernier, Corine; Gharbi, Tijani; Boulahdour, Hatem; Delage-Mourroux, Régis; Pudlo, Marc

2017-02-01

Carbon nanotubes represent promising transporters for delivery of DNA and other biomolecules into living cells. Various methods of CNTs surface functionalization have been developed. These are essential to improve CNTs dispersibility and permit their interactions with biological structures that broaden their use in advanced biomedical applications. The present review discusses the different single walled carbon nanotubes and multiwalled carbon nanotubes functionalization methods, leading to the formation of optimized and functionalized-CNT complexes with DNA. F-CNTs are recognized as efficient and promising gene carriers. Emphasis is then placed on the processes used by f-CNTs/DNA complexes to cross cell membranes. Energy independent pathways and uptake mechanisms dependent on energy, such as endocytosis or phagocytosis, are reported by many studies, and if these mechanisms seem contradictory at first sight, a detailed review of the literature illustrates that they are rather complementary. Preferential use of one or the other depends on the DNA and CNTs chemical nature and physical parameters, experimental procedures and cell types. Efficient non-viral gene delivery is desirable, yet challenging. CNTs appear as a promising solution to penetrate into cells and successfully deliver DNA. Moreover, the field of use of CNTs as gene carrier is large and is currently growing. This critical review summarizes the development and evaluation of CNTs as intracellular gene delivery system and provides an overview of functionalized CNTs/DNA cellular uptake mechanisms, depending on several parameters of CNTs/DNA complexes. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Dynamic coding of vertical facilitated vergence by premotor saccadic burst neurons.

PubMed

Van Horn, Marion R; Cullen, Kathleen E

2008-10-01

To redirect our gaze in three-dimensional space we frequently combine saccades and vergence. These eye movements, known as disconjugate saccades, are characterized by eyes rotating by different amounts, with markedly different dynamics, and occur whenever gaze is shifted between near and far objects. How the brain ensures the precise control of binocular positioning remains controversial. It has been proposed that the traditionally assumed "conjugate" saccadic premotor pathway does not encode conjugate commands but rather encodes monocular commands for the right or left eye during saccades. Here, we directly test this proposal by recording from the premotor neurons of the horizontal saccade generator during a dissociation task that required a vergence but no horizontal conjugate saccadic command. Specifically, saccadic burst neurons (SBNs) in the paramedian pontine reticular formation were recorded while rhesus monkeys made vertical saccades made between near and far targets. During this task, we first show that peak vergence velocities were enhanced to saccade-like speeds (e.g., >150 vs. <100 degrees/s during saccade-free movements for comparable changes in vergence angle). We then quantified the discharge dynamics of SBNs during these movements and found that the majority of the neurons preferentially encode the velocity of the ipsilateral eye. Notably, a given neuron typically encoded the movement of the same eye during horizontal saccades that were made in depth. Taken together, our findings demonstrate that the brain stem saccadic burst generator encodes integrated conjugate and vergence commands, thus providing strong evidence for the proposal that the classic saccadic premotor pathway controls gaze in three-dimensional space.

Genomic survey, expression profile and co-expression network analysis of OsWD40 family in rice

PubMed Central

2012-01-01

Background WD40 proteins represent a large family in eukaryotes, which have been involved in a broad spectrum of crucial functions. Systematic characterization and co-expression analysis of OsWD40 genes enable us to understand the networks of the WD40 proteins and their biological processes and gene functions in rice. Results In this study, we identify and analyze 200 potential OsWD40 genes in rice, describing their gene structures, genome localizations, and evolutionary relationship of each member. Expression profiles covering the whole life cycle in rice has revealed that transcripts of OsWD40 were accumulated differentially during vegetative and reproductive development and preferentially up or down-regulated in different tissues. Under phytohormone treatments, 25 OsWD40 genes were differentially expressed with treatments of one or more of the phytohormone NAA, KT, or GA3 in rice seedlings. We also used a combined analysis of expression correlation and Gene Ontology annotation to infer the biological role of the OsWD40 genes in rice. The results suggested that OsWD40 genes may perform their diverse functions by complex network, thus were predictive for understanding their biological pathways. The analysis also revealed that OsWD40 genes might interact with each other to take part in metabolic pathways, suggesting a more complex feedback network. Conclusions All of these analyses suggest that the functions of OsWD40 genes are diversified, which provide useful references for selecting candidate genes for further functional studies. PMID:22429805

Unsaturated flow processes in structurally-variable pathways in wildfire-affected soils and ash

NASA Astrophysics Data System (ADS)

Ebel, B. A.

2016-12-01

Prediction of flash flood and debris flow generation in wildfire-affected soils and ash hinges on understanding unsaturated flow processes. Water resources issues, such as groundwater recharge, also rely on our ability to quantify subsurface flow. Soil-hydraulic property data provide insight into unsaturated flow processes and timescales. A literature review and synthesis of existing data from the literature for wildfire-affected soils, including ash and unburned soils, facilitated calculating metrics and timescales of hydrologic response related to infiltration and surface runoff generation. Sorptivity (S) and the Green-Ampt wetting front parameter (Ψf) were significantly lower in burned soils compared to unburned soils, while field-saturated hydraulic conductivity (Kfs) was not significantly different. The magnitude and duration of the influence of capillarity was substantially reduced in burned soils, leading to faster ponding times in response to rainfall. Ash had large values of S and Kfs compared to unburned and burned soils but intermediate values of Ψf, suggesting that ash has long ponding times in response to rainfall. The ratio of S2/Kfs was nearly constant ( 100 mm) for unburned soils, but was more variable in burned soils. Post-wildfire changes in this ratio suggested that unburned soils had a balance between gravity and capillarity contributions to infiltration, which may depend on soil organic matter, while burning shifted infiltration more towards gravity contributions by reducing S. Taken together, the changes in post-wildfire soil-hydraulic properties increased the propensity for surface runoff generation and may have enhanced subsurface preferential flow through pathways altered by wildfire.

The effects of environmental physical factors on the microbial communities and the distribution of different CO2 fixation pathways in a limestone landscape

NASA Astrophysics Data System (ADS)

Wun, S. R.; Huang, T. Y.; Hsu, B. M.; Fan, C. W.

2017-12-01

We aimed to study the effects of physical factors on the relative abundance of bacteria and their preferential admissions of autotrophic CO2 fixation pathways after subjected to environmental long-term influence. The Narrow-Sky located in upper part of Takangshan is a small gulch of Pleistocene coralline limestone formation in southern Taiwan. The physical parameters such as illumination, humidity, and temperature were varied largely in habitats around the gulch, namely on the limestone wall at the opening of gulch, on the coordinate ground soil, on the wall inside the gulch, and the water drip from limestone wall. The total organic carbon was measured in solid samples to evaluate the biomass of the habitats. A metagenomic approach was carried out to reveal their microbial community structure. After the metagenomic library of operational taxonomic units (OTUs) was constructed, a BLAST search by "nomenclature of bacteria" instead of sequences between the OTU libraries and KEGG database was carried out to generate libraries of "model microbial communities", which the complete genomes of the entire bacterial populations were available. Our results showed the biomass of habitats in the opening of gulch was twice higher than the inside, suggesting the illumination played an important role in biosynthesis. In quantitative comparison in key enzymes of CO2 fixation pathways by model communities, 70% to 90% of bacteria possessed key enzymes of Fuchs-Holo cycle, while only 5% to 20% of bacteria contained key enzymes of Calvin-Benson cycle. The key enzymes for hydroxypropionate/ hydroxybutyrate and dicarboxylate/ 4-hydroxybutyrate cycles were not found in this study. In the water sample, approximate 10% of bacteria consisted of the key enzyme for Arnon-Buchanan cycle. Less than 2% of bacteria in all habitats take the reductive acetyl-CoA cycle for CO2 fixation. This study provides a novel method to study biosynthetic process of microbial communities in natural habitats.

Linking soil moisture balance and source-responsive models to estimate diffuse and preferential components of groundwater recharge

USGS Publications Warehouse

Cuthbert, M.O.; Mackay, R.; Nimmo, J.R.

2012-01-01

Results are presented of a detailed study into the vadose zone and shallow water table hydrodynamics of a field site in Shropshire, UK. A conceptual model is developed and tested using a range of numerical models, including a modified soil moisture balance model (SMBM) for estimating groundwater recharge in the presence of both diffuse and preferential flow components. Tensiometry reveals that the loamy sand topsoil wets up via macropore flow and subsequent redistribution of moisture into the soil matrix. Recharge does not occur until near-positive pressures are achieved at the top of the sandy glaciofluvial outwash material that underlies the topsoil, about 1 m above the water table. Once this occurs, very rapid water table rises follow. This threshold behaviour is attributed to the vertical discontinuity in the macropore system due to seasonal ploughing of the topsoil, and a lower permeability plough/iron pan restricting matrix flow between the topsoil and the lower outwash deposits. Although the wetting process in the topsoil is complex, a SMBM is shown to be effective in predicting the initiation of preferential flow from the base of the topsoil into the lower outwash horizon. The rapidity of the response at the water table and a water table rise during the summer period while flow gradients in the unsaturated profile were upward suggest that preferential flow is also occurring within the outwash deposits below the topsoil. A variation of the source-responsive model proposed by Nimmo (2010) is shown to reproduce the observed water table dynamics well in the lower outwash horizon when linked to a SMBM that quantifies the potential recharge from the topsoil. The results reveal new insights into preferential flow processes in cultivated soils and provide a useful and practical approach to accounting for preferential flow in studies of groundwater recharge estimation.

Stokes Approach to Preferential Flow at the Darcy-Scale

NASA Astrophysics Data System (ADS)

Germann, Peter; Bogner, Christina

2017-04-01

Preferential Flow in soils is fast, limited to infiltration and occupies but a small portion of porosity. However, how fast is it, how much water is involved, what is its flow rate, and how far is it carried? Supported with numerous measurements a Stokes approach to preferential flow provides the answers at the operational Darcy-scale. The approach to preferential flow in permeable media (pm) stresses momentum dissipation during viscous flow. Thus, a laminar water film percolates through a pm. The dynamic film is initially determined by the thickness F (m) and the specific contact area L (m2 m-3) per unit volume of the medium. Input to the medium's surface is a pulse with volume flux density q (ms-1) that starts and ends at times TB and TE. A specific pulse and the intrinsic properties of a pm determine F and L. A water content wave (WCW) envelops the spatio-temporal evolution of a water film. A WCW is completely described with a set of analytical relationships that are based on F, L, and the water's viscosity. The approach is an extension of Hagen-Poiseuille's law of flow in concentric conduits. It also evolves seamlessly from extending Darcy's law into non-saturated pm. Experimental determination of F and L follows either from drainage flow or from rapid soil moisture recordings during the passing of a WCW, for instance, with TDR-equipment. Parameters from numerous infiltration experiments in the field, in soil columns, in sand boxes, and lysimeters demonstrate the approach's broad applicability, thus framing the spatio-temporal extensions, velocities and volume flux densities of preferential flows. The specific contact area L is considered the locus of water, heat, particle and solute transfer between a WCW and the sessile parts of a pm. A recent analysis of delayed Br-breakthrough with respect to drainage flow supports the feasibility of the Stokes approach to preferential flow at the Darcy-scale. A perspective of modeling sequences of input pulses will conclude the presentation.

The inhibiting effect of dislocation helices on the stress-induced orientation of S' precipitates in Al–Cu–Mg alloy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guo, Xiaobin; Deng, Yunlai, E-mail: luckdeng@csu.edu.cn; State Key Laboratory of High Performance and Complex Manufacturing, Central South University, Changsha

The phenomenon of restrained stress-induced preferential orientation of S′ precipitates is investigated using a single-crystal of Al–1.23Cu–0.43 Mg alloy. Al–1.23Cu–0.43 Mg single-crystal specimens are subjected to stress aging, and the microstructure is analyzed by transmission electron microscopy (TEM). It is found that the stress-induced preferential orientation of S′ precipitates is restrained owing to the dislocations produced by a higher stress. The effect of dislocations on the oriented precipitates depends on the total length of the intersection lines for precipitate habit planes and dislocation glide planes. This investigation not only provides important insight into solving the anisotropy problem attributed to precipitationmore » strengthening, but also offers a benchmark for choosing the appropriate stress range in manufacturing of Al–Cu–Mg alloys. - Highlights: • Single crystals of an Al–Cu–Mg alloy were prepared for the investigations. • A phenomenon of restrained stress-induced preferential orientation of S′ precipitates was found. • The influence of dislocation helices on precipitation during stress-aging was studied. • Difference of orientation degree of S′ precipitates and θ′ precipitates was explained. • A basis for choosing the appropriate stress range in manufacturing of Al–Cu–Mg alloys is provided.« less

Multiple Export Mechanisms for mRNAs

PubMed Central

Delaleau, Mildred; Borden, Katherine L. B.

2015-01-01

Nuclear mRNA export plays an important role in gene expression. We describe the mechanisms of mRNA export including the importance of mRNP assembly, docking with the nuclear basket of the nuclear pore complex (NPC), transit through the central channel of the NPC and cytoplasmic release. We describe multiple mechanisms of mRNA export including NXF1 and CRM1 mediated pathways. Selective groups of mRNAs can be preferentially transported in order to respond to cellular stimuli. RNAs can be selected based on the presence of specific cis-acting RNA elements and binding of specific adaptor proteins. The role that dysregulation of this process plays in human disease is also discussed. PMID:26343730

Objective monitoring of mTOR inhibitor therapy by three-dimensional facial analysis.

PubMed

Baynam, Gareth S; Walters, Mark; Dawkins, Hugh; Bellgard, Matthew; Halbert, Anne R; Claes, Peter

2013-08-01

With advances in therapeutics for rare, genetic and syndromic diseases, there is an increasing need for objective assessments of phenotypic endpoints. These assessments will preferentially be high precision, non-invasive, non-irradiating, and relatively inexpensive and portable. We report a case of a child with an extensive lymphatic vascular malformation of the head and neck, treated with an mammalian target of Rapamycin (mTOR) inhibitor that was assessed using 3D facial analysis. This case illustrates that this technology is prospectively a cost-effective modality for treatment monitoring, and it supports that it may also be used for novel explorations of disease biology for conditions associated with disturbances in the mTOR, and interrelated, pathways.

Mn-silicide nanostructures aligned on massively parallel silicon nano-ribbons

NASA Astrophysics Data System (ADS)

De Padova, Paola; Ottaviani, Carlo; Ronci, Fabio; Colonna, Stefano; Olivieri, Bruno; Quaresima, Claudio; Cricenti, Antonio; Dávila, Maria E.; Hennies, Franz; Pietzsch, Annette; Shariati, Nina; Le Lay, Guy

2013-01-01

The growth of Mn nanostructures on a 1D grating of silicon nano-ribbons is investigated at atomic scale by means of scanning tunneling microscopy, low energy electron diffraction and core level photoelectron spectroscopy. The grating of silicon nano-ribbons represents an atomic scale template that can be used in a surface-driven route to control the combination of Si with Mn in the development of novel materials for spintronics devices. The Mn atoms show a preferential adsorption site on silicon atoms, forming one-dimensional nanostructures. They are parallel oriented with respect to the surface Si array, which probably predetermines the diffusion pathways of the Mn atoms during the process of nanostructure formation.

Mn-silicide nanostructures aligned on massively parallel silicon nano-ribbons.

PubMed

De Padova, Paola; Ottaviani, Carlo; Ronci, Fabio; Colonna, Stefano; Olivieri, Bruno; Quaresima, Claudio; Cricenti, Antonio; Dávila, Maria E; Hennies, Franz; Pietzsch, Annette; Shariati, Nina; Le Lay, Guy

2013-01-09

The growth of Mn nanostructures on a 1D grating of silicon nano-ribbons is investigated at atomic scale by means of scanning tunneling microscopy, low energy electron diffraction and core level photoelectron spectroscopy. The grating of silicon nano-ribbons represents an atomic scale template that can be used in a surface-driven route to control the combination of Si with Mn in the development of novel materials for spintronics devices. The Mn atoms show a preferential adsorption site on silicon atoms, forming one-dimensional nanostructures. They are parallel oriented with respect to the surface Si array, which probably predetermines the diffusion pathways of the Mn atoms during the process of nanostructure formation.

Evidence of a sewer vapor transport pathway at the USEPA vapor intrusion research duplex.

PubMed

McHugh, Thomas; Beckley, Lila; Sullivan, Terry; Lutes, Chris; Truesdale, Robert; Uppencamp, Rob; Cosky, Brian; Zimmerman, John; Schumacher, Brian

2017-11-15

The role of sewer lines as preferential pathways for vapor intrusion is poorly understood. Although the importance of sewer lines for volatile organic compound (VOC) transport has been documented at a small number of sites with vapor intrusion, sewer lines are not routinely sampled during most vapor intrusion investigations. We have used a tracer study and VOC concentration measurements to evaluate the role of the combined sanitary/storm sewer line in VOC transport at the USEPA vapor intrusion research duplex in Indianapolis, Indiana. The results from the tracer study demonstrated gas migration from the sewer main line into the duplex. The migration pathway appears to be complex and may include leakage from the sewer lateral at a location below the building foundation. Vapor samples collected from the sewer line demonstrated the presence of tetrachloroethene (PCE) and chloroform in the sewer main in front of the duplex and at multiple sample locations within the sewer line upstream of the duplex. These test results combined with results from the prior multi-year study of the duplex indicate that the sewer line plays an important role in transport of VOCs from the subsurface source to the immediate vicinity of the duplex building envelope. Copyright © 2017 Elsevier B.V. All rights reserved.

AMPK governs lineage specification through Tfeb-dependent regulation of lysosomes.

PubMed

Young, Nathan P; Kamireddy, Anwesh; Van Nostrand, Jeanine L; Eichner, Lillian J; Shokhirev, Maxim Nikolaievich; Dayn, Yelena; Shaw, Reuben J

2016-03-01

Faithful execution of developmental programs relies on the acquisition of unique cell identities from pluripotent progenitors, a process governed by combinatorial inputs from numerous signaling cascades that ultimately dictate lineage-specific transcriptional outputs. Despite growing evidence that metabolism is integrated with many molecular networks, how pathways that control energy homeostasis may affect cell fate decisions is largely unknown. Here, we show that AMP-activated protein kinase (AMPK), a central metabolic regulator, plays critical roles in lineage specification. Although AMPK-deficient embryonic stem cells (ESCs) were normal in the pluripotent state, these cells displayed profound defects upon differentiation, failing to generate chimeric embryos and preferentially adopting an ectodermal fate at the expense of the endoderm during embryoid body (EB) formation. AMPK(-/-) EBs exhibited reduced levels of Tfeb, a master transcriptional regulator of lysosomes, leading to diminished endolysosomal function. Remarkably, genetic loss of Tfeb also yielded endodermal defects, while AMPK-null ESCs overexpressing this transcription factor normalized their differential potential, revealing an intimate connection between Tfeb/lysosomes and germ layer specification. The compromised endolysosomal system resulting from AMPK or Tfeb inactivation blunted Wnt signaling, while up-regulating this pathway restored expression of endodermal markers. Collectively, these results uncover the AMPK pathway as a novel regulator of cell fate determination during differentiation. © 2016 Young et al.; Published by Cold Spring Harbor Laboratory Press.

Metabolic engineering of Corynebacterium crenatium for enhancing production of higher alcohols

PubMed Central

Su, Haifeng; Lin, Jiafu; Wang, GuangWei

2016-01-01

Biosynthesis approaches for the production of higher alcohols as a source of alternative fossil fuels have garnered increasing interest recently. However, there is little information available in the literature about using undirected whole-cell mutagenesis (UWCM) in vivo to improve higher alcohols production. In this study, for the first time, we approached this question from two aspects: first preferentially improving the capacity of expression host, and subsequently optimizing metabolic pathways using multiple genetic mutations to shift metabolic flux toward the biosynthetic pathway of target products to convert intermediate 2-keto acid compounds into diversified C4~C5 higher alcohols using UWCM in vivo, with the aim of improving the production. The results demonstrated the production of higher alcohols including isobutanol, 2-methyl-1-butanol, 3-methyl-1-butanol from glucose and duckweed under simultaneous saccharification and fermentation (SSF) scheme were higher based on the two aspects compared with only the use of wild-type stain as expression host. These findings showed that the improvement via UWCM in vivo in the two aspects for expression host and metabolic flux can facilitate the increase of higher alcohols production before using gene editing technology. Our work demonstrates that a multi-faceted approach for the engineering of novel synthetic pathways in microorganisms for improving biofuel production is feasible. PMID:27996038

Evidence of a sewer vapor transport pathway at the USEPA vapor intrusion research duplex

DOE PAGES

McHugh, Thomas; Beckley, Lila; Sullivan, Terry; ...

2017-04-26

We report the role of sewer lines as preferential pathways for vapor intrusion is poorly understood. Although the importance of sewer lines for volatile organic compound (VOC) transport has been documented at a small number of sites with vapor intrusion, sewer lines are not routinely sampled during most vapor intrusion investigations. We have used a tracer study and VOC concentration measurements to evaluate the role of the combined sanitary/storm sewer line in VOC transport at the USEPA vapor intrusion research duplex in Indianapolis, Indiana. The results from the tracer study demonstrated gas migration from the sewer main line into themore » duplex. The migration pathway appears to be complex and may include leakage from the sewer lateral at a location below the building foundation. Vapor samples collected from the sewer line demonstrated the presence of tetrachloroethene (PCE) and chloroform in the sewer main in front of the duplex and at multiple sample locations within the sewer line upstream of the duplex. Finally, these test results combined with results from the prior multi-year study of the duplex indicate that the sewer line plays an important role in transport of VOCs from the subsurface source to the immediate vicinity of the duplex building envelope.« less

Metabolic engineering of Corynebacterium crenatium for enhancing production of higher alcohols

NASA Astrophysics Data System (ADS)

Su, Haifeng; Lin, Jiafu; Wang, Guangwei

2016-12-01

Biosynthesis approaches for the production of higher alcohols as a source of alternative fossil fuels have garnered increasing interest recently. However, there is little information available in the literature about using undirected whole-cell mutagenesis (UWCM) in vivo to improve higher alcohols production. In this study, for the first time, we approached this question from two aspects: first preferentially improving the capacity of expression host, and subsequently optimizing metabolic pathways using multiple genetic mutations to shift metabolic flux toward the biosynthetic pathway of target products to convert intermediate 2-keto acid compounds into diversified C4~C5 higher alcohols using UWCM in vivo, with the aim of improving the production. The results demonstrated the production of higher alcohols including isobutanol, 2-methyl-1-butanol, 3-methyl-1-butanol from glucose and duckweed under simultaneous saccharification and fermentation (SSF) scheme were higher based on the two aspects compared with only the use of wild-type stain as expression host. These findings showed that the improvement via UWCM in vivo in the two aspects for expression host and metabolic flux can facilitate the increase of higher alcohols production before using gene editing technology. Our work demonstrates that a multi-faceted approach for the engineering of novel synthetic pathways in microorganisms for improving biofuel production is feasible.

Tuning complement activation and pathway through controlled molecular architecture of dextran chains in nanoparticle corona.

PubMed

Coty, Jean-Baptiste; Eleamen Oliveira, Elquio; Vauthier, Christine

2017-11-05

The understanding of complement activation by nanomaterials is a key to a rational design of safe and efficient nanomedicines. This work proposed a systematic study investigating how molecular design of nanoparticle coronas made of dextran impacts on mechanisms that trigger complement activation. The nanoparticles used for this work consisted of dextran-coated poly(isobutylcyanoacrylate) (PIBCA) nanoparticles have already been thoroughly characterized. Their different capacity to trigger complement activation established on the cleavage of the protein C3 was also already described making these nanoparticles good models to investigate the relation between the molecular feature of their corona and the mechanism by which they triggered complement activation. Results of this new study show that complement activation pathways can be selected by distinct architectures formed by dextran chains composing the nanoparticle corona. Assumptions that explain the relation between complement activation mechanisms triggered by the nanoparticles and the nanoparticle corona molecular feature were proposed. These results are of interest to better understand how the design of dextran-coated nanomaterials will impact interactions with the complement system. It can open perspectives with regard to the selection of a preferential complement activation pathway or prevent the nanoparticles to activate the complement system, based on a rational choice of the corona configuration. Copyright © 2017 Elsevier B.V. All rights reserved.

Evidence of a sewer vapor transport pathway at the USEPA vapor intrusion research duplex

DOE Office of Scientific and Technical Information (OSTI.GOV)

McHugh, Thomas; Beckley, Lila; Sullivan, Terry

We report the role of sewer lines as preferential pathways for vapor intrusion is poorly understood. Although the importance of sewer lines for volatile organic compound (VOC) transport has been documented at a small number of sites with vapor intrusion, sewer lines are not routinely sampled during most vapor intrusion investigations. We have used a tracer study and VOC concentration measurements to evaluate the role of the combined sanitary/storm sewer line in VOC transport at the USEPA vapor intrusion research duplex in Indianapolis, Indiana. The results from the tracer study demonstrated gas migration from the sewer main line into themore » duplex. The migration pathway appears to be complex and may include leakage from the sewer lateral at a location below the building foundation. Vapor samples collected from the sewer line demonstrated the presence of tetrachloroethene (PCE) and chloroform in the sewer main in front of the duplex and at multiple sample locations within the sewer line upstream of the duplex. Finally, these test results combined with results from the prior multi-year study of the duplex indicate that the sewer line plays an important role in transport of VOCs from the subsurface source to the immediate vicinity of the duplex building envelope.« less

HIV-2 integrase polymorphisms and longitudinal genotypic analysis of HIV-2 infected patients failing a raltegravir-containing regimen.

PubMed

Cavaco-Silva, Joana; Abecasis, Ana; Miranda, Ana Cláudia; Poças, José; Narciso, Jorge; Águas, Maria João; Maltez, Fernando; Almeida, Isabel; Germano, Isabel; Diniz, António; Gonçalves, Maria de Fátima; Gomes, Perpétua; Cunha, Celso; Camacho, Ricardo Jorge

2014-01-01

To characterize the HIV-2 integrase gene polymorphisms and the pathways to resistance of HIV-2 patients failing a raltegravir-containing regimen, we studied 63 integrase strand transfer inhibitors (INSTI)-naïve patients, and 10 heavily pretreated patients exhibiting virological failure while receiving a salvage raltegravir-containing regimen. All patients were infected by HIV-2 group A. 61.4% of the integrase residues were conserved, including the catalytic motif residues. No INSTI-major resistance mutations were detected in the virus population from naïve patients, but two amino acids that are secondary resistance mutations to INSTIs in HIV-1 were observed. The 10 raltegravir-experienced patients exhibited resistance mutations via three main genetic pathways: N155H, Q148R, and eventually E92Q - T97A. The 155 pathway was preferentially used (7/10 patients). Other mutations associated to raltegravir resistance in HIV-1 were also observed in our HIV-2 population (V151I and D232N), along with several novel mutations previously unreported. Data retrieved from this study should help build a more robust HIV-2-specific algorithm for the genotypic interpretation of raltegravir resistance, and contribute to improve the clinical monitoring of HIV-2-infected patients.

Academic performance of young competitive swimmers is associated with physical activity intensity and its predominant metabolic pathway: a pilot study.

PubMed

Ayan, Carlos; Cancela Carral, Jose; Montero, Carlos

2014-09-01

The relationship between physical activity (PA) and academic performance has been previously studied. However, there is a need to determine if the intensity of the PA performed and its predominant metabolic pathway show any degree of association with the academic achievement. Cross-sectional data were gathered from Spanish young competitive swimmers. Academic achievement was based on individual grades for each student; the PA level was measured by means of the Physical Activity Questionnaire for Adolescents. Swimmers were classified according to the preferential energetic cost of the event in which they competed. A total of 254 swimmers finished the study; 62.8% of them were considered moderate active. The statistical analysis showed that the higher the level of PA performed, the better the average grades achieved. This relationship was significant among the girls (P = .04). No significant differences were found regarding the influence of the kind of swimming event. However, taking part in aerobic events proved to have a significant influence on the academic achievement for girls (P = .01). The link between academic achievement and PA depends on the intensity in which the PA is performed, as well as on its predominant metabolic pathway. However, such associations seem to be gender-dependent.

Syringyl lignin is unaltered by severe sinapyl alcohol dehydrogenase suppression in tobacco.

PubMed

Barakate, Abdellah; Stephens, Jennifer; Goldie, Alison; Hunter, William N; Marshall, David; Hancock, Robert D; Lapierre, Catherine; Morreel, Kris; Boerjan, Wout; Halpin, Claire

2011-12-01

The manipulation of lignin could, in principle, facilitate efficient biofuel production from plant biomass. Despite intensive study of the lignin pathway, uncertainty exists about the enzyme catalyzing the last step in syringyl (S) monolignol biosynthesis, the reduction of sinapaldehyde to sinapyl alcohol. Traditional schemes of the pathway suggested that both guaiacyl (G) and S monolignols are produced by a single substrate-versatile enzyme, cinnamyl alcohol dehydrogenase (CAD). This was challenged by the discovery of a novel sinapyl alcohol dehydrogenase (SAD) that preferentially uses sinapaldehyde as a substrate and that was claimed to regulate S lignin biosynthesis in angiosperms. Consequently, most pathway schemes now show SAD (or SAD and CAD) at the sinapaldehyde reduction step, although functional evidence is lacking. We cloned SAD from tobacco (Nicotiana tabacum) and suppressed it in transgenic plants using RNA interference-inducing vectors. Characterization of lignin in the woody stems shows no change to content, composition, or structure, and S lignin is normal. By contrast, plants additionally suppressed in CAD have changes to lignin structure and S:G ratio and have increased sinapaldehyde in lignin, similar to plants suppressed in CAD alone. These data demonstrate that CAD, not SAD, is the enzyme responsible for S lignin biosynthesis in woody angiosperm xylem.

Syringyl Lignin Is Unaltered by Severe Sinapyl Alcohol Dehydrogenase Suppression in Tobacco[W

PubMed Central

Barakate, Abdellah; Stephens, Jennifer; Goldie, Alison; Hunter, William N.; Marshall, David; Hancock, Robert D.; Lapierre, Catherine; Morreel, Kris; Boerjan, Wout; Halpin, Claire

2011-01-01

The manipulation of lignin could, in principle, facilitate efficient biofuel production from plant biomass. Despite intensive study of the lignin pathway, uncertainty exists about the enzyme catalyzing the last step in syringyl (S) monolignol biosynthesis, the reduction of sinapaldehyde to sinapyl alcohol. Traditional schemes of the pathway suggested that both guaiacyl (G) and S monolignols are produced by a single substrate-versatile enzyme, cinnamyl alcohol dehydrogenase (CAD). This was challenged by the discovery of a novel sinapyl alcohol dehydrogenase (SAD) that preferentially uses sinapaldehyde as a substrate and that was claimed to regulate S lignin biosynthesis in angiosperms. Consequently, most pathway schemes now show SAD (or SAD and CAD) at the sinapaldehyde reduction step, although functional evidence is lacking. We cloned SAD from tobacco (Nicotiana tabacum) and suppressed it in transgenic plants using RNA interference–inducing vectors. Characterization of lignin in the woody stems shows no change to content, composition, or structure, and S lignin is normal. By contrast, plants additionally suppressed in CAD have changes to lignin structure and S:G ratio and have increased sinapaldehyde in lignin, similar to plants suppressed in CAD alone. These data demonstrate that CAD, not SAD, is the enzyme responsible for S lignin biosynthesis in woody angiosperm xylem. PMID:22158465

HIV-2 Integrase Polymorphisms and Longitudinal Genotypic Analysis of HIV-2 Infected Patients Failing a Raltegravir-Containing Regimen

PubMed Central

Cavaco-Silva, Joana; Abecasis, Ana; Miranda, Ana Cláudia; Poças, José; Narciso, Jorge; Águas, Maria João; Maltez, Fernando; Almeida, Isabel; Germano, Isabel; Diniz, António; Gonçalves, Maria de Fátima; Gomes, Perpétua; Cunha, Celso; Camacho, Ricardo Jorge

2014-01-01

To characterize the HIV-2 integrase gene polymorphisms and the pathways to resistance of HIV-2 patients failing a raltegravir-containing regimen, we studied 63 integrase strand transfer inhibitors (INSTI)-naïve patients, and 10 heavily pretreated patients exhibiting virological failure while receiving a salvage raltegravir-containing regimen. All patients were infected by HIV-2 group A. 61.4% of the integrase residues were conserved, including the catalytic motif residues. No INSTI-major resistance mutations were detected in the virus population from naïve patients, but two amino acids that are secondary resistance mutations to INSTIs in HIV-1 were observed. The 10 raltegravir-experienced patients exhibited resistance mutations via three main genetic pathways: N155H, Q148R, and eventually E92Q - T97A. The 155 pathway was preferentially used (7/10 patients). Other mutations associated to raltegravir resistance in HIV-1 were also observed in our HIV-2 population (V151I and D232N), along with several novel mutations previously unreported. Data retrieved from this study should help build a more robust HIV-2-specific algorithm for the genotypic interpretation of raltegravir resistance, and contribute to improve the clinical monitoring of HIV-2-infected patients. PMID:24681625

Preferential sites for InAsP/InP quantum wire nucleation using molecular dynamics

NASA Astrophysics Data System (ADS)

Nuñez-Moraleda, Bernardo; Pizarro, Joaquin; Guerrero, Elisa; Guerrero-Lebrero, Maria P.; Yáñez, Andres; Molina, Sergio Ignacio; Galindo, Pedro Luis

2014-11-01

In this paper, stress fields at the surface of the capping layer of self-assembled InAsP quantum wires grown on an InP (001) substrate have been determined from atomistic models using molecular dynamics and Stillinger-Weber potentials. To carry out these calculations, the quantum wire compositional distribution was extracted from previous works, where the As and P distributions were determined by electron energy loss spectroscopy and high-resolution aberration-corrected Z-contrast imaging. Preferential sites for the nucleation of wires on the surface of the capping layer were studied and compared with (i) previous simulations using finite element analysis to solve anisotropic elastic theory equations and (ii) experimentally measured locations of stacked wires. Preferential nucleation sites of stacked wires were determined by the maximum stress location at the MD model surface in good agreement with experimental results and those derived from finite element analysis. This indicates that MD simulations based on empirical potentials provide a suitable and flexible tool to study strain dependent atom processes.

A novel assay reveals preferential binding between Rabs, kinesins, and specific endosomal subpopulations

PubMed Central

Bentley, Marvin; Decker, Helena; Luisi, Julie

2015-01-01

Identifying the proteins that regulate vesicle trafficking is a fundamental problem in cell biology. In this paper, we introduce a new assay that involves the expression of an FKBP12-rapamycin–binding domain–tagged candidate vesicle-binding protein, which can be inducibly linked to dynein or kinesin. Vesicles can be labeled by any convenient method. If the candidate protein binds the labeled vesicles, addition of the linker drug results in a predictable, highly distinctive change in vesicle localization. This assay generates robust and easily interpretable results that provide direct experimental evidence of binding between a candidate protein and the vesicle population of interest. We used this approach to compare the binding of Kinesin-3 family members with different endosomal populations. We found that KIF13A and KIF13B bind preferentially to early endosomes and that KIF1A and KIF1Bβ bind preferentially to late endosomes and lysosomes. This assay may have broad utility for identifying the trafficking proteins that bind to different vesicle populations. PMID:25624392

The application of in situ analytical transmission electron microscopy to the study of preferential intergranular oxidation in Alloy 600.

PubMed

Burke, M G; Bertali, G; Prestat, E; Scenini, F; Haigh, S J

2017-05-01

In situ analytical transmission electron microscopy (TEM) can provide a unique perspective on dynamic reactions in a variety of environments, including liquids and gases. In this study, in situ analytical TEM techniques have been applied to examine the localised oxidation reactions that occur in a Ni-Cr-Fe alloy, Alloy 600, using a gas environmental cell at elevated temperatures. The initial stages of preferential intergranular oxidation, shown to be an important precursor phenomenon for intergranular stress corrosion cracking in pressurized water reactors (PWRs), have been successfully identified using the in situ approach. Furthermore, the detailed observations correspond to the ex situ results obtained from bulk specimens tested in hydrogenated steam and in high temperature PWR primary water. The excellent agreement between the in situ and ex situ oxidation studies demonstrates that this approach can be used to investigate the initial stages of preferential intergranular oxidation relevant to nuclear power systems. Copyright © 2016 Elsevier B.V. All rights reserved.

How to Enhance Gas Removal from Porous Electrodes?

PubMed Central

Kadyk, Thomas; Bruce, David; Eikerling, Michael

2016-01-01

This article presents a structure-based modeling approach to optimize gas evolution at an electrolyte-flooded porous electrode. By providing hydrophobic islands as preferential nucleation sites on the surface of the electrode, it is possible to nucleate and grow bubbles outside of the pore space, facilitating their release into the electrolyte. Bubbles that grow at preferential nucleation sites act as a sink for dissolved gas produced in electrode reactions, effectively suctioning it from the electrolyte-filled pores. According to the model, high oversaturation is necessary to nucleate bubbles inside of the pores. The high oversaturation allows establishing large concentration gradients in the pores that drive a diffusion flux towards the preferential nucleation sites. This diffusion flux keeps the pores bubble-free, avoiding deactivation of the electrochemically active surface area of the electrode as well as mechanical stress that would otherwise lead to catalyst degradation. The transport regime of the dissolved gas, viz. diffusion control vs. transfer control at the liquid-gas interface, determines the bubble growth law. PMID:28008914

Information filtering via preferential diffusion.

PubMed

Lü, Linyuan; Liu, Weiping

2011-06-01

Recommender systems have shown great potential in addressing the information overload problem, namely helping users in finding interesting and relevant objects within a huge information space. Some physical dynamics, including the heat conduction process and mass or energy diffusion on networks, have recently found applications in personalized recommendation. Most of the previous studies focus overwhelmingly on recommendation accuracy as the only important factor, while overlooking the significance of diversity and novelty that indeed provide the vitality of the system. In this paper, we propose a recommendation algorithm based on the preferential diffusion process on a user-object bipartite network. Numerical analyses on two benchmark data sets, MovieLens and Netflix, indicate that our method outperforms the state-of-the-art methods. Specifically, it can not only provide more accurate recommendations, but also generate more diverse and novel recommendations by accurately recommending unpopular objects.

Information filtering via preferential diffusion

NASA Astrophysics Data System (ADS)

Lü, Linyuan; Liu, Weiping

2011-06-01

Recommender systems have shown great potential in addressing the information overload problem, namely helping users in finding interesting and relevant objects within a huge information space. Some physical dynamics, including the heat conduction process and mass or energy diffusion on networks, have recently found applications in personalized recommendation. Most of the previous studies focus overwhelmingly on recommendation accuracy as the only important factor, while overlooking the significance of diversity and novelty that indeed provide the vitality of the system. In this paper, we propose a recommendation algorithm based on the preferential diffusion process on a user-object bipartite network. Numerical analyses on two benchmark data sets, MovieLens and Netflix, indicate that our method outperforms the state-of-the-art methods. Specifically, it can not only provide more accurate recommendations, but also generate more diverse and novel recommendations by accurately recommending unpopular objects.

Efficiency of a borehole seal by means of pre-compacted bentonite blocks

NASA Astrophysics Data System (ADS)

Van Geet, M.; Volckaert, G.; Bastiaens, W.; Maes, N.; Weetjens, E.; Sillen, X.; Vallejan, B.; Gens, A.

The backfilling and sealing of shafts and galleries is an essential part of the design of underground repositories for high-level radioactive waste. Part of the EC funded project RESEAL studied the feasibility of sealing off a borehole in plastic Boom Clay by means of pre-compacted bentonite blocks. Two bentonites, namely the FoCa and Serrata clay, have been used. Based on laboratory tests, the bentonite blocks had an initial dry density of about 1.8 g/cm 3 to obtain a swelling pressure of about 4.4 MPa, corresponding to the in situ lithostatic stress, at full saturation. The set-up was equipped with several sensors to follow-up the behaviour of the seal and the surrounding host rock during hydration. Full saturation was reached after five months and was mainly reached by natural hydration. Swelling pressure was lower than originally foreseen due to the slow reconsolidation of the host rock. Later on, the efficiency of the seal with respect to water, gas and radionuclide migration was tested. The in situ measured permeability of the seals was about 5 × 10 -13 m/s. A gas breakthrough experiment did not show any preferential gas migration through the seal. No evidences of a preferential pathway could be detected from 125I tracer test results.

Can a fractured caprock self-heal?

NASA Astrophysics Data System (ADS)

Elkhoury, Jean E.; Detwiler, Russell L.; Ameli, Pasha

2015-05-01

The ability of geologic seals to prevent leakage of fluids injected into the deep subsurface is critical for mitigating risks associated with greenhouse-gas sequestration and natural-gas production. Fractures caused by tectonic or injection-induced stresses create potential leakage pathways that may be further enhanced by mineral dissolution. We present results from reactive-flow experiments in fractured caprock (dolomitic anhydrite), where additional dissolution occurs in the rock matrix adjacent to the fracture surfaces. Preferential dissolution of anhydrite left a compacted layer of dolomite in the fractures. At lower flow rate, rock-fluid reactions proceeded to near equilibrium within the fracture with preferential flow paths persisting over the 6-month duration of the experiment and a negligible change in permeability. At higher flow rate, permeability decreased by a dramatic two orders of magnitude. This laboratory-scale observation of self-healing argues against the likelihood of runaway permeability growth in fractured porous caprock composed of minerals with different solubilities and reaction kinetics. However, scaling arguments suggest that at larger length scales this self-healing process may be offset by the formation of dissolution channels. Our results have relevance beyond the greenhouse-gas sequestration problem. Chemical disequilibrium at waste injection sites and in hydrothermal reservoirs will lead to reactive flows that may also significantly alter formation permeability.

Functional Differentiation of Bundle Sheath and Mesophyll Maize Chloroplasts Determined by Comparative ProteomicsW⃞

PubMed Central

Majeran, Wojciech; Cai, Yang; Sun, Qi; van Wijk, Klaas J.

2005-01-01

Chloroplasts of maize (Zea mays) leaves differentiate into specific bundle sheath (BS) and mesophyll (M) types to accommodate C4 photosynthesis. Consequences for other plastid functions are not well understood but are addressed here through a quantitative comparative proteome analysis of purified M and BS chloroplast stroma. Three independent techniques were used, including cleavable stable isotope coded affinity tags. Enzymes involved in lipid biosynthesis, nitrogen import, and tetrapyrrole and isoprenoid biosynthesis are preferentially located in the M chloroplasts. By contrast, enzymes involved in starch synthesis and sulfur import preferentially accumulate in BS chloroplasts. The different soluble antioxidative systems, in particular peroxiredoxins, accumulate at higher levels in M chloroplasts. We also observed differential accumulation of proteins involved in expression of plastid-encoded proteins (e.g., EF-Tu, EF-G, and mRNA binding proteins) and thylakoid formation (VIPP1), whereas others were equally distributed. Enzymes related to the C4 shuttle, the carboxylation and regeneration phase of the Calvin cycle, and several regulators (e.g., CP12) distributed as expected. However, enzymes involved in triose phosphate reduction and triose phosphate isomerase are primarily located in the M chloroplasts, indicating that the M-localized triose phosphate shuttle should be viewed as part of the BS-localized Calvin cycle, rather than a parallel pathway. PMID:16243905

Calreticulin mutation-specific immunostaining in myeloproliferative neoplasms: pathogenetic insight and diagnostic value

PubMed Central

Vannucchi, A M; Rotunno, G; Bartalucci, N; Raugei, G; Carrai, V; Balliu, M; Mannarelli, C; Pacilli, A; Calabresi, L; Fjerza, R; Pieri, L; Bosi, A; Manfredini, R; Guglielmelli, P

2014-01-01

Mutations in the gene calreticulin (CALR) occur in the majority of JAK2- and MPL-unmutated patients with essential thrombocythemia (ET) and primary myelofibrosis (PMF); identifying CALR mutations contributes to the diagnostic pathway of ET and PMF. CALR mutations are heterogeneous spanning over the exon 9, but all result in a novel common protein C terminus. We developed a polyclonal antibody against a 17-amino-acid peptide derived from mutated calreticulin that was used for immunostaining of bone marrow biopsies. We show that this antibody specifically recognized patients harboring different types of CALR mutation with no staining in healthy controls and JAK2- or MPL-mutated ET and PMF. The labeling was mostly localized in megakaryocytes, whereas myeloid and erythroid cells showed faint staining, suggesting a preferential expression of calreticulin in megakaryocytes. Megakaryocytic-restricted expression of calreticulin was also demonstrated using an antibody against wild-type calreticulin and by measuring the levels of calreticulin RNA by gene expression analysis. Immunostaining using an antibody specific for mutated calreticulin may become a rapid, simple and cost-effective method for identifying CALR-mutated patients complementing molecular analysis; furthermore, the labeling pattern supports the preferential expansion of megakaryocytic cell lineage as a result of CALR mutation in an immature hematopoietic stem cell. PMID:24618731

The Role of Spatial Dispersion of Repolarization in Inherited and Acquired Sudden Cardiac Death Syndromes

PubMed Central

Antzelevitch, Charles

2007-01-01

This review examines the role of spatial electrical heterogeneity within ventricular myocardium on the function of the heart in health and disease. The cellular basis for transmural dispersion of repolarization (TDR) is reviewed and the hypothesis that amplification of spatial dispersion of repolarization underlies the development of life-threatening ventricular arrhythmias associated with inherited ion channelopathies is evaluated. The role of TDR in the long QT, short QT and Brugada syndromes as well as catecholaminergic polymorphic ventricular tachycardia (CPVT) are critically examined. In the long QT Syndrome, amplification of TDR is often secondary to preferential prolongation of the action potential duration (APD) of M cells, whereas in the Brugada Syndrome, it is thought to be due to selective abbreviation of the APD of right ventricular (RV) epicardium. Preferential abbreviation of APD of either endocardium or epicardium appears to be responsible for amplification of TDR in the short QT syndrome. In catecholaminergic polymorphic VT, reversal of the direction of activation of the ventricular wall is responsible for the increase in TDR. In conclusion, the long QT, short QT, Brugada and catecholaminergic polymorphic VT syndromes are pathologies with very different phenotypes and etiologies, but which share a common final pathway in causing sudden cardiac death. PMID:17586620

Antitumor activity and mechanism of action of the cyclopenta[b]benzofuran, silvestrol.

PubMed

Cencic, Regina; Carrier, Marilyn; Galicia-Vázquez, Gabriela; Bordeleau, Marie-Eve; Sukarieh, Rami; Bourdeau, Annie; Brem, Brigitte; Teodoro, Jose G; Greger, Harald; Tremblay, Michel L; Porco, John A; Pelletier, Jerry

2009-01-01

Flavaglines are a family of natural products from the genus Aglaia that exhibit anti-cancer activity in vitro and in vivo and inhibit translation initiation. They have been shown to modulate the activity of eIF4A, the DEAD-box RNA helicase subunit of the eukaryotic initiation factor (eIF) 4F complex, a complex that stimulates ribosome recruitment during translation initiation. One flavagline, silvestrol, is capable of modulating chemosensitivity in a mechanism-based mouse model. Among a number of flavagline family members tested herein, we find that silvestrol is the more potent translation inhibitor among these. We find that silvestrol impairs the ribosome recruitment step of translation initiation by affecting the composition of the eukaryotic initiation factor (eIF) 4F complex. We show that silvestrol exhibits significant anticancer activity in human breast and prostate cancer xenograft models, and that this is associated with increased apoptosis, decreased proliferation, and inhibition of angiogenesis. We demonstrate that targeting translation by silvestrol results in preferential inhibition of weakly initiating mRNAs. Our results indicate that silvestrol is a potent anti-cancer compound in vivo that exerts its activity by affecting survival pathways as well as angiogenesis. We propose that silvestrol mediates its effects by preferentially inhibiting translation of malignancy-related mRNAs. Silvestrol appears to be well tolerated in animals.

Preliminary Test Results of Heshe Hydrogeological Experimental Well Station in Taiwan

NASA Astrophysics Data System (ADS)

Chuang, P.; Liu, C.; Lin, M.; Chan, W.; Lee, T.; Chia, Y.; Teng, M.; Liu, C.

2013-12-01

Safe disposal of radioactive waste is a critical issue for the development of nuclear energy. The design of final disposal system is based on the concept of multiple barriers which integrate the natural barriers and engineering barriers for long-term isolation of radioactive wastes. As groundwater is the major medium that can transport radionuclides to our living environment, it is essential to characterize groundwater flow at the disposal site. Taiwan is located at the boundary between the Eurasian plate and the Philippine Sea plate. Geologic formations are often fractured due to tectonic compression and extension. In this study, a well station for the research and development of hydrogeological techniques was established at the Experimental Forest of the National Taiwan University in central Taiwan. There are 10 testing wells, ranging in depth from 25 m to 100 m, at the station. The bedrock beneath the regolith is highly fractured mudstone. As fracture is the preferential pathway of the groundwater flow, the focus of in-situ tests is to investigate the location of permeable fractures and the connection of permeable fractures. Several field tests have been conducted, including geophysical logging, heat-pulse flowmeter, hydraulic test, tracer test and double packer test, for the development of advanced technologies to detect the preferential groundwater flow in fractured rocks.

The large-scale investigation of gene expression in Leymus chinensis stigmas provides a valuable resource for understanding the mechanisms of poaceae self-incompatibility.

PubMed

Zhou, Qingyuan; Jia, Junting; Huang, Xing; Yan, Xueqing; Cheng, Liqin; Chen, Shuangyan; Li, Xiaoxia; Peng, Xianjun; Liu, Gongshe

2014-05-26

Many Poaceae species show a gametophytic self-incompatibility (GSI) system, which is controlled by at least two independent and multiallelic loci, S and Z. Until currently, the gene products for S and Z were unknown. Grass SI plant stigmas discriminate between pollen grains that land on its surface and support compatible pollen tube growth and penetration into the stigma, whereas recognizing incompatible pollen and thus inhibiting pollination behaviors. Leymus chinensis (Trin.) Tzvel. (sheepgrass) is a Poaceae SI species. A comprehensive analysis of sheepgrass stigma transcriptome may provide valuable information for understanding the mechanism of pollen-stigma interactions and grass SI. The transcript abundance profiles of mature stigmas, mature ovaries and leaves were examined using high-throughput next generation sequencing technology. A comparative transcriptomic analysis of these tissues identified 1,025 specifically or preferentially expressed genes in sheepgrass stigmas. These genes contained a significant proportion of genes predicted to function in cell-cell communication and signal transduction. We identified 111 putative transcription factors (TFs) genes and the most abundant groups were MYB, C2H2, C3H, FAR1, MADS. Comparative analysis of the sheepgrass, rice and Arabidopsis stigma-specific or preferential datasets showed broad similarities and some differences in the proportion of genes in the Gene Ontology (GO) functional categories. Potential SI candidate genes identified in other grasses were also detected in the sheepgrass stigma-specific or preferential dataset. Quantitative real-time PCR experiments validated the expression pattern of stigma preferential genes including homologous grass SI candidate genes. This study represents the first large-scale investigation of gene expression in the stigmas of an SI grass species. We uncovered many notable genes that are potentially involved in pollen-stigma interactions and SI mechanisms, including genes encoding receptor-like protein kinases (RLK), CBL (calcineurin B-like proteins) interacting protein kinases, calcium-dependent protein kinase, expansins, pectinesterase, peroxidases and various transcription factors. The availability of a pool of stigma-specific or preferential genes for L. chinensis offers an opportunity to elucidate the mechanisms of SI in Poaceae.

Cholinergic left-right asymmetry in the habenulo-interpeduncular pathway.

PubMed

Hong, Elim; Santhakumar, Kirankumar; Akitake, Courtney A; Ahn, Sang Jung; Thisse, Christine; Thisse, Bernard; Wyart, Claire; Mangin, Jean-Marie; Halpern, Marnie E

2013-12-24

The habenulo-interpeduncular pathway, a highly conserved cholinergic system, has emerged as a valuable model to study left-right asymmetry in the brain. In larval zebrafish, the bilaterally paired dorsal habenular nuclei (dHb) exhibit prominent left-right differences in their organization, gene expression, and connectivity, but their cholinergic nature was unclear. Through the discovery of a duplicated cholinergic gene locus, we now show that choline acetyltransferase and vesicular acetylcholine transporter homologs are preferentially expressed in the right dHb of larval zebrafish. Genes encoding the nicotinic acetylcholine receptor subunits α2 and β4 are transcribed in the target interpeduncular nucleus (IPN), suggesting that the asymmetrical cholinergic pathway is functional. To confirm this, we activated channelrhodopsin-2 specifically in the larval dHb and performed whole-cell patch-clamp recording of IPN neurons. The response to optogenetic or electrical stimulation of the right dHb consisted of an initial fast glutamatergic excitatory postsynaptic current followed by a slow-rising cholinergic current. In adult zebrafish, the dHb are divided into discrete cholinergic and peptidergic subnuclei that differ in size between the left and right sides of the brain. After exposing adults to nicotine, fos expression was activated in subregions of the IPN enriched for specific nicotinic acetylcholine receptor subunits. Our studies of the newly identified cholinergic gene locus resolve the neurotransmitter identity of the zebrafish habenular nuclei and reveal functional asymmetry in a major cholinergic neuromodulatory pathway of the vertebrate brain.

SP600125 has a remarkable anticancer potential against undifferentiated thyroid cancer through selective action on ROCK and p53 pathways.

PubMed

Grassi, Elisa Stellaria; Vezzoli, Valeria; Negri, Irene; Lábadi, Árpád; Fugazzola, Laura; Vitale, Giovanni; Persani, Luca

2015-11-03

Thyroid cancer is the most common endocrine malignancy with increasing incidence worldwide.The majority of thyroid cancer cases are well differentiated with favorable outcome. However, undifferentiated thyroid cancers are one of the most lethal human malignancies because of their invasiveness, metastatization and refractoriness even to the most recently developed therapies.In this study we show for the first time a significant hyperactivation of ROCK/HDAC6 pathway in thyroid cancer tissues, and its negative correlation with p53 DNA binding ability.We demonstrate that a small compound, SP600125 (SP), is able to induce cell death selectively in undifferentiated thyroid cancer cell lines by specifically acting on the pathogenic pathways of cancer development. In detail, SP acts on the ROCK/HDAC6 pathway involved in dedifferentiation and invasiveness of undifferentiated human cancers, by restoring its physiological activity level. As main consequence, cancer cell migration is inhibited and, at the same time, cell death is induced through the mitotic catastrophe. Moreover, SP exerts a preferential action on the mutant p53 by increasing its DNA binding ability. In TP53-mutant cells that survive mitotic catastrophe this process results in p21 induction and eventually lead to premature senescence. In conclusion, SP has been proved to be able to simultaneously block cell replication and migration, the two main processes involved in cancer development and dissemination, making it an ideal candidate for developing new drugs against anaplastic thyroid cancer.

The Pathways for Intelligible Speech: Multivariate and Univariate Perspectives

PubMed Central

Evans, S.; Kyong, J.S.; Rosen, S.; Golestani, N.; Warren, J.E.; McGettigan, C.; Mourão-Miranda, J.; Wise, R.J.S.; Scott, S.K.

2014-01-01

An anterior pathway, concerned with extracting meaning from sound, has been identified in nonhuman primates. An analogous pathway has been suggested in humans, but controversy exists concerning the degree of lateralization and the precise location where responses to intelligible speech emerge. We have demonstrated that the left anterior superior temporal sulcus (STS) responds preferentially to intelligible speech (Scott SK, Blank CC, Rosen S, Wise RJS. 2000. Identification of a pathway for intelligible speech in the left temporal lobe. Brain. 123:2400–2406.). A functional magnetic resonance imaging study in Cerebral Cortex used equivalent stimuli and univariate and multivariate analyses to argue for the greater importance of bilateral posterior when compared with the left anterior STS in responding to intelligible speech (Okada K, Rong F, Venezia J, Matchin W, Hsieh IH, Saberi K, Serences JT,Hickok G. 2010. Hierarchical organization of human auditory cortex: evidence from acoustic invariance in the response to intelligible speech. 20: 2486–2495.). Here, we also replicate our original study, demonstrating that the left anterior STS exhibits the strongest univariate response and, in decoding using the bilateral temporal cortex, contains the most informative voxels showing an increased response to intelligible speech. In contrast, in classifications using local “searchlights” and a whole brain analysis, we find greater classification accuracy in posterior rather than anterior temporal regions. Thus, we show that the precise nature of the multivariate analysis used will emphasize different response profiles associated with complex sound to speech processing. PMID:23585519

Insights to Engineered Geothermal System Performance Using Gringarten-Witherspoon-Ohnishi Analytical Solutions and Fracture Network Models

NASA Astrophysics Data System (ADS)

Doe, T.; McLaren, R.; Finilla, A.

2017-12-01

An enduring legacy of Paul Witherspoon and his students and colleagues has been both the development of geothermal energy and the bases of modern fractured-rock hydrogeology. One of the seminal contributions to the geothermal field was Gringarten, Witherspoon, and Ohnishi's analytical models for enhanced geothermal systems. Although discrete fracture network (DFN) modeling developed somewhat independently in the late 1970s, Paul Witherspoon's foresight in promoting underground in situ testing at the Stripa Mine in Sweden was a major driver in Lawrence Berkeley Laboratory's contributions to its development.This presentation looks extensions of Gringarten's analytical model into discrete fracture network modeling as a basis for providing further insights into the challenges and opportunities of engineered geothermal systems. The analytical solution itself has many insightful applications beyond those presented in the original paper. The definition of dimensionless time by itself shows that thermal breakthrough has a second power dependence on surface area and on flow rate. The fracture intensity also plays a strong role, as it both increases the surface area and decrease his flow rate per fracture. The improvement of EGS performance with fracture intensity reaches a limit where thermal depletion of the rock lags only slightly behind the thermal breakthrough of cold water in the fracture network.Simple network models, which couple a DFN generator (FracMan) with a hydrothermally coupled flow solver (HydroGeoSphere) expand on Gringarten's concepts to show that realistic heterogeneity of spacing and transmissivity significantly degrades EGS performance. EGS production in networks of stimulated fractures initially follows Gringarten's type curves, with a later deviation is the smaller rock blocks thermally deplete and the entire stimulated volume acts as a single sink. Three-dimensional models of EGS performance show the critical importance of the relative magnitudes of fluid pressure and stress gradients, preferential growth and aperture enhancement may change with depth creating preferential pathways through rock this cooler than the injection depth.

He-3-rich flares - A possible explanation

NASA Technical Reports Server (NTRS)

Fisk, L. A.

1978-01-01

A plasma mechanism is proposed to explain the dramatic enhancements in He-3 observed in He-3-rich flares. It is shown that a common current instability in the corona may heat ambient He-3(2+) over any other ion and thus may preferentially inject He-3 into the flare acceleration process. This mechanism operates when the abundance of He-4 and heavier elements is larger than normal in the coronal plasma. It may also preferentially heat and thus inject certain ions of iron. The mechanism thus provides a possible explanation for the observed correlation between He-3 and heavy enhancements in He-3-rich flares.

Quantifying Preferential Flow and Seasonal Storage in an Unsaturated Fracture-Facial Domain

NASA Astrophysics Data System (ADS)

Nimmo, J. R.; Malek-Mohammadi, S.

2012-12-01

Preferential flow through deep unsaturated zones of fractured rock is hydrologically important to a variety of contaminant transport and water-resource issues. The unsaturated zone of the English Chalk Aquifer provides an important opportunity for a case study of unsaturated preferential flow in isolation from other flow modes. The chalk matrix has low hydraulic conductivity and stays saturated, owing to its fine uniform pores and the wet climate of the region. Therefore the substantial fluxes observed in the unsaturated chalk must be within fractures and interact minimally with matrix material. Price et al. [2000] showed that irregularities on fracture surfaces provide a significant storage capacity in the chalk unsaturated zone, likely accounting for volumes of water required to explain unexpected dry-season water-table stability during substantial continuing streamflow observed by Lewis et al. [1993] In this presentation we discuss and quantify the dynamics of replenishment and drainage of this unsaturated zone fracture-face storage domain using a modification of the source-responsive model of Nimmo [2010]. This model explains the processes in terms of two interacting flow regimes: a film or rivulet preferential flow regime on rough fracture faces, active on an individual-storm timescale, and a regime of adsorptive and surface-tension influences, resembling traditional diffuse formulations of unsaturated flow, effective mainly on a seasonal timescale. The modified model identifies hydraulic parameters for an unsaturated fracture-facial domain lining the fractures. Besides helping to quantify the unsaturated zone storage described by Price et al., these results highlight the importance of research on the topic of unsaturated-flow relations within a near-fracture-surface domain. This model can also facilitate understanding of mechanisms for reinitiation of preferential flow after temporary cessation, which is important in multi-year preferential flow through deep unsaturated zones [Pruess, 1999]. Lewis, M.A., H.K. Jones, D.M.J. Macdonald, M. Price, J.A. Barker, T.R. Shearer, A.J. Wesselink, and D.J. Evans (1993), Groundwater storage in British aquifers--Chalk, National Rivers Authority R&D Note, 169, Bristol, UK. Nimmo, J.R. (2010), Theory for Source-Responsive and Free-Surface Film Modeling of Unsaturated Flow, Vadose Zone Journal, 9(2), 295-306, doi:10.2136/vzj2009.0085. Price, M., R.G. Low, and C. McCann (2000), Mechanisms of water storage and flow in the unsaturated zone of the Chalk aquifer, Journal of Hydrology, 233(1-4), 54-71. Pruess, K. (1999), A mechanistic model for water seepage through thick unsaturated zones in fractured rocks of low matrix permeability, Water Resources Research, 35(4), 1039-1051.

Anthropogenic impacts on deep submarine canyons of the western Mediterranean Sea

NASA Astrophysics Data System (ADS)

Sanchez-Vidal, A.; Tubau, X.; Llorca, M.; Woodall, L.; Canals, M.; Farré, M.; Barceló, D.; Thompson, R.

2016-02-01

Submarine canyons are seafloor geomorphic features connecting the shallow coastal ocean to the deep continental margin and basin. Often considered biodiversity hotspots, submarine canyons have been identified as preferential pathways for water, sediment, pollutant and litter transfers from the coastal to the deep ocean. Here we provide insights on the presence of some of the most insidious man-made debris and substances in submarine canyons of the western Mediterranean Sea, which are relevant to achieve a "Good Environmental Status" by 2020 as outlined in the European Union's ambitious Marine Strategy Framework Directive. Ranked by size on a decreasing basis, we review the origin, distribution and transport mechanisms of i) marine litter, including plastic, lost fishing gear and metallic objects; ii) microplastics in the form of fibers of rayon, polyester, polyamide and acetates; and iii) persistent organic pollutants including the toxic and persistent perfluoroalkyl substances. This integrated analysis allows us to understand the pivotal role of atmospheric driven oceanographic processes occurring in Mediterranean deep canyons (dense shelf water cascading, coastal storms) in spreading any type of man-made compound to the deep sea, where they sink and accumulate before getting buried.

Maternal Bias and Escape from X Chromosome Imprinting in the Midgestation Mouse Placenta

PubMed Central

Finn, Elizabeth H; Smith, Cheryl L; Rodriguez, Jesse; Sidow, Arend; Baker, Julie C

2014-01-01

To investigate the epigenetic landscape at the interface between mother and fetus, we provide a comprehensive analysis of parent-of-origin bias in the mouse placenta. Using F1 interspecies hybrids between mus musculus (C57BL/6J) and mus musculus castaneus, we sequenced RNA from 23 individual midgestation placentas, five late stage placentas, and two yolk sac samples and then used SNPs to determine whether transcripts were preferentially generated from the maternal or paternal allele. In the placenta, we find 103 genes that show significant and reproducible parent-of-origin bias, of which 78 are novel candidates. Most (96%) show a strong maternal bias which we demonstrate, via multiple mathematical models, pyrosequencing, and FISH, is not due to maternal decidual contamination. Analysis of the X chromosome also reveals paternal expression of Xist and several genes that escape inactivation, most significantly Alas2, Fhl1, and Slc38a5. Finally, sequencing individual placentas allowed us to reveal notable expression similarity between littermates. In all, we observe a striking preference for maternal transcription in the midgestation mouse placenta and a dynamic imprinting landscape in extraembryonic tissues, reflecting the complex nature of epigenetic pathways in the placenta. PMID:24594094

CRISPR interference and priming varies with individual spacer sequences

PubMed Central

Xue, Chaoyou; Seetharam, Arun S.; Musharova, Olga; Severinov, Konstantin; J. Brouns, Stan J.; Severin, Andrew J.; Sashital, Dipali G.

2015-01-01

CRISPR–Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) systems allow bacteria to adapt to infection by acquiring ‘spacer’ sequences from invader DNA into genomic CRISPR loci. Cas proteins use RNAs derived from these loci to target cognate sequences for destruction through CRISPR interference. Mutations in the protospacer adjacent motif (PAM) and seed regions block interference but promote rapid ‘primed’ adaptation. Here, we use multiple spacer sequences to reexamine the PAM and seed sequence requirements for interference and priming in the Escherichia coli Type I-E CRISPR–Cas system. Surprisingly, CRISPR interference is far more tolerant of mutations in the seed and the PAM than previously reported, and this mutational tolerance, as well as priming activity, is highly dependent on spacer sequence. We identify a large number of functional PAMs that can promote interference, priming or both activities, depending on the associated spacer sequence. Functional PAMs are preferentially acquired during unprimed ‘naïve’ adaptation, leading to a rapid priming response following infection. Our results provide numerous insights into the importance of both spacer and target sequences for interference and priming, and reveal that priming is a major pathway for adaptation during initial infection. PMID:26586800

Geoelectrical monitoring of simulated subsurface leakage to support high-hazard nuclear decommissioning at the Sellafield Site, UK.

PubMed

Kuras, Oliver; Wilkinson, Paul B; Meldrum, Philip I; Oxby, Lucy S; Uhlemann, Sebastian; Chambers, Jonathan E; Binley, Andrew; Graham, James; Smith, Nicholas T; Atherton, Nick

2016-10-01

A full-scale field experiment applying 4D (3D time-lapse) cross-borehole Electrical Resistivity Tomography (ERT) to the monitoring of simulated subsurface leakage was undertaken at a legacy nuclear waste silo at the Sellafield Site, UK. The experiment constituted the first application of geoelectrical monitoring in support of decommissioning work at a UK nuclear licensed site. Images of resistivity changes occurring since a baseline date prior to the simulated leaks revealed likely preferential pathways of silo liquor simulant flow in the vadose zone and upper groundwater system. Geophysical evidence was found to be compatible with historic contamination detected in permeable facies in sediment cores retrieved from the ERT boreholes. Results indicate that laterally discontinuous till units forming localized hydraulic barriers substantially affect flow patterns and contaminant transport in the shallow subsurface at Sellafield. We conclude that only geophysical imaging of the kind presented here has the potential to provide the detailed spatial and temporal information at the (sub-)meter scale needed to reduce the uncertainty in models of subsurface processes at nuclear sites. Copyright © 2016 British Geological Survey, NERC. Published by Elsevier B.V. All rights reserved.

Phase transformation mechanism in lithium manganese nickel oxide revealed by single-crystal hard X-ray microscopy

DOE PAGES

Kuppan, Saravanan; Xu, Yahong; Liu, Yijin; ...

2017-02-01

Understanding the reaction pathway and kinetics of solid-state phase transformation is critical in designing advanced electrode materials with better performance and stability. Despite the first-order phase transition with a large lattice mismatch between the involved phases, spinel LiMn 1.5Ni 0.5O 4 is capable of fast rate even at large particle size, presenting an enigma yet to be understood. The present study uses advanced two-dimensional and three-dimensional nano-tomography on a series of well-formed LixMn 1.5Ni 0.5O 4 (0 ≤ x ≤ 1) crystals to visualize the mesoscale phase distribution, as a function of Li content at the sub-particle level. Inhomogeneity alongmore » with the coexistence of Li-rich and Li-poor phases are broadly observed on partially delithiated crystals, providing direct evidence for a concurrent nucleation and growth process instead of a shrinking-core or a particle-by-particle process. As a result, superior kinetics of (100) facets at the vertices of truncated octahedral particles promote preferential delithiation, whereas the observation of strain-induced cracking suggests mechanical degradation in the material.« less

Risky business for a juvenile marine predator? Testing the influence of foraging strategies on size and growth rate under natural conditions

PubMed Central

DiBattista, Joseph D.; Moore, Jonathan W.; Ward, Eric J.; Fisk, Aaron T.; Kessel, Steven; Guttridge, Tristan L.; Feldheim, Kevin A.; Franks, Bryan R.; Gruber, Samuel H.; Weideli, Ornella C.; Chapman, Demian D.

2017-01-01

Mechanisms driving selection of body size and growth rate in wild marine vertebrates are poorly understood, thus limiting knowledge of their fitness costs at ecological, physiological and genetic scales. Here, we indirectly tested whether selection for size-related traits of juvenile sharks that inhabit a nursery hosting two dichotomous habitats, protected mangroves (low predation risk) and exposed seagrass beds (high predation risk), is influenced by their foraging behaviour. Juvenile sharks displayed a continuum of foraging strategies between mangrove and seagrass areas, with some individuals preferentially feeding in one habitat over another. Foraging habitat was correlated with growth rate, whereby slower growing, smaller individuals fed predominantly in sheltered mangroves, whereas larger, faster growing animals fed over exposed seagrass. Concomitantly, tracked juveniles undertook variable movement behaviours across both the low and high predation risk habitat. These data provide supporting evidence for the hypothesis that directional selection favouring smaller size and slower growth rate, both heritable traits in this shark population, may be driven by variability in foraging behaviour and predation risk. Such evolutionary pathways may be critical to adaptation within predator-driven marine ecosystems. PMID:28381626

Autocrine selection of a GLP-1R G-protein biased agonist with potent antidiabetic effects.

PubMed

Zhang, Hongkai; Sturchler, Emmanuel; Zhu, Jiang; Nieto, Ainhoa; Cistrone, Philip A; Xie, Jia; He, LinLing; Yea, Kyungmoo; Jones, Teresa; Turn, Rachel; Di Stefano, Peter S; Griffin, Patrick R; Dawson, Philip E; McDonald, Patricia H; Lerner, Richard A

2015-12-01

Glucagon-like peptide-1 (GLP-1) receptor (GLP-1R) agonists have emerged as treatment options for type 2 diabetes mellitus (T2DM). GLP-1R signals through G-protein-dependent, and G-protein-independent pathways by engaging the scaffold protein β-arrestin; preferential signalling of ligands through one or the other of these branches is known as 'ligand bias'. Here we report the discovery of the potent and selective GLP-1R G-protein-biased agonist, P5. We identified P5 in a high-throughput autocrine-based screening of large combinatorial peptide libraries, and show that P5 promotes G-protein signalling comparable to GLP-1 and Exendin-4, but exhibited a significantly reduced β-arrestin response. Preclinical studies using different mouse models of T2DM demonstrate that P5 is a weak insulin secretagogue. Nevertheless, chronic treatment of diabetic mice with P5 increased adipogenesis, reduced adipose tissue inflammation as well as hepatic steatosis and was more effective at correcting hyperglycaemia and lowering haemoglobin A1c levels than Exendin-4, suggesting that GLP-1R G-protein-biased agonists may provide a novel therapeutic approach to T2DM.

Risky business for a juvenile marine predator? Testing the influence of foraging strategies on size and growth rate under natural conditions.

PubMed

Hussey, Nigel E; DiBattista, Joseph D; Moore, Jonathan W; Ward, Eric J; Fisk, Aaron T; Kessel, Steven; Guttridge, Tristan L; Feldheim, Kevin A; Franks, Bryan R; Gruber, Samuel H; Weideli, Ornella C; Chapman, Demian D

2017-04-12

Mechanisms driving selection of body size and growth rate in wild marine vertebrates are poorly understood, thus limiting knowledge of their fitness costs at ecological, physiological and genetic scales. Here, we indirectly tested whether selection for size-related traits of juvenile sharks that inhabit a nursery hosting two dichotomous habitats, protected mangroves (low predation risk) and exposed seagrass beds (high predation risk), is influenced by their foraging behaviour. Juvenile sharks displayed a continuum of foraging strategies between mangrove and seagrass areas, with some individuals preferentially feeding in one habitat over another. Foraging habitat was correlated with growth rate, whereby slower growing, smaller individuals fed predominantly in sheltered mangroves, whereas larger, faster growing animals fed over exposed seagrass. Concomitantly, tracked juveniles undertook variable movement behaviours across both the low and high predation risk habitat. These data provide supporting evidence for the hypothesis that directional selection favouring smaller size and slower growth rate, both heritable traits in this shark population, may be driven by variability in foraging behaviour and predation risk. Such evolutionary pathways may be critical to adaptation within predator-driven marine ecosystems. © 2017 The Author(s).

Protein-solvent preferential interactions, protein hydration, and the modulation of biochemical reactions by solvent components.

PubMed

Timasheff, Serge N

2002-07-23

Solvent additives (cosolvents, osmolytes) modulate biochemical reactions if, during the course of the reaction, there is a change in preferential interactions of solvent components with the reacting system. Preferential interactions can be expressed in terms of preferential binding of the cosolvent or its preferential exclusion (preferential hydration). The driving force is the perturbation by the protein of the chemical potential of the cosolvent. It is shown that the measured change of the amount of water in contact with protein during the course of the reaction modulated by an osmolyte is a change in preferential hydration that is strictly a measure of the cosolvent chemical potential perturbation by the protein in the ternary water-protein-cosolvent system. It is not equal to the change in water of hydration, because water of hydration is a reflection strictly of protein-water forces in a binary system. There is no direct relation between water of preferential hydration and water of hydration.

Methods to Quantify Cell Signaling and GPCR Receptor Ligand Bias: Characterization of Drugs that Target the Endocannabinoid Receptors in Huntington's Disease.

PubMed

Bagher, Amina M; Laprairie, Robert B; Kelly, Melanie E M; Denovan-Wright, Eileen M

2018-01-01

G protein-coupled receptors (GPCRs) interact with multiple intracellular effector proteins such that different ligands may preferentially activate one signal pathway over others, a phenomenon known as signaling bias. Signaling bias can be quantified to optimize drug selection for preclinical research. Here, we describe moderate-throughput methods to quantify signaling bias of known and novel compounds. In the example provided, we describe a method to define cannabinoid-signaling bias in a cell culture model of Huntington's disease (HD). Decreasing type 1 cannabinoid receptor (CB 1 ) levels is correlated with chorea and cognitive deficits in HD. There is evidence that elevating CB 1 levels and/or signaling may be beneficial for HD patients while decreasing CB 1 levels and/or signaling may be detrimental. Recent studies have found that Gα i/o -biased CB 1 agonists activate extracellular signal-regulated kinase (ERK), increase CB 1 protein levels, and improve viability of cells expressing mutant huntingtin. In contrast, CB 1 agonists that are β-arrestin1-biased were found to reduce CB 1 protein levels and cell viability. Measuring agonist bias of known and novel CB 1 agonists will provide important data that predict CB 1 -specific agonists that might be beneficial in animal models of HD and, following animal testing, in HD patients. This method can also be applied to study signaling bias for other GPCRs.

Proteome-wide covalent ligand discovery in native biological systems

PubMed Central

Backus, Keriann M.; Correia, Bruno E.; Lum, Kenneth M.; Forli, Stefano; Horning, Benjamin D.; González-Páez, Gonzalo E.; Chatterjee, Sandip; Lanning, Bryan R.; Teijaro, John R.; Olson, Arthur J.; Wolan, Dennis W.; Cravatt, Benjamin F.

2016-01-01

Small molecules are powerful tools for investigating protein function and can serve as leads for new therapeutics. Most human proteins, however, lack small-molecule ligands, and entire protein classes are considered “undruggable” 1,2. Fragment-based ligand discovery (FBLD) can identify small-molecule probes for proteins that have proven difficult to target using high-throughput screening of complex compound libraries 1,3. Although reversibly binding ligands are commonly pursued, covalent fragments provide an alternative route to small-molecule probes 4–10, including those that can access regions of proteins that are difficult to access through binding affinity alone 5,10,11. In this manuscript, we report a quantitative analysis of cysteine-reactive small-molecule fragments screened against thousands of proteins. Covalent ligands were identified for >700 cysteines found in both druggable proteins and proteins deficient in chemical probes, including transcription factors, adaptor/scaffolding proteins, and uncharacterized proteins. Among the atypical ligand-protein interactions discovered were compounds that react preferentially with pro- (inactive) caspases. We used these ligands to distinguish extrinsic apoptosis pathways in human cell lines versus primary human T-cells, showing that the former is largely mediated by caspase-8 while the latter depends on both caspase-8 and −10. Fragment-based covalent ligand discovery provides a greatly expanded portrait of the ligandable proteome and furnishes compounds that can illuminate protein functions in native biological systems. PMID:27309814

Structural controls on a geothermal system in the Tarutung Basin, north central Sumatra

NASA Astrophysics Data System (ADS)

Nukman, Mochamad; Moeck, Inga

2013-09-01

The Sumatra Fault System provides a unique geologic setting to evaluate the influence of structural controls on geothermal activity. Whereas most of the geothermal systems in Indonesia are controlled by volcanic activity, geothermal systems at the Sumatra Fault System might be controlled by faults and fractures. Exploration strategies for these geothermal systems need to be verified because the typical pattern of heat source and alteration clays are missing so that conventional exploration with magnetotelluric surveys might not provide sufficient data to delineate favorable settings for drilling. We present field geological, structural and geomorphological evidence combined with mapping of geothermal manifestations to allow constraints between fault dynamics and geothermal activity in the Tarutung Basin in north central Sumatra. Our results indicate that the fault pattern in the Tarutung Basin is generated by a compressional stress direction acting at a high angle to the right-lateral Sumatra Fault System. NW-SE striking normal faults possibly related to negative flower structures and NNW-SSE to NNE-SSW oriented dilative Riedel shears are preferential fluid pathways whereas ENE-WSW striking faults act as barriers in this system. The dominant of geothermal manifestations at the eastern part of the basin indicates local extension due to clockwise block rotation in the Sumatra Fault System. Our results support the effort to integrate detailed field geological surveys to refined exploration strategies even in tropical areas where outcrops are limited.

Transcriptional Repression of ATF4 Gene by CCAAT/Enhancer-binding Protein β (C/EBPβ) Differentially Regulates Integrated Stress Response*

PubMed Central

Dey, Souvik; Savant, Sudha; Teske, Brian F.; Hatzoglou, Maria; Calkhoven, Cornelis F.; Wek, Ronald C.

2012-01-01

Different environmental stresses induce the phosphorylation of eIF2 (eIF2∼P), repressing global protein synthesis coincident with preferential translation of ATF4. ATF4 is a transcriptional activator of genes involved in metabolism and nutrient uptake, antioxidation, and regulation of apoptosis. Because ATF4 is a common downstream target that integrates signaling from different eIF2 kinases and their respective stress signals, the eIF2∼P/ATF4 pathway is collectively referred to as the integrated stress response. Although eIF2∼P elicits translational control in response to many different stresses, there are selected stresses, such as exposure to UV irradiation, that do not increase ATF4 expression despite robust eIF2∼P. The rationale for this discordant induction of ATF4 expression and eIF2∼P in response to UV irradiation is that transcription of ATF4 is repressed, and therefore ATF4 mRNA is not available for preferential translation. In this study, we show that C/EBPβ is a transcriptional repressor of ATF4 during UV stress. C/EBPβ binds to critical elements in the ATF4 promoter, resulting in its transcriptional repression. Expression of C/EBPβ increases in response to UV stress, and the liver-enriched inhibitory protein (LIP) isoform of C/EBPβ, but not the liver-enriched activating protein (LAP) version, represses ATF4 transcription. Loss of the liver-enriched inhibitory protein isoform results in increased ATF4 mRNA levels in response to UV irradiation and subsequent recovery of ATF4 translation, leading to enhanced expression of its target genes. Together these results illustrate how eIF2∼P and translational control combined with transcription factors regulated by alternative signaling pathways can direct programs of gene expression that are specifically tailored to each environmental stress. PMID:22556424

Transcriptional Analysis of Fracture Healing and the Induction of Embryonic Stem Cell–Related Genes

PubMed Central

Bais, Manish; McLean, Jody; Sebastiani, Paola; Young, Megan; Wigner, Nathan; Smith, Temple; Kotton, Darrell N.; Einhorn, Thomas A.; Gerstenfeld, Louis C.

2009-01-01

Fractures are among the most common human traumas. Fracture healing represents a unique temporarily definable post-natal process in which to study the complex interactions of multiple molecular events that regulate endochondral skeletal tissue formation. Because of the regenerative nature of fracture healing, it is hypothesized that large numbers of post-natal stem cells are recruited and contribute to formation of the multiple cell lineages that contribute to this process. Bayesian modeling was used to generate the temporal profiles of the transcriptome during fracture healing. The temporal relationships between ontologies that are associated with various biologic, metabolic, and regulatory pathways were identified and related to developmental processes associated with skeletogenesis, vasculogenesis, and neurogenesis. The complement of all the expressed BMPs, Wnts, FGFs, and their receptors were related to the subsets of transcription factors that were concurrently expressed during fracture healing. We further defined during fracture healing the temporal patterns of expression for 174 of the 193 genes known to be associated with human genetic skeletal disorders. In order to identify the common regulatory features that might be present in stem cells that are recruited during fracture healing to other types of stem cells, we queried the transcriptome of fracture healing against that seen in embryonic stem cells (ESCs) and mesenchymal stem cells (MSCs). Approximately 300 known genes that are preferentially expressed in ESCs and ∼350 of the known genes that are preferentially expressed in MSCs showed induction during fracture healing. Nanog, one of the central epigenetic regulators associated with ESC stem cell maintenance, was shown to be associated in multiple forms or bone repair as well as MSC differentiation. In summary, these data present the first temporal analysis of the transcriptome of an endochondral bone formation process that takes place during fracture healing. They show that neurogenesis as well as vasculogenesis are predominant components of skeletal tissue formation and suggest common pathways are shared between post-natal stem cells and those seen in ESCs. PMID:19415118

Absorption, accumulation and biological effects of depleted uranium in Peyer's patches of rats.

PubMed

Dublineau, I; Grison, S; Grandcolas, L; Baudelin, C; Tessier, C; Suhard, D; Frelon, S; Cossonnet, C; Claraz, M; Ritt, J; Paquet, P; Voisin, P; Gourmelon, P

2006-10-29

The digestive tract is the entry route for radionuclides following the ingestion of contaminated food and/or water wells. It was recently characterized that the small intestine was the main area of uranium absorption throughout the gastrointestinal tract. This study was designed to determine the role played by the Peyer's patches in the intestinal absorption of uranium, as well as the possible accumulation of this radionuclide in lymphoid follicles and the toxicological or pathological consequences on the Peyer's patch function subsequent to the passage and/or accumulation of uranium. Results of experiments performed in Ussing chambers indicate that the apparent permeability to uranium in the intestine was higher (10-fold) in the mucosa than in Peyer's patches ((6.21+/-1.21 to 0.55+/-0.35)x10(-6)cm/s, respectively), demonstrating that the small intestinal epithelium was the preferential pathway for the transmucosal passage of uranium. A quantitative analysis of uranium by ICP-MS following chronic contamination with depleted uranium during 3 or 9 months showed a preferential accumulation of uranium in Peyer's patches (1355% and 1266%, respectively, at 3 and 9 months) as compared with epithelium (890% and 747%, respectively, at 3 and 9 months). Uranium was also detected in the mesenteric lymph nodes ( approximately 5-fold after contamination with DU). The biological effects of this accumulation of depleted uranium after chronic contamination were investigated in Peyer's patches. There was no induction of the apoptosis pathway after chronic DU contamination in Peyer's patches. The results indicate no change in the cytokine expression (Il-10, TGF-beta, IFN-gamma, TNF-alpha, MCP-1) in Peyer's patches and in mesenteric lymph nodes, and no modification in the uptake of yeast cells by Peyer's patches. In conclusion, this study shows that the Peyer's patches were a site of retention for uranium following the chronic ingestion of this radionuclide, without any biological consequences of such accumulation on Peyer's patch functions.

Platinum(IV) complex LA-12 exerts higher ability than cisplatin to enhance TRAIL-induced cancer cell apoptosis via stimulation of mitochondrial pathway.

PubMed

Jelínková, Iva; Šafaříková, Barbora; Vondálová Blanářová, Olga; Skender, Belma; Hofmanová, Jiřina; Sova, Petr; Moyer, Mary Pat; Kozubík, Alois; Kolář, Zdeněk; Ehrmann, Jiří; Hyršlová Vaculová, Alena

2014-12-01

In search for novel strategies in colon cancer treatment, we investigated the unique ability of platinum(IV) complex LA-12 to efficiently enhance the killing effects of tumor necrosis factor-related apoptosis inducing ligand (TRAIL), and compared it with the sensitizing action of cisplatin. We provide the first evidence that LA-12 primes human colon cancer cells for TRAIL-induced cytotoxicity by p53-independent activation of the mitochondrial apoptotic pathway. The cooperative action of LA-12 and TRAIL was associated with stimulation of Bax/Bak activation, drop of mitochondrial membrane potential, caspase-9 activation, and a shift of the balance among Bcl-2 family proteins in favor of the pro-apoptotic members. In contrast to cisplatin, LA-12 was a potent inducer of ERK-mediated Noxa and BimL protein upregulation, and more effectively enhanced TRAIL-induced apoptosis in the absence of Bax. The cooperative action of LA-12 and TRAIL was augmented following the siRNA-mediated silencing of Mcl-1 in both Bax proficient/deficient cells. We newly demonstrated that LA-12 induced ERK-mediated c-Myc upregulation, and proved that c-Myc silencing inhibited the mitochondrial activation and apoptosis in colon cancer cells treated with LA-12 and TRAIL. The LA-12-mediated sensitization to TRAIL-induced apoptosis was demonstrated in several colon cancer cell lines, further underscoring the general relevance of our findings. The selective action of LA-12 was documented by preferential priming of cancer but not normal colon cancer cells to TRAIL killing effects. Our work highlights the promising potential of LA-12 over cisplatin to enhance the colon cancer cell sensitivity to TRAIL-induced apoptosis, and provides new mechanistic insights into their cooperative action. Copyright © 2014 Elsevier Inc. All rights reserved.

Structural basis of the heterodimerization of the MST and RASSF SARAH domains in the Hippo signalling pathway

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hwang, Eunha; Korea University, Seoul 136-701; Cheong, Hae-Kap

2014-07-01

The heterodimeric structure of the MST1 and RASSF5 SARAH domains is presented. A comparison of homodimeric and heterodimeric interactions provides a structural basis for the preferential association of the SARAH heterodimer. Despite recent progress in research on the Hippo signalling pathway, the structural information available in this area is extremely limited. Intriguingly, the homodimeric and heterodimeric interactions of mammalian sterile 20-like (MST) kinases through the so-called ‘SARAH’ (SAV/RASSF/HPO) domains play a critical role in cellular homeostasis, dictating the fate of the cell regarding cell proliferation or apoptosis. To understand the mechanism of the heterodimerization of SARAH domains, the three-dimensional structuresmore » of an MST1–RASSF5 SARAH heterodimer and an MST2 SARAH homodimer were determined by X-ray crystallography and were analysed together with that previously determined for the MST1 SARAH homodimer. While the structure of the MST2 homodimer resembled that of the MST1 homodimer, the MST1–RASSF5 heterodimer showed distinct structural features. Firstly, the six N-terminal residues (Asp432–Lys437), which correspond to the short N-terminal 3{sub 10}-helix h1 kinked from the h2 helix in the MST1 homodimer, were disordered. Furthermore, the MST1 SARAH domain in the MST1–RASSF5 complex showed a longer helical structure (Ser438–Lys480) than that in the MST1 homodimer (Val441–Lys480). Moreover, extensive polar and nonpolar contacts in the MST1–RASSF5 SARAH domain were identified which strengthen the interactions in the heterodimer in comparison to the interactions in the homodimer. Denaturation experiments performed using urea also indicated that the MST–RASSF heterodimers are substantially more stable than the MST homodimers. These findings provide structural insights into the role of the MST1–RASSF5 SARAH domain in apoptosis signalling.« less

Transcriptomic analysis reveals Toxoplasma gondii strain-specific differences in host cell response to dense granule protein GRA15.

PubMed

Liu, Qing; Gao, Wen-Wei; Elsheikha, Hany M; He, Jun-Jun; Li, Fa-Cai; Yang, Wen-Bin; Zhu, Xing-Quan

2018-06-19

Growth and replication of the protozoan parasite Toxoplasma gondii within host cell entail the production of several effector proteins, which the parasite exploits for counteracting the host's immune response. Despite considerable research to define the host signaling pathways manipulated by T. gondii and their effectors, there has been limited progress into understanding how individual members of the dense granule proteins (GRAs) modulate gene expression within host cells. The aim of this study was to evaluate whether T. gondii GRA15 protein plays any role in regulating host gene expression. Baby hamster kidney cells (BHK-21) were transfected with plasmids encoding GRA15 genes of either type I GT1 strain (GRA15 I ) or type II PRU strain (GRA15 II ). Gene expression patterns of transfected and nontransfected BHK-21 cells were investigated using RNA-sequencing analysis. GRA15 I and GRA15 II induced both known and novel transcriptional changes in the transfected BHK-21 cells compared with nontransfected cells. Pathway analysis revealed that GRA15 II was mainly involved in the regulation of tumor necrosis factor (TNF), NF-κB, HTLV-I infection, and NOD-like receptor signaling pathways. GRA15 I preferentially influenced the synthesis of unsaturated fatty acids in host cells. Our findings support the hypothesis that certain functions of GRA15 protein are strain dependent and that GRA15 modulates the expression of signaling pathways and genes with important roles in T. gondii pathophysiology. A greater understanding of host signaling pathways influenced by T. gondii effectors would allow the development of more efficient anti-T. gondii therapeutic schemes, capitalizing on disrupting parasite virulence factors to advance the treatment of toxoplasmosis.

Effects of individual popularity on information spreading in complex networks

NASA Astrophysics Data System (ADS)

Gao, Lei; Li, Ruiqi; Shu, Panpan; Wang, Wei; Gao, Hui; Cai, Shimin

2018-01-01

In real world, human activities often exhibit preferential selection mechanism based on the popularity of individuals. However, this mechanism is seldom taken into account by previous studies about spreading dynamics on networks. Thus in this work, an information spreading model is proposed by considering the preferential selection based on individuals' current popularity, which is defined as the number of individuals' cumulative contacts with informed neighbors. A mean-field theory is developed to analyze the spreading model. Through systematically studying the information spreading dynamics on uncorrelated configuration networks as well as real-world networks, we find that the popularity preference has great impacts on the information spreading. On the one hand, the information spreading is facilitated, i.e., a larger final prevalence of information and a smaller outbreak threshold, if nodes with low popularity are preferentially selected. In this situation, the effective contacts between informed nodes and susceptible nodes are increased, and nodes almost have uniform probabilities of obtaining the information. On the other hand, if nodes with high popularity are preferentially selected, the final prevalence of information is reduced, the outbreak threshold is increased, and even the information cannot outbreak. In addition, the heterogeneity of the degree distribution and the structure of real-world networks do not qualitatively affect the results. Our research can provide some theoretical supports for the promotion of spreading such as information, health related behaviors, and new products, etc.

Solubility of lysozyme in the presence of aqueous chloride salts: common-ion effect and its role on solubility and crystal thermodynamics.

PubMed

Annunziata, Onofrio; Payne, Andrew; Wang, Ying

2008-10-08

Understanding protein solubility is important for a rational design of the conditions of protein crystallization. We report measurements of lysozyme solubility in aqueous solutions as a function of NaCl, KCl, and NH4Cl concentrations at 25 degrees C and pH 4.5. Our solubility results are directly compared to preferential-interaction coefficients of these ternary solutions determined in the same experimental conditions by ternary diffusion. This comparison has provided new important insight on the dependence of protein solubility on salt concentration. We remark that the dependence of the preferential-interaction coefficient as a function of salt concentration is substantially shaped by the common-ion effect. This effect plays a crucial role also on the observed behavior of lysozyme solubility. We find that the dependence of solubility on salt type and concentration strongly correlates with the corresponding dependence of the preferential-interaction coefficient. Examination of both preferential-interaction coefficients and second virial coefficients has allowed us to demonstrate that the solubility dependence on salt concentration is substantially affected by the corresponding change of protein chemical potential in the crystalline phase. We propose a simple model for the crystalline phase based on salt partitioning between solution and the hydrated protein crystal. A novel solubility equation is reported that quantitatively explains the observed experimental dependence of protein solubility on salt concentration.

Molecular characterization of DNA repair protein Ku70 from Vitis vinifera and its purification from transgenic tobacco.

PubMed

Tak, Himanshu; Mhatre, Minal

2013-08-01

The DNA double strand break repair in plants is preferentially by non homologous end joining (NHEJ) pathway. A key protein of NHEJ pathway is Ku70. We have identified Ku70 homolog (VvKu70) from grapevine genome database. In this report we characterize a Ku70 homologue from Vitis vinifera cv. Mango. The VvKu70 expression was found to increase strongly in response to gamma radiation. The transcript level of VvKu70 was found to increase up to 36 h in gamma irradiated shoots of grapevine. The expression of VvKu70 was found in many organs like stem, leaves and roots. A GFP fused VvKu70 protein was found to be nuclear localized which indicates that the VvKu70 is a nuclear localized protein. The VvKu70 identified by in silico approaches is present as a single copy number in V. vinifera cv. Mango genome. The VvKu70-GFP fused protein possesses ATPase activity and fails to bind dsDNA but binds ssDNA.

PD-1–Mediated Attrition of Polyfunctional Memory CD8+ T Cells in Chronic Toxoplasma Infection

PubMed Central

Bhadra, Rajarshi; Gigley, Jason P.; Khan, Imtiaz A.

2012-01-01

We reported earlier that during chronic toxoplasmosis CD8+ T cells become functionally exhausted with concomitant PD-1 upregulation, leading to eventual host mortality. However, how immune exhaustion specifically mediates attrition of CD8 polyfunctionality, a hallmark of potent T-cell response, during persistent infections has not been addressed. In this study, we demonstrate that PD-1 is preferentially expressed on polyfunctional memory CD8+ T cells, which renders them susceptible to apoptosis. In vitro blockade of the PD-1–PD-L1 pathway dramatically reduces apoptosis of polyfunctional and interferon γ+/granzyme B− memory but not effector CD8+ T cells. In summary, the present report underscores the critical role of the PD-1–PD-L1 pathway in mediating attrition of this important CD8+ T-cell subset and addresses the mechanistic basis of how αPD-L1 therapy reinvigorates polyfunctional CD8 response during chronic infections. The conclusions of this study can have profound immunotherapeutic implications in combating recrudescent toxoplasmosis as well other chronic infections. PMID:22539813

Analysis of the morphology, stability, and folding pathways of ring polymers with supramolecular topological constraints using molecular simulation and nonlinear manifold learning

NASA Astrophysics Data System (ADS)

Wang, Jiang; Ferguson, Andrew

Ring polymers offer a wide range of natural and engineered functions and applications, including as circular bacterial DNA, crown ethers for cation chelation, and ``molecular machines'' such as mechanical nanoswitches. The morphology and dynamics of ring polymers are governed by the chemistry and degree of polymerization of the ring, and intramolecular and supramolecular topological constraints such as knots or mechanically-interlocked rings. We perform molecular dynamics simulations of polyethylene ring polymers as a function of degree of polymerization and in different topological states, including a knotted state, catenane state (two interlocked rings), and borromean state (three interlocked rings). Applying nonlinear manifold learning to our all-atom simulation trajectories, we extract low-dimensional free energy surfaces governing the accessible conformational states and their relative thermodynamic stability. The free energy surfaces reveal how degree of polymerization and topological constraints affect the thermally accessible conformations, chiral symmetry breaking, and folding and collapse pathways of the rings, and present a means to rationally engineer ring size and topology to preferentially stabilize particular conformational states.

Increases in cAMP, MAPK Activity and CREB Phosphorylation during REM Sleep: Implications for REM Sleep and Memory Consolidation

PubMed Central

Luo, Jie; Phan, Trongha X.; Yang, Yimei; Garelick, Michael G.; Storm, Daniel R.

2013-01-01

The cyclic adenosine monophosphate (cAMP), mitogen-activated protein kinase (MAPK) and cAMP response element-binding protein (CREB) transcriptional pathway is required for consolidation of hippocampus-dependent memory. In mice, this pathway undergoes a circadian oscillation required for memory persistence that reaches a peak during the daytime. Since mice exhibit polyphasic sleep patterns during the day, this suggested the interesting possibility that cAMP, MAPK activity and CREB phosphorylation may be elevated during sleep. Here, we report that cAMP, phospho-p44/42 MAPK and phospho-CREB are higher in rapid eye movement (REM) sleep compared to awake mice but are not elevated in non-rapid eye movement (NREM) sleep. This peak of activity during REM sleep does not occur in mice lacking calmodulin-stimulated adenylyl cyclases, a mouse strain that learns but cannot consolidate hippocampus-dependent memory. We conclude that a preferential increase in cAMP, MAPK activity and CREB phosphorylation during REM sleep may contribute to hippocampus-dependent memory consolidation. PMID:23575844

Genomic analyses identify molecular subtypes of pancreatic cancer.

PubMed

Bailey, Peter; Chang, David K; Nones, Katia; Johns, Amber L; Patch, Ann-Marie; Gingras, Marie-Claude; Miller, David K; Christ, Angelika N; Bruxner, Tim J C; Quinn, Michael C; Nourse, Craig; Murtaugh, L Charles; Harliwong, Ivon; Idrisoglu, Senel; Manning, Suzanne; Nourbakhsh, Ehsan; Wani, Shivangi; Fink, Lynn; Holmes, Oliver; Chin, Venessa; Anderson, Matthew J; Kazakoff, Stephen; Leonard, Conrad; Newell, Felicity; Waddell, Nick; Wood, Scott; Xu, Qinying; Wilson, Peter J; Cloonan, Nicole; Kassahn, Karin S; Taylor, Darrin; Quek, Kelly; Robertson, Alan; Pantano, Lorena; Mincarelli, Laura; Sanchez, Luis N; Evers, Lisa; Wu, Jianmin; Pinese, Mark; Cowley, Mark J; Jones, Marc D; Colvin, Emily K; Nagrial, Adnan M; Humphrey, Emily S; Chantrill, Lorraine A; Mawson, Amanda; Humphris, Jeremy; Chou, Angela; Pajic, Marina; Scarlett, Christopher J; Pinho, Andreia V; Giry-Laterriere, Marc; Rooman, Ilse; Samra, Jaswinder S; Kench, James G; Lovell, Jessica A; Merrett, Neil D; Toon, Christopher W; Epari, Krishna; Nguyen, Nam Q; Barbour, Andrew; Zeps, Nikolajs; Moran-Jones, Kim; Jamieson, Nigel B; Graham, Janet S; Duthie, Fraser; Oien, Karin; Hair, Jane; Grützmann, Robert; Maitra, Anirban; Iacobuzio-Donahue, Christine A; Wolfgang, Christopher L; Morgan, Richard A; Lawlor, Rita T; Corbo, Vincenzo; Bassi, Claudio; Rusev, Borislav; Capelli, Paola; Salvia, Roberto; Tortora, Giampaolo; Mukhopadhyay, Debabrata; Petersen, Gloria M; Munzy, Donna M; Fisher, William E; Karim, Saadia A; Eshleman, James R; Hruban, Ralph H; Pilarsky, Christian; Morton, Jennifer P; Sansom, Owen J; Scarpa, Aldo; Musgrove, Elizabeth A; Bailey, Ulla-Maja Hagbo; Hofmann, Oliver; Sutherland, Robert L; Wheeler, David A; Gill, Anthony J; Gibbs, Richard A; Pearson, John V; Waddell, Nicola; Biankin, Andrew V; Grimmond, Sean M

2016-03-03

Integrated genomic analysis of 456 pancreatic ductal adenocarcinomas identified 32 recurrently mutated genes that aggregate into 10 pathways: KRAS, TGF-β, WNT, NOTCH, ROBO/SLIT signalling, G1/S transition, SWI-SNF, chromatin modification, DNA repair and RNA processing. Expression analysis defined 4 subtypes: (1) squamous; (2) pancreatic progenitor; (3) immunogenic; and (4) aberrantly differentiated endocrine exocrine (ADEX) that correlate with histopathological characteristics. Squamous tumours are enriched for TP53 and KDM6A mutations, upregulation of the TP63∆N transcriptional network, hypermethylation of pancreatic endodermal cell-fate determining genes and have a poor prognosis. Pancreatic progenitor tumours preferentially express genes involved in early pancreatic development (FOXA2/3, PDX1 and MNX1). ADEX tumours displayed upregulation of genes that regulate networks involved in KRAS activation, exocrine (NR5A2 and RBPJL), and endocrine differentiation (NEUROD1 and NKX2-2). Immunogenic tumours contained upregulated immune networks including pathways involved in acquired immune suppression. These data infer differences in the molecular evolution of pancreatic cancer subtypes and identify opportunities for therapeutic development.

Phase structure within a fracture network beneath a surface pond: Field experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

GLASS JR.,ROBERT J.; NICHOLL,M.J.

2000-05-09

The authors performed a simple experiment to elucidate phase structure within a pervasively fractured welded tuff. Dyed water was infiltrated from a surface pond over a 36 minute period while a geophysical array monitored the wetted region within vertical planes directly beneath. They then excavated the rock mass to a depth of {approximately}5 m and mapped the fracture network and extent of dye staining in a series of horizontal pavements. Near the pond the network was fully stained. Below, the phase structure immediately expanded and with depth, the structure became fragmented and complicated exhibiting evidence of preferential flow, fingers, irregularmore » wetting patterns, and varied behavior at fracture intersections. Limited transient geophysical data suggested that strong vertical pathways form first followed by increased horizontal expansion and connection within the network. These rapid pathways are also the first to drain. Estimates also suggest that the excavation captured from {approximately}10% to 1% or less of the volume of rock interrogated by the infiltration slug and thus the penetration depth could have been quite large.« less

Connectivity in modelling subsurface stormflow and tracer transport in a forested hillslope

NASA Astrophysics Data System (ADS)

Laine-Kaulio, Hanne; Koivusalo, Harri

2016-04-01

Preferential flow characterizes subsurface water movement in forested hillslopes. Connectivity of preferential flowpaths in soil, as well as connections between the preferential flowpaths and the soil matrix, control the flow patterns in hillslopes. We simulated subsurface stormflow and tracer transport within a forested hillslope section in Eastern Finland with a modifiable and detailed, physically-based 3-D dual-permeability model. The objective was to investigate the role of flowpath connectivity in capturing the observed migration velocity and concentration status of a tracer plume during the different stages of an irrigation experiment. Hypotheses to explain the observed transport behaviour were formulated based on observed spatial variations in the soil properties. The hypotheses were then tested by running corresponding model versions against spatial high-frequency data from the irrigation experiment. The 3-D distribution of preferential flowpaths, and the connections and disconnections between them, had the most crucial role in capturing the observed transport event with the model. Lateral by-pass flow in the preferential flow network and the transmissivity feedback phenomenon dominated the tracer transport. However, disconnections in lateral preferential flow restrained the transport, making the transport route devious instead of being directly lateral. These disconnections were caused by spots of cemented soil material. Stones had an opposite effect on the flow route formation compared to the cemented spots because preferential flowpaths were present on stone surfaces. Preferential flowpaths related to stones were linked with other types of preferential flowpaths in soil, facilitating the connectivity of preferential flowpaths within the entire hillslope. To take into account the discontinuity in lateral preferential flow and the tortuosity of the dominant flow routes in the model, an explicit representation of the 3-D distribution of saturated hydraulic conductivity in the preferential flow network was required. In addition, with-depth changing porosity values of both pore domains of soil, i.e., the preferential flowpaths and the soil matrix, as well as explicit descriptions of local water losses into the underlying bedrock, were found important for successful simulations. Other investigated model features, including complexity in the values of the rest of the model parameters and in the calculation routines used in describing the flow connections between the preferential flowpaths and the soil matrix, were not found beneficial for the model outcome.

Investigation of the functional role of CSLD proteins in plant cell wall deposition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nielsen, Erik Etlar

The overall goal of this research proposal was to characterize the molecular machinery responsible for polarized secretion of cell wall components in Arabidopsis thaliana. We have used the polarized expansion that occurs during root hair cell growth to identify membrane trafficking pathways involved in polarized secretion of cell wall components to the expanding tips of these cells, and we have recently shown that CSLD3 is preferentially targeted to the apical plasma membranes in root hair cells, where it plays essential roles during cell wall deposition in these cells. The specific aims of the project are designed to answer the followingmore » objective: Identification of the cell wall polysaccharide class that CSLD proteins synthesize.« less

Conformer-specific hydrogen atom tunnelling in trifluoromethylhydroxycarbene

NASA Astrophysics Data System (ADS)

Mardyukov, Artur; Quanz, Henrik; Schreiner, Peter R.

2017-01-01

Conformational control of organic reactions is at the heart of the biomolecular sciences. To achieve a particular reactivity, one of many conformers may be selected, for instance, by a (bio)catalyst, as the geometrically most suited and appropriately reactive species. The equilibration of energetically close-lying conformers is typically assumed to be facile and less energetically taxing than the reaction under consideration itself: this is termed the 'Curtin-Hammett principle'. Here, we show that the trans conformer of trifluoromethylhydroxycarbene preferentially rearranges through a facile quantum-mechanical hydrogen tunnelling pathway, while its cis conformer is entirely unreactive. Hence, this presents the first example of a conformer-specific hydrogen tunnelling reaction. The Curtin-Hammett principle is not applicable, due to the high barrier between the two conformers.

Influence of very short patch mismatch repair on SOS inducing lesions after aminoglycoside treatment in Escherichia coli.

PubMed

Baharoglu, Zeynep; Mazel, Didier

2014-01-01

Low concentrations of aminoglycosides induce the SOS response in Vibrio cholerae but not in Escherichia coli. In order to determine whether a specific factor present in E. coli prevents this induction, we developed a genetic screen where only SOS inducing mutants are viable. We identified the vsr gene coding for the Vsr protein of the very short patch mismatch repair (VSPR) pathway. The effect of mismatch repair (MMR) mutants was also studied. We propose that lesions formed upon aminoglycoside treatment are preferentially repaired by VSPR without SOS induction in E. coli and by MMR when VSPR is impaired. Copyright © 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Modeling Preferential Admissions at Elite Liberal Arts Colleges

ERIC Educational Resources Information Center

Cockburn, Sally; Hewitt, Gordon; Kelly, Timothy

2013-01-01

This paper presents the results of a model that simulates the effects of varying preferential admissions policies on the academic profile of a set of 35 small liberal arts colleges. An underlying assumption is that all schools in the set use the same ratio of preferential to non-preferential admissions. The model predicts that even drastic changes…

Spreading dynamics of an e-commerce preferential information model on scale-free networks

NASA Astrophysics Data System (ADS)

Wan, Chen; Li, Tao; Guan, Zhi-Hong; Wang, Yuanmei; Liu, Xiongding

2017-02-01

In order to study the influence of the preferential degree and the heterogeneity of underlying networks on the spread of preferential e-commerce information, we propose a novel susceptible-infected-beneficial model based on scale-free networks. The spreading dynamics of the preferential information are analyzed in detail using the mean-field theory. We determine the basic reproductive number and equilibria. The theoretical analysis indicates that the basic reproductive number depends mainly on the preferential degree and the topology of the underlying networks. We prove the global stability of the information-elimination equilibrium. The permanence of preferential information and the global attractivity of the information-prevailing equilibrium are also studied in detail. Some numerical simulations are presented to verify the theoretical results.

The mechanism for enhanced oxidation degradation of dioxin-like PCBs (PCB-77) in the atmosphere by the solvation effect.

PubMed

Xin, Mei-Ling; Yang, Jia-Wen; Li, Yu

2017-07-11

The reaction pathways of PCB-77 in the atmosphere with ·OH, O 2 , NO x , and 1 O 2 were inferred based on density functional theory calculations with the 6-31G* basis set. The structures the reactants, transition states, intermediates, and products were optimized. The energy barriers and reaction heats were obtained to determine the energetically favorable reaction pathways. To study the solvation effect, the energy barriers and reaction rates for PCB-77 with different polar and nonpolar solvents (cyclohexane, benzene, carbon tetrachloride, chloroform, acetone, dichloromethane, ethanol, methanol, acetonitrile, dimethylsulfoxide, and water) were calculated. The results showed that ·OH preferentially added to the C5 atom of PCB-77, which has no Cl atom substituent, to generate the intermediate IM5. This intermediate subsequently reacted with O 2 via pathway A to generate IM5a, with an energy barrier of 7.27 kcal/mol and total reaction rate of 8.45 × 10 -8  cm 3 /molecule s. Pathway B involved direct dehydrogenation of IM5 to produce the OH-PCBs intermediate IM5b, with an energy barrier of 28.49 kcal/mol and total reaction rate of 1.15 × 10 -5  cm 3 /molecule s. The most likely degradation pathway of PCB-77 in the atmosphere is pathway A to produce IM5a. The solvation effect results showed that cyclohexane, carbon tetrachloride, and benzene could reduce the reaction energy barrier of pathway A. Among these solvents, the solvation effect of benzene was the largest, and could reduce the total reaction energy barrier by 25%. Cyclohexane, carbon tetrachloride, benzene, dichloromethane, acetone, and ethanol could increase the total reaction rate of pathway A. The increase in the reaction rate of pathway A with benzene was 8%. The effect of solvents on oxidative degradation of PCB-77 in the atmosphere is important. Graphical abstract The reaction pathways of PCB-77 in the atmosphere with •OH, O2, NOx, and 1O2 were inferred based on density functional theory calculations with the 6-31G* basis set. Different polar and nonpolar solvents: cyclohexane, benzene, carbon tetrachloride, chloroform, acetone, dichloromethane, ethanol, methanol, acetonitrile, dimethylsulfoxide, and water were selected to study the solvation effect on the favorable reaction pathways. The investigated results showed what kind of pathway was most likely to occur and the solvent effect on the reaction pathway.

Identifying variably saturated water-flow patterns in a steep hillslope under intermittent heavy rainfall

USGS Publications Warehouse

El-Kadi, A. I.; Torikai, J.D.

2001-01-01

The objective of this paper is to identify water-flow patterns in part of an active landslide, through the use of numerical simulations and data obtained during a field study. The approaches adopted include measuring rainfall events and pore-pressure responses in both saturated and unsaturated soils at the site. To account for soil variability, the Richards equation is solved within deterministic and stochastic frameworks. The deterministic simulations considered average water-retention data, adjusted retention data to account for stones or cobbles, retention functions for a heterogeneous pore structure, and continuous retention functions for preferential flow. The stochastic simulations applied the Monte Carlo approach which considers statistical distribution and autocorrelation of the saturated conductivity and its cross correlation with the retention function. Although none of the models is capable of accurately predicting field measurements, appreciable improvement in accuracy was attained using stochastic, preferential flow, and heterogeneous pore-structure models. For the current study, continuum-flow models provide reasonable accuracy for practical purposes, although they are expected to be less accurate than multi-domain preferential flow models.

Dynamic preferential allocation to arbuscular mycorrhizal fungi explains fungal succession and coexistence.

PubMed

Bachelot, Benedicte; Lee, Charlotte T

2018-02-01

Evidence accumulates about the role of arbuscular mycorrhizal (AM) fungi in shaping plant communities, but little is known about the factors determining the biomass and coexistence of several types of AM fungi in a plant community. Here, using a consumer-resource framework that treats the relationship between plants and fungi as simultaneous, reciprocal exploitation, we investigated what patterns of dynamic preferential plant carbon allocation to empirically-defined fungal types (on-going partner choice) would be optimal for plants, and how these patterns depend on successional dynamics. We found that ruderal AM fungi can dominate under low steady-state nutrient availability, and competitor AM fungi can dominate at higher steady-state nutrient availability; these are conditions characteristic of early and late succession, respectively. We also found that dynamic preferential allocation alone can maintain a diversity of mutualists, suggesting that on-going partner choice is a new coexistence mechanism for mutualists. Our model can therefore explain both mutualist coexistence and successional strategy, providing a powerful tool to derive testable predictions. © 2017 by the Ecological Society of America.

Reinterpreting the Anomalous Mole Fraction Effect: The Ryanodine Receptor Case Study

PubMed Central

Gillespie, Dirk; Giri, Janhavi; Fill, Michael

2009-01-01

Abstract The origin of the anomalous mole fraction effect (AMFE) in calcium channels is explored with a model of the ryanodine receptor. This model predicted and experiments verified new AMFEs in the cardiac isoform. In mole fraction experiments, conductance is measured in mixtures of ion species X and Y as their relative amounts (mole fractions) vary. This curve can have a minimum (an AMFE). The traditional interpretation of the AMFE is that multiple interacting ions move through the pore in a single file. Mole fraction curves without minima (no AMFEs) are generally interpreted as X displacing Y from the pore in a proportion larger than its bath mole fraction (preferential selectivity). We find that the AMFE is also caused by preferential selectivity of X over Y, if X and Y have similar conductances. This is a prediction applicable to any channel and provides a fundamentally different explanation of the AMFE that does not require single filing or multiple occupancy: preferential selectivity causes the resistances to current flow in the baths, channel vestibules, and selectivity filter to change differently with mole fraction, and produce the AMFE. PMID:19843453

JAK1/STAT3 Activation through a Proinflammatory Cytokine Pathway Leads to Resistance to Molecularly Targeted Therapy in Non-Small Cell Lung Cancer.

PubMed

Shien, Kazuhiko; Papadimitrakopoulou, Vassiliki A; Ruder, Dennis; Behrens, Carmen; Shen, Li; Kalhor, Neda; Song, Juhee; Lee, J Jack; Wang, Jing; Tang, Ximing; Herbst, Roy S; Toyooka, Shinichi; Girard, Luc; Minna, John D; Kurie, Jonathan M; Wistuba, Ignacio I; Izzo, Julie G

2017-10-01

Molecularly targeted drugs have yielded significant therapeutic advances in oncogene-driven non-small cell lung cancer (NSCLC), but a majority of patients eventually develop acquired resistance. Recently, the relation between proinflammatory cytokine IL6 and resistance to targeted drugs has been reported. We investigated the functional contribution of IL6 and the other members of IL6 family proinflammatory cytokine pathway to resistance to targeted drugs in NSCLC cells. In addition, we examined the production of these cytokines by cancer cells and cancer-associated fibroblasts (CAF). We also analyzed the prognostic significance of these molecule expressions in clinical NSCLC samples. In NSCLC cells with acquired resistance to targeted drugs, we observed activation of the IL6-cytokine pathway and STAT3 along with epithelial-to-mesenchymal transition (EMT) features. In particular, IL6 family cytokine oncostatin-M (OSM) induced a switch to the EMT phenotype and protected cells from targeted drug-induced apoptosis in OSM receptors (OSMRs)/JAK1/STAT3-dependent manner. The cross-talk between NSCLC cells and CAFs also preferentially activated the OSM/STAT3 pathway via a paracrine mechanism and decreased sensitivity to targeted drugs. The selective JAK1 inhibitor filgotinib effectively suppressed STAT3 activation and OSMR expression, and cotargeting inhibition of the oncogenic pathway and JAK1 reversed resistance to targeted drugs. In the analysis of clinical samples, OSMR gene expression appeared to be associated with worse prognosis in patients with surgically resected lung adenocarcinoma. Our data suggest that the OSMRs/JAK1/STAT3 axis contributes to resistance to targeted drugs in oncogene-driven NSCLC cells, implying that this pathway could be a therapeutic target. Mol Cancer Ther; 16(10); 2234-45. ©2017 AACR . ©2017 American Association for Cancer Research.

Determining the frequency, depth and velocity of preferential flow by high frequency soil moisture monitoring

NASA Astrophysics Data System (ADS)

Hardie, Marcus; Lisson, Shaun; Doyle, Richard; Cotching, William

2013-01-01

Preferential flow in agricultural soils has been demonstrated to result in agrochemical mobilisation to shallow ground water. Land managers and environmental regulators need simple cost effective techniques for identifying soil - land use combinations in which preferential flow occurs. Existing techniques for identifying preferential flow have a range of limitations including; often being destructive, non in situ, small sampling volumes, or are subject to artificial boundary conditions. This study demonstrated that high frequency soil moisture monitoring using a multi-sensory capacitance probe mounted within a vertically rammed access tube, was able to determine the occurrence, depth, and wetting front velocity of preferential flow events following rainfall. Occurrence of preferential flow was not related to either rainfall intensity or rainfall amount, rather preferential flow occurred when antecedent soil moisture content was below 226 mm soil moisture storage (0-70 cm). Results indicate that high temporal frequency soil moisture monitoring may be used to identify soil type - land use combinations in which the presence of preferential flow increases the risk of shallow groundwater contamination by rapid transport of agrochemicals through the soil profile. However use of high frequency based soil moisture monitoring to determine agrochemical mobilisation risk may be limited by, inability to determine the volume of preferential flow, difficulty observing macropore flow at high antecedent soil moisture content, and creation of artificial voids during installation of access tubes in stony soils.

Liposomal Fasudil, a Rho-Kinase Inhibitor, for Prolonged Pulmonary Preferential Vasodilation in Pulmonary Arterial Hypertension

PubMed Central

Gupta, Vivek; Gupta, Nilesh; Shaik, Imam H.; Mehvar, Reza; McMurtry, Ivan F.; Oka, Masahiko; Nozik-Grayck, Eva; Komatsu, Masanobu; Ahsan, Fakhrul

2013-01-01

Current pharmacological interventions for pulmonary arterial hypertension (PAH) require continuous infusions, multiple inhalations, or oral administration of drugs that act on various pathways involved in the pathogenesis of PAH. However, invasive methods of administration, short duration of action, and lack of pulmonary selectivity result in noncompliance and poor patient outcomes. In this study, we tested the hypothesis that encapsulation of an investigational anti-PAH molecule fasudil (HA-1077), a Rho-kinase inhibitor, into liposomal vesicles results in prolonged vasodilation in distal pulmonary arterioles. Liposomes were prepared by hydration and extrusion method and fasudil was loaded by ammonium sulfate-induced transmembrane electrochemical gradient. Liposomes were then characterized for various physicochemical properties. Optimized formulations were tested for pulmonary absorption and their pharmacological efficacy in a monocrotaline (MCT) induced rat model of PAH. The entrapment efficiency of optimized liposomal fasudil formulations was between 68.1±0.8% and 73.6±2.3%, and the cumulative release at 37°C was 98–99% over a period of 5 days. Compared to intravenous (IV) fasudil, a ~10 fold increase in the terminal plasma half-life was observed when liposomal fasudil was administered as aerosols. The t1/2 of IV fasudil was 0.39±0.12 h. and when given as liposomes via pulmonary route, the t1/2 extended to 4.71±0.72 h. One h after intratracheal instillation of liposomal fasudil, mean pulmonary arterial pressure (MPAP) was reduced by 37.6±5.7% and continued to decrease for about 3 h, suggesting that liposomal formulations produced pulmonary preferential vasodilation in MCT induced PAH rats. Overall, this study established the proof-of-principle that aerosolized liposomal fasudil is a feasible option for a non-invasive, controlled release and pulmonary preferential treatment of PAH. PMID:23353807

Glaucocalyxin A Inhibits Platelet Activation and Thrombus Formation Preferentially via GPVI Signaling Pathway

PubMed Central

Li, Qiang; Ren, Lijie; Liu, Xiaohui; Chu, Chunjun; Ozaki, Yukio; Zhang, Jian; Zhu, Li

2013-01-01

Platelets play a pivotal role in atherothrombosis and the antiplatelet agents have been proved to be useful in preventing onset of acute clinical events including myocardial infarction and stroke. Increasing number of natural compounds has been identified to be potential antiplatelet agents. Here we report the antiplatelet effect of glaucocalyxin A (GLA), an ent-diterpenoid that we isolated and purified from the aerial parts of Rabdosia japonica (Burm. f.) var. glaucocalyx (Maxim.) Hara, and investigate the molecular mechanisms by which GLA inhibits platelet activation and thrombus formation. The effect of GLA on platelet activation was measured using platelets freshly isolated from peripheral blood of healthy donors. Results showed that pretreatment of human platelets with lower concentrations of GLA (0.01μg/ml, 0.1μg/ml) significantly inhibited platelet aggregation induced by collagen (P<0.001) and CRP (P<0.01), a synthetic GPVI ligand, but not by ADP and U46619. Accordingly, GLA inhibited collagen-stimulated tyrosine phosphorylation of Syk, LAT, and phospholipase Cγ2, the signaling events in collagen receptor GPⅥ pathway. GLA also inhibited platelet p-selectin secretion and integrin activation by convulxin, a GPVI selective ligand. Additionally, GLA was found to inhibit low-dose thrombin-induced platelet activation. Using a flow chamber device, GLA was found to attenuate platelet adhesion on collagen surfaces in high shear condition. In vivo studies showed that GLA administration increased the time for complete occlusion upon vascular injury in mice, but did not extend tail-bleeding time when mice were administered with relatively lower doses of GLA. Therefore, the present results provide the molecular basis for the inhibition effect of GLA on platelet activation and its in vivo effect on thrombus formation, suggesting that GLA could potentially be developed as an antiplatelet and antithrombotic agent. PMID:24386454

Alternative Methods for Assessing Contaminant Transport from the Vadose Zone to Indoor Air

NASA Astrophysics Data System (ADS)

Baylor, K. J.; Lee, A.; Reddy, P.; Plate, M.

2010-12-01

Vapor intrusion, which is the transport of contaminant vapors from groundwater and the vadose zone to indoor air, has emerged as a significant human health risk near hazardous waste sites. Volatile organic compounds (VOCs) such as trichloroethylene (TCE) and tetrachloroethylene (PCE) can volatilize from groundwater and from residual sources in the vadose zone and enter homes and commercial buildings through cracks in the slab, plumbing conduits, or other preferential pathways. Assessment of the vapor intrusion pathway typically requires collection of groundwater, soil gas, and indoor air samples, a process which can be expensive and time-consuming. We evaluated three alternative vapor intrusion assessment methods, including 1) use of radon as a surrogate for vapor intrusion, 2) use of pressure differential measurements between indoor/outdoor and indoor/subslab to assess the potential for vapor intrusion, and 3) use of passive, longer-duration sorbent methods to measure indoor air VOC concentrations. The primary test site, located approximately 30 miles south of San Francisco, was selected due to the presence of TCE (10 - 300 ug/L) in shallow groundwater (5 to 10 feet bgs). At this test site, we found that radon was not a suitable surrogate to asses vapor intrusion and that pressure differential measurements are challenging to implement and equipment-intensive. More significantly, we found that the passive, longer-duration sorbent methods are easy to deploy and compared well quantitatively with standard indoor air sampling methods. The sorbent technique is less than half the cost of typical indoor air methods, and also provides a longer duration sample, typically 3 to 14 days rather than 8 to 24 hours for standard methods. The passive sorbent methods can be a reliable, cost-effective, and easy way to sample for TCE, PCE and other VOCs as part of a vapor intrusion investigation.

Sulforaphane preconditioning of the Nrf2/HO-1 defense pathway protects the cerebral vasculature against blood-brain barrier disruption and neurological deficits in stroke.

PubMed

Alfieri, Alessio; Srivastava, Salil; Siow, Richard C M; Cash, Diana; Modo, Michel; Duchen, Michael R; Fraser, Paul A; Williams, Steven C R; Mann, Giovanni E

2013-12-01

Disruption of the blood-brain barrier (BBB) and cerebral edema are the major pathogenic mechanisms leading to neurological dysfunction and death after ischemic stroke. The brain protects itself against infarction via activation of endogenous antioxidant defense mechanisms, and we here report the first evidence that sulforaphane-mediated preactivation of nuclear factor erythroid 2-related factor 2 (Nrf2) and its downstream target heme oxygenase-1 (HO-1) in the cerebral vasculature protects the brain against stroke. To induce ischemic stroke, Sprague-Dawley rats were subjected to 70 min middle cerebral artery occlusion (MCAo) followed by 4, 24, or 72 h reperfusion. Nrf2 and HO-1 protein expression was upregulated in cerebral microvessels of peri-infarct regions after 4-72 h, with HO-1 preferentially associated with perivascular astrocytes rather than the cerebrovascular endothelium. In naïve rats, treatment with sulforaphane increased Nrf2 expression in cerebral microvessels after 24h. Upregulation of Nrf2 by sulforaphane treatment prior to transient MCAo (1h) was associated with increased HO-1 expression in perivascular astrocytes in peri-infarct regions and cerebral endothelium in the infarct core. BBB disruption, lesion progression, as analyzed by MRI, and neurological deficits were reduced by sulforaphane pretreatment. As sulforaphane pretreatment led to a moderate increase in peroxynitrite generation, we suggest that hormetic preconditioning underlies sulforaphane-mediated protection against stroke. In conclusion, we propose that pharmacological or dietary interventions aimed to precondition the brain via activation of the Nrf2 defense pathway in the cerebral microvasculature provide a novel therapeutic approach for preventing BBB breakdown and neurological dysfunction in stroke. Crown Copyright © 2013. Published by Elsevier Inc. All rights reserved.

“Selfish spermatogonial selection”: a novel mechanism for the association between advanced paternal age and neurodevelopmental disorders

PubMed Central

Goriely, Anne; McGrath, John J.; Hultman, Christina M.; Wilkie, Andrew O.M.; Malaspina, Dolores

2014-01-01

Objectives There is robust evidence from epidemiological studies that the offspring of older fathers have an increased risk of neurodevelopmental disorders such as schizophrenia and autism. Here we present a novel mechanism that may contribute to this association. Methods Narrative review. Results Because the male germ cell undergoes many more cell divisions across the reproductive age range, copy-errors taking place in the paternal germline are associated with de novo mutations in the offspring of older men. Recently it has been recognized that somatic mutations in male germ cells that modify proliferation via dysregulation of the RAS pathway can lead to within-testis expansion of mutant clonal lines. First identified in association with rare paternal age-effect disorders (e.g. Apert syndrome, achondroplasia), this process is known as ‘selfish spermatogonial selection’. This mechanism will (a) favor propagation of germ cells carrying pathogenic mutations, (b) increasingly skew the mutational profile of sperm as men age, and (c) result in an enrichment of de novo mutations in the offspring of older fathers that preferentially impact on specific cellular signaling pathways. This mechanism offers a parsimonious explanation not only for the association between advanced paternal age and various neurodevelopmental disorders, but also provides insights into the genetic architecture (role of de novo mutations), neurobiological correlates (altered cell cycle) and some epidemiological features of these disorders. We outline hypotheses to test this model. Conclusions In light of our current understanding of the genetic networks involved in neurocognitive disorders and the principles of selfish spermatogonial selection, we speculate that some pathogenic mutations associated with these disorders are the consequence of a selfish mechanism originating in the aging testis. Given the secular changes for delayed parenthood in most societies, this hypothesis has important public health implications. PMID:23639989

Organic Acids: The Pools of Fixed Carbon Involved in Redox Regulation and Energy Balance in Higher Plants

PubMed Central

Igamberdiev, Abir U.; Eprintsev, Alexander T.

2016-01-01

Organic acids are synthesized in plants as a result of the incomplete oxidation of photosynthetic products and represent the stored pools of fixed carbon accumulated due to different transient times of conversion of carbon compounds in metabolic pathways. When redox level in the cell increases, e.g., in conditions of active photosynthesis, the tricarboxylic acid (TCA) cycle in mitochondria is transformed to a partial cycle supplying citrate for the synthesis of 2-oxoglutarate and glutamate (citrate valve), while malate is accumulated and participates in the redox balance in different cell compartments (via malate valve). This results in malate and citrate frequently being the most accumulated acids in plants. However, the intensity of reactions linked to the conversion of these compounds can cause preferential accumulation of other organic acids, e.g., fumarate or isocitrate, in higher concentrations than malate and citrate. The secondary reactions, associated with the central metabolic pathways, in particularly with the TCA cycle, result in accumulation of other organic acids that are derived from the intermediates of the cycle. They form the additional pools of fixed carbon and stabilize the TCA cycle. Trans-aconitate is formed from citrate or cis-aconitate, accumulation of hydroxycitrate can be linked to metabolism of 2-oxoglutarate, while 4-hydroxy-2-oxoglutarate can be formed from pyruvate and glyoxylate. Glyoxylate, a product of either glycolate oxidase or isocitrate lyase, can be converted to oxalate. Malonate is accumulated at high concentrations in legume plants. Organic acids play a role in plants in providing redox equilibrium, supporting ionic gradients on membranes, and acidification of the extracellular medium. PMID:27471516

Determinants of the Thrombogenic Potential of Multiwalled Carbon Nanotubes

PubMed Central

Burke, Andrew; Singh, Ravi; Carroll, David L.; Owen, John; Kock, Nancy D.; D’Agostino, Ralph; Torti, Frank M.; Torti, Suzy V.

2011-01-01

Multiwalled carbon nanotubes (MWCNTs) are cylindrical tubes of graphitic carbon with unique physical and electrical properties. MWCNTs are being explored for a variety of diagnostic and therapeutic applications. Successful biomedical application of MWCNTs will require compatibility with normal circulatory components, including constituents of the hemostatic cascades. In this manuscript, we compare the thrombotic activity of MWCNTs in vitro and in vivo. We also assess the influence of functionalization of MWCNTs on thrombotic activity. In vitro, MWCNT activate the intrinsic pathway of coagulation as measured by activated partial thromboplastin time (aPTT) assays. Functionalization by amidation or carboxylation enhances this procoagulant activity. Mechanistic studies demonstrate that MWCNTs enhance propagation of the intrinsic pathway via a non-classical mechanism strongly dependent on factor IX. MWCNTs preferentially associate with factor IXa and may provide a platform for its activation. In addition to their effects on the coagulation cascade, MWCNTs activate platelets in vitro, with amidated MWCNTs exhibiting greater platelet activation than carboxylated or pristine MWCNTs. However, contrasting trends are obtained in vivo, where functionalization tends to diminish rather than enhance pro-coagulant activity. Thus, following systemic injection of MWCNTs in mice, pristine MWCNTs decreased platelet counts, increased vWF, and increased D-dimers. In contrast, carboxylated MWCNTS exhibited little procoagulant tendency in vivo, eliciting only a mild and transient decrease in platelets. Amidated MWCNTs elicited no statistically significant change in platelet count. Further, neither carboxylated nor amidated MWCNTs increased vWF or D-dimers in mouse plasma. We conclude that the pro-coagulant tendencies of MWCNTs observed in vitro are not necessarily recapitulated in vivo. Further, functionalization can markedly attenuate the procoagulant activity of MWCNTs in vivo. This work will inform the rational development of biocompatible MWCNTs for systemic delivery. PMID:21663954

Gremlin 2 promotes differentiation of embryonic stem cells to atrial fate by activation of the JNK signaling pathway

PubMed Central

Tanwar, Vineeta; Bylund, Jeffery B.; Hu, Jianyong; Yan, Jingbo; Walthall, Joel M.; Mukherjee, Amrita; Heaton, William H.; Wang, Wen-Der; Potet, Franck; Rai, Meena; Kupershmidt, Sabina; Knapik, Ela W.; Hatzopoulos, Antonis K.

2014-01-01

The Bone Morphogenetic Protein antagonist Gremlin 2 (Grem2) is required for atrial differentiation and establishment of cardiac rhythm during embryonic development. A human Grem2 variant has been associated with familial atrial fibrillation, suggesting that abnormal Grem2 activity causes arrhythmias. However, it is not known how Grem2 integrates into signaling pathways to direct atrial cardiomyocyte differentiation. Here, we demonstrate that Grem2 expression is induced concurrently with the emergence of cardiovascular progenitor cells during differentiation of mouse embryonic (ES) stem cells. Grem2 exposure enhances the cardiogenic potential of ES cells by ~20–120 fold, preferentially inducing genes expressed in atrial myocytes such as Myl7, Nppa and Sarcolipin. We show that Grem2 acts upstream to upregulate pro-atrial transcriptional factors CoupTFII and Hey1 and downregulate atrial fate repressors Irx4 and Hey2. The molecular phenotype of Grem2-induced atrial cardiomyocytes was further supported by induction of ion channels encoded by Kcnj3, Kcnj5, and Cacna1D genes and establishment of atrial-like action potentials shown by electrophysiological recordings. We show that promotion of atrial-like cardiomyocyte is specific to the Gremlin subfamily of BMP antagonists. Grem2 pro-atrial differentiation activity is conveyed by non-canonical BMP signaling through phosphorylation of JNK and can be reversed by specific JNK inhibitors, but not by dorsomorphin, an inhibitor of canonical BMP signaling. Taken together, our data provide novel mechanistic insights into atrial cardiomyocyte differentiation from pluripotent stem cells and will assist the development of future approaches to study and treat arrhythmias. PMID:24648383

Molecular Characteristics of Malignant Ovarian Germ Cell Tumors and Comparison With Testicular Counterparts: Implications for Pathogenesis

PubMed Central

Kraggerud, Sigrid Marie; Hoei-Hansen, Christina E.; Alagaratnam, Sharmini; Skotheim, Rolf I.; Abeler, Vera M.

2013-01-01

This review focuses on the molecular characteristics and development of rare malignant ovarian germ cell tumors (mOGCTs). We provide an overview of the genomic aberrations assessed by ploidy, cytogenetic banding, and comparative genomic hybridization. We summarize and discuss the transcriptome profiles of mRNA and microRNA (miRNA), and biomarkers (DNA methylation, gene mutation, individual protein expression) for each mOGCT histological subtype. Parallels between the origin of mOGCT and their male counterpart testicular GCT (TGCT) are discussed from the perspective of germ cell development, endocrinological influences, and pathogenesis, as is the GCT origin in patients with disorders of sex development. Integrated molecular profiles of the 3 main histological subtypes, dysgerminoma (DG), yolk sac tumor (YST), and immature teratoma (IT), are presented. DGs show genomic aberrations comparable to TGCT. In contrast, the genome profiles of YST and IT are different both from each other and from DG/TGCT. Differences between DG and YST are underlined by their miRNA/mRNA expression patterns, suggesting preferential involvement of the WNT/β-catenin and TGF-β/bone morphogenetic protein signaling pathways among YSTs. Characteristic protein expression patterns are observed in DG, YST and IT. We propose that mOGCT develop through different developmental pathways, including one that is likely shared with TGCT and involves insufficient sexual differentiation of the germ cell niche. The molecular features of the mOGCTs underline their similarity to pluripotent precursor cells (primordial germ cells, PGCs) and other stem cells. This similarity combined with the process of ovary development, explain why mOGCTs present so early in life, and with greater histological complexity, than most somatic solid tumors. PMID:23575763

Gene identification and substrate regulation provide insights into sulfur accumulation during bioleaching with the psychrotolerant acidophile Acidithiobacillus ferrivorans.

PubMed

Liljeqvist, Maria; Rzhepishevska, Olena I; Dopson, Mark

2013-02-01

The psychrotolerant acidophile Acidithiobacillus ferrivorans has been identified from cold environments and has been shown to use ferrous iron and inorganic sulfur compounds as its energy sources. A bioinformatic evaluation presented in this study suggested that Acidithiobacillus ferrivorans utilized a ferrous iron oxidation pathway similar to that of the related species Acidithiobacillus ferrooxidans. However, the inorganic sulfur oxidation pathway was less clear, since the Acidithiobacillus ferrivorans genome contained genes from both Acidithiobacillus ferrooxidans and Acidithiobacillus caldus encoding enzymes whose assigned functions are redundant. Transcriptional analysis revealed that the petA1 and petB1 genes (implicated in ferrous iron oxidation) were downregulated upon growth on the inorganic sulfur compound tetrathionate but were on average 10.5-fold upregulated in the presence of ferrous iron. In contrast, expression of cyoB1 (involved in inorganic sulfur compound oxidation) was decreased 6.6-fold upon growth on ferrous iron alone. Competition assays between ferrous iron and tetrathionate with Acidithiobacillus ferrivorans SS3 precultured on chalcopyrite mineral showed a preference for ferrous iron oxidation over tetrathionate oxidation. Also, pure and mixed cultures of psychrotolerant acidophiles were utilized for the bioleaching of metal sulfide minerals in stirred tank reactors at 5 and 25°C in order to investigate the fate of ferrous iron and inorganic sulfur compounds. Solid sulfur accumulated in bioleaching cultures growing on a chalcopyrite concentrate. Sulfur accumulation halted mineral solubilization, but sulfur was oxidized after metal release had ceased. The data indicated that ferrous iron was preferentially oxidized during growth on chalcopyrite, a finding with important implications for biomining in cold environments.

Improvement and efficient display of Bacillus thuringiensis toxins on M13 phages and ribosomes.

PubMed

Pacheco, Sabino; Cantón, Emiliano; Zuñiga-Navarrete, Fernando; Pecorari, Frédéric; Bravo, Alejandra; Soberón, Mario

2015-12-01

Bacillus thuringiensis (Bt) produces insecticidal proteins that have been used worldwide in the control of insect-pests in crops and vectors of human diseases. However, different insect species are poorly controlled by the available Bt toxins or have evolved resistance to these toxins. Evolution of Bt toxicity could provide novel toxins to control insect pests. To this aim, efficient display systems to select toxins with increased binding to insect membranes or midgut proteins involved in toxicity are likely to be helpful. Here we describe two display systems, phage display and ribosome display, that allow the efficient display of two non-structurally related Bt toxins, Cry1Ac and Cyt1Aa. Improved display of Cry1Ac and Cyt1Aa on M13 phages was achieved by changing the commonly used peptide leader sequence of the coat pIII-fusion protein, that relies on the Sec translocation pathway, for a peptide leader sequence that relies on the signal recognition particle pathway (SRP) and by using a modified M13 helper phage (Phaberge) that has an amber mutation in its pIII genomic sequence and preferentially assembles using the pIII-fusion protein. Also, both Cry1Ac and Cyt1Aa were efficiently displayed on ribosomes, which could allow the construction of large libraries of variants. Furthermore, Cry1Ac or Cyt1Aa displayed on M13 phages or ribosomes were specifically selected from a mixture of both toxins depending on which antigen was immobilized for binding selection. These improved systems may allow the selection of Cry toxin variants with improved insecticidal activities that could counter insect resistances.

HTLV-I Tax Increases Genetic Instability by Inducing DNA Double Strand Breaks during DNA Replication and Switching Repair to NHEJ

PubMed Central

Baydoun, Hicham H.; Bai, Xue Tao; Shelton, Shary; Nicot, Christophe

2012-01-01

Background Appropriate responses to damaged DNA are indispensible for preserving genome stability and preventing cancer. Tumor viruses often target DNA repair machinery to achieve transformation. The Human T-cell leukemia virus type I (HTLV-I) is the only known transforming human retrovirus and the etiological agent of Adult T-cell Leukemia (ATLL). Although HTLV-I-transformed leukemic cells have numerous genetic lesions, the precise role of the viral tax gene in this process is not fully understood. Results Our results show a novel function of HTLV-I oncoprotein Tax as an inducer of genomic DNA double strand breaks (DDSB) during DNA replication. We also found that Tax acts as a potent inhibitor of homologous recombination (HR) DNA repair through the activation of the NF-kB pathway. These results were confirmed using HTLV-I molecular clones expressing Tax at physiological levels in a natural context. We further found that HTLV-I- and Tax-transformed cells are not more susceptible to DNA damaging agents and repair DNA lesions at a rate similar to that of normal cells. Finally, we demonstrated that during S phase, Tax-associated DDSB are preferentially repaired using the error-prone non-homologous end joining (NHEJ) pathway. Conclusions This study provides new insights in Tax effects on DNA repair and genome instability. Although it may not be self sufficient, the creation of DNA breaks and subsequent abnormal use of the non-conservative NHEJ DNA repair during the S phase in HTLV-I-infected Tax-expressing cells may cooperate with other factors to increase genetic and genome instability and favor transformation. PMID:22916124

Nanoridges that characterize the surface morphology of flowers require the synthesis of cutin polyester

PubMed Central

Li-Beisson, Yonghua; Pollard, Mike; Sauveplane, Vincent; Pinot, Franck; Ohlrogge, John; Beisson, Fred

2009-01-01

Distinctive nanoridges on the surface of flowers have puzzled plant biologists ever since their discovery over 75 years ago. Although postulated to help attract insect pollinators, the function, chemical nature, and ontogeny of these surface nanostructures remain uncertain. Studies have been hampered by the fact that no ridgeless mutants have been identified. Here, we describe two mutants lacking nanoridges and define the biosynthetic pathway for 10,16-dihydroxypalmitate, a major cutin monomer in nature. Using gene expression profiling, two candidates for the formation of floral cutin were identified in the model plant Arabidopsis thaliana: the glycerol-3-phosphate acyltransferase 6 (GPAT6) and a member of a cytochrome P450 family with unknown biological function (CYP77A6). Plants carrying null mutations in either gene produced petals with no nanoridges and no cuticle could be observed by either scanning or transmission electron microscopy. A strong reduction in cutin content was found in flowers of both mutants. In planta overexpression suggested GPAT6 preferentially uses palmitate derivatives in cutin synthesis. Comparison of cutin monomer profiles in knockouts for CYP77A6 and the fatty acid ω-hydroxylase CYP86A4 provided genetic evidence that CYP77A6 is an in-chain hydroxylase acting subsequently to CYP86A4 in the synthesis of 10,16-dihydroxypalmitate. Biochemical activity of CYP77A6 was demonstrated by production of dihydroxypalmitates from 16-hydroxypalmitate, using CYP77A6-expressing yeast microsomes. These results define the biosynthetic pathway for an abundant and widespread monomer of the cutin polyester, show that the morphology of floral surfaces depends on the synthesis of cutin, and identify target genes to investigate the function of nanoridges in flower biology. PMID:19959665

Nanoridges that characterize the surface morphology of flowers require the synthesis of cutin polyester.

PubMed

Li-Beisson, Yonghua; Pollard, Mike; Sauveplane, Vincent; Pinot, Franck; Ohlrogge, John; Beisson, Fred

2009-12-22

Distinctive nanoridges on the surface of flowers have puzzled plant biologists ever since their discovery over 75 years ago. Although postulated to help attract insect pollinators, the function, chemical nature, and ontogeny of these surface nanostructures remain uncertain. Studies have been hampered by the fact that no ridgeless mutants have been identified. Here, we describe two mutants lacking nanoridges and define the biosynthetic pathway for 10,16-dihydroxypalmitate, a major cutin monomer in nature. Using gene expression profiling, two candidates for the formation of floral cutin were identified in the model plant Arabidopsis thaliana: the glycerol-3-phosphate acyltransferase 6 (GPAT6) and a member of a cytochrome P450 family with unknown biological function (CYP77A6). Plants carrying null mutations in either gene produced petals with no nanoridges and no cuticle could be observed by either scanning or transmission electron microscopy. A strong reduction in cutin content was found in flowers of both mutants. In planta overexpression suggested GPAT6 preferentially uses palmitate derivatives in cutin synthesis. Comparison of cutin monomer profiles in knockouts for CYP77A6 and the fatty acid omega-hydroxylase CYP86A4 provided genetic evidence that CYP77A6 is an in-chain hydroxylase acting subsequently to CYP86A4 in the synthesis of 10,16-dihydroxypalmitate. Biochemical activity of CYP77A6 was demonstrated by production of dihydroxypalmitates from 16-hydroxypalmitate, using CYP77A6-expressing yeast microsomes. These results define the biosynthetic pathway for an abundant and widespread monomer of the cutin polyester, show that the morphology of floral surfaces depends on the synthesis of cutin, and identify target genes to investigate the function of nanoridges in flower biology.

Magnetic Tracking of Gas Hydrate Deposits.

NASA Astrophysics Data System (ADS)

Lowe, C.; Enkin, R. J.; Judith, B.; Dallimore, S. R.

2005-12-01

Analysis of recovered core from the Mallik gas hydrate field in the Mackenzie Delta, Northwest Territories, Canada demonstrates that the magnetic properties of hydrate-bearing strata differ significantly from those strata lacking gas hydrate. The recovered core, which extends from just above (885 m) to just below (1152 m) observed gas hydrate occurrences (891-1107 m), comprises a series of six stratigraphic units that are either sand or silt dominated. Gas hydrate is preferentially concentrated in the higher porosity, sand-dominated units. Although the sediment source region for the Mackenzie Delta is sufficiently large that silts and sands have similar primary mineralogy, their magnetic properties are distinct. Magnetite, apparent in silt units with porosities too low to accommodate significant gas hydrate deposits, is reduced to iron sulphide in the gas hydrate-bearing sand horizons. The degree of the observed magnetic reduction increases with increasing gas hydrate concentration. Furthermore, silts retain their primary magnetism, whereas sands are remagnetized. Two independent investigations of marine gas hydrate occurrences (Blake Ridge, offshore eastern USA and Cascadia, offshore western Canada) demonstrate similar magnetic reduction within known gas hydrate fields, and an even larger depletion of magnetic minerals in vent zones where methane is actively fluxing to surface. Collectively, the findings from these three regions indicate that porosity and structure are fundamental controls on methane pathways. Investigations are presently underway to determine the precise triggers and chemical pathways of the observed magnetic reductions. However, findings to date indicate that magnetic studies of host sediments in gas hydrate systems provide a powerful lithologic correlation tool, a window into the processes associated with gas hydrate formation, and form the basis of quantitative analysis of magnetic surveys over gas hydrate deposits.

The Endocannabinoid, Anandamide, Augments Notch-1 Signaling in Cultured Cortical Neurons Exposed to Amyloid-β and in the Cortex of Aged Rats*

PubMed Central

Tanveer, Riffat; Gowran, Aoife; Noonan, Janis; Keating, Sinead E.; Bowie, Andrew G.; Campbell, Veronica A.

2012-01-01

Aberrant Notch signaling has recently emerged as a possible mechanism for the altered neurogenesis, cognitive impairment, and learning and memory deficits associated with Alzheimer disease (AD). Recently, targeting the endocannabinoid system in models of AD has emerged as a potential approach to slow the progression of the disease process. Although studies have identified neuroprotective roles for endocannabinoids, there is a paucity of information on modulation of the pro-survival Notch pathway by endocannabinoids. In this study the influence of the endocannabinoids, anandamide (AEA) and 2-arachidonoylglycerol, on the Notch-1 pathway and on its endogenous regulators were investigated in an in vitro model of AD. We report that AEA up-regulates Notch-1 signaling in cultured neurons. We also provide evidence that although Aβ1–42 increases expression of the endogenous inhibitor of Notch-1, numb (Nb), this can be prevented by AEA and 2-arachidonoylglycerol. Interestingly, AEA up-regulated Nct expression, a component of γ-secretase, and this was found to play a crucial role in the enhanced Notch-1 signaling mediated by AEA. The stimulatory effects of AEA on Notch-1 signaling persisted in the presence of Aβ1–42. AEA was found to induce a preferential processing of Notch-1 over amyloid precursor protein to generate Aβ1–40. Aging, a natural process of neurodegeneration, was associated with a reduction in Notch-1 signaling in rat cortex and hippocampus, and this was restored with chronic treatment with URB 597. In summary, AEA has the proclivity to enhance Notch-1 signaling in an in vitro model of AD, which may have relevance for restoring neurogenesis and cognition in AD. PMID:22891244

Gene Identification and Substrate Regulation Provide Insights into Sulfur Accumulation during Bioleaching with the Psychrotolerant Acidophile Acidithiobacillus ferrivorans

PubMed Central

Liljeqvist, Maria; Rzhepishevska, Olena I.

2013-01-01

The psychrotolerant acidophile Acidithiobacillus ferrivorans has been identified from cold environments and has been shown to use ferrous iron and inorganic sulfur compounds as its energy sources. A bioinformatic evaluation presented in this study suggested that Acidithiobacillus ferrivorans utilized a ferrous iron oxidation pathway similar to that of the related species Acidithiobacillus ferrooxidans. However, the inorganic sulfur oxidation pathway was less clear, since the Acidithiobacillus ferrivorans genome contained genes from both Acidithiobacillus ferrooxidans and Acidithiobacillus caldus encoding enzymes whose assigned functions are redundant. Transcriptional analysis revealed that the petA1 and petB1 genes (implicated in ferrous iron oxidation) were downregulated upon growth on the inorganic sulfur compound tetrathionate but were on average 10.5-fold upregulated in the presence of ferrous iron. In contrast, expression of cyoB1 (involved in inorganic sulfur compound oxidation) was decreased 6.6-fold upon growth on ferrous iron alone. Competition assays between ferrous iron and tetrathionate with Acidithiobacillus ferrivorans SS3 precultured on chalcopyrite mineral showed a preference for ferrous iron oxidation over tetrathionate oxidation. Also, pure and mixed cultures of psychrotolerant acidophiles were utilized for the bioleaching of metal sulfide minerals in stirred tank reactors at 5 and 25°C in order to investigate the fate of ferrous iron and inorganic sulfur compounds. Solid sulfur accumulated in bioleaching cultures growing on a chalcopyrite concentrate. Sulfur accumulation halted mineral solubilization, but sulfur was oxidized after metal release had ceased. The data indicated that ferrous iron was preferentially oxidized during growth on chalcopyrite, a finding with important implications for biomining in cold environments. PMID:23183980

Sensitivity Analysis of the Agricultural Policy/Environmental eXtender (APEX) for Phosphorus Loads in Tile-Drained Landscapes.

PubMed

Ford, W; King, K; Williams, M; Williams, J; Fausey, N

2015-07-01

Numerical modeling is an economical and feasible approach for quantifying the effects of best management practices on dissolved reactive phosphorus (DRP) loadings from agricultural fields. However, tools that simulate both surface and subsurface DRP pathways are limited and have not been robustly evaluated in tile-drained landscapes. The objectives of this study were to test the ability of the Agricultural Policy/Environmental eXtender (APEX), a widely used field-scale model, to simulate surface and tile P loadings over management, hydrologic, biologic, tile, and soil gradients and to better understand the behavior of P delivery at the edge-of-field in tile-drained midwestern landscapes. To do this, a global, variance-based sensitivity analysis was performed, and model outputs were compared with measured P loads obtained from 14 surface and subsurface edge-of-field sites across central and northwestern Ohio. Results of the sensitivity analysis showed that response variables for DRP were highly sensitive to coupled interactions between presumed important parameters, suggesting nonlinearity of DRP delivery at the edge-of-field. Comparison of model results to edge-of-field data showcased the ability of APEX to simulate surface and subsurface runoff and the associated DRP loading at monthly to annual timescales; however, some high DRP concentrations and fluxes were not reflected in the model, suggesting the presence of preferential flow. Results from this study provide new insights into baseline tile DRP loadings that exceed thresholds for algal proliferation. Further, negative feedbacks between surface and subsurface DRP delivery suggest caution is needed when implementing DRP-based best management practices designed for a specific flow pathway. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Mechanisms of cross-talk between G-protein-coupled receptors resulting in enhanced release of intracellular Ca2+.

PubMed Central

Werry, Tim D; Wilkinson, Graeme F; Willars, Gary B

2003-01-01

Alteration in [Ca(2+)](i) (the intracellular concentration of Ca(2+)) is a key regulator of many cellular processes. To allow precise regulation of [Ca(2+)](i) and a diversity of signalling by this ion, cells possess many mechanisms by which they are able to control [Ca(2+)](i) both globally and at the subcellular level. Among these are many members of the superfamily of GPCRs (G-protein-coupled receptors), which are characterized by the presence of seven transmembrane domains. Typically, those receptors able to activate PLC (phospholipase C) enzymes cause release of Ca(2+) from intracellular stores and influence Ca(2+) entry across the plasma membrane. It has been well documented that Ca(2+) signalling by one type of GPCR can be influenced by stimulation of a different type of GPCR. Indeed, many studies have demonstrated heterologous desensitization between two different PLC-coupled GPCRs. This is not surprising, given our current understanding of negative-feedback regulation and the likely shared components of the signalling pathway. However, there are also many documented examples of interactions between GPCRs, often coupling preferentially to different signalling pathways, which result in a potentiation of Ca(2+) signalling. Such interactions have important implications for both the control of cell function and the interpretation of in vitro cell-based assays. However, there is currently no single mechanism that adequately accounts for all examples of this type of cross-talk. Indeed, many studies either have not addressed this issue or have been unable to determine the mechanism(s) involved. This review seeks to explore a range of possible mechanisms to convey their potential diversity and to provide a basis for further experimental investigation. PMID:12790797

CXCR7/CXCR4 heterodimer constitutively recruits beta-arrestin to enhance cell migration.

PubMed

Décaillot, Fabien M; Kazmi, Manija A; Lin, Ying; Ray-Saha, Sarmistha; Sakmar, Thomas P; Sachdev, Pallavi

2011-09-16

G protein-coupled receptor hetero-oligomerization is emerging as an important regulator of ligand-dependent transmembrane signaling, but precisely how receptor heteromers affect receptor pharmacology remains largely unknown. In this study, we have attempted to identify the functional significance of the heteromeric complex between CXCR4 and CXCR7 chemokine receptors. We demonstrate that co-expression of CXCR7 with CXCR4 results in constitutive recruitment of β-arrestin to the CXCR4·CXCR7 complex and simultaneous impairment of G(i)-mediated signaling. CXCR7/CXCR4 co-expression also results in potentiation of CXCL12 (SDF-1)-mediated downstream β-arrestin-dependent cell signaling pathways, including ERK1/2, p38 MAPK, and SAPK as judged from the results of experiments using siRNA knockdown to deplete β-arrestin. Interestingly, CXCR7/CXCR4 co-expression enhances cell migration in response to CXCL12 stimulation. Again, inhibition of β-arrestin using either siRNA knockdown or a dominant negative mutant abrogates the enhanced CXCL12-dependent migration of CXCR4/CXCR7-expressing cells. These results show how CXCR7, which cannot signal directly through G protein-linked pathways, can nevertheless affect cellular signaling networks by forming a heteromeric complex with CXCR4. The CXCR4·CXCR7 heterodimer complex recruits β-arrestin, resulting in preferential activation of β-arrestin-linked signaling pathways over canonical G protein pathways. CXCL12-dependent signaling of CXCR4 and its role in cellular physiology, including cancer metastasis, should be evaluated in the context of potential functional hetero-oligomerization with CXCR7.

CXCR7/CXCR4 Heterodimer Constitutively Recruits β-Arrestin to Enhance Cell Migration*

PubMed Central

Décaillot, Fabien M.; Kazmi, Manija A.; Lin, Ying; Ray-Saha, Sarmistha; Sakmar, Thomas P.; Sachdev, Pallavi

2011-01-01

G protein-coupled receptor hetero-oligomerization is emerging as an important regulator of ligand-dependent transmembrane signaling, but precisely how receptor heteromers affect receptor pharmacology remains largely unknown. In this study, we have attempted to identify the functional significance of the heteromeric complex between CXCR4 and CXCR7 chemokine receptors. We demonstrate that co-expression of CXCR7 with CXCR4 results in constitutive recruitment of β-arrestin to the CXCR4·CXCR7 complex and simultaneous impairment of Gi-mediated signaling. CXCR7/CXCR4 co-expression also results in potentiation of CXCL12 (SDF-1)-mediated downstream β-arrestin-dependent cell signaling pathways, including ERK1/2, p38 MAPK, and SAPK as judged from the results of experiments using siRNA knockdown to deplete β-arrestin. Interestingly, CXCR7/CXCR4 co-expression enhances cell migration in response to CXCL12 stimulation. Again, inhibition of β-arrestin using either siRNA knockdown or a dominant negative mutant abrogates the enhanced CXCL12-dependent migration of CXCR4/CXCR7-expressing cells. These results show how CXCR7, which cannot signal directly through G protein-linked pathways, can nevertheless affect cellular signaling networks by forming a heteromeric complex with CXCR4. The CXCR4·CXCR7 heterodimer complex recruits β-arrestin, resulting in preferential activation of β-arrestin-linked signaling pathways over canonical G protein pathways. CXCL12-dependent signaling of CXCR4 and its role in cellular physiology, including cancer metastasis, should be evaluated in the context of potential functional hetero-oligomerization with CXCR7. PMID:21730065

Novel fragmentation pathways of anionic adducts of steroids formed by electrospray anion attachment involving regioselective attachment, regiospecific decompositions, charge-induced pathways, and ion-dipole complex intermediates.

PubMed

Rannulu, Nalaka S; Cole, Richard B

2012-09-01

The analysis of several bifunctional neutral steroids, 5-α-pregnane diol (5-α-pregnane-3α-20βdiol), estradiol (3,17α-dihydroxy-1,3,5(10)-estratriene), progesterone (4-pregnene-3,20-dione), lupeol (3β-hydroxy-20(29)-lupene), pregnenolone (5-pregnen-3β-ol-20-one), and pregnenolone acetate (5-pregnen-3β-ol-20-one acetate) was accomplished by negative ion electrospray mass spectrometry (ESI-MS) employing adduct formation with various anions: fluoride, bicarbonate, acetate, and chloride. Fluoride yielded higher abundances of anionic adducts and more substantial abundances of deprotonated molecules compared with other investigated anions. Collision-induced dissociation (CID) of precursor [M + anion](-) adducts of these steroids revealed that fluoride adduct [M + F](-) precursors first lose HF to produce [M - H](-) and then undergo consecutive decompositions to yield higher abundances of structurally-informative product ions than the other tested anions. In addition to charge-remote fragmentations, the majority of CID pathways of estradiol are deduced to occur via charge-induced fragmentation. Most interestingly, certain anions exhibit preferential attachment to a specific site on these bifunctional steroid molecules, which we are calling "regioselective anion attachment." Regioselective anion attachment is evidenced by subsequent regiospecific decomposition. Regioselective attachment of fluoride (and acetate) anions to low (and moderate) acidity functional groups of pregnenolone, respectively, is demonstrated using deuterated compounds. Moreover, the formation of unique intermediate ion-dipole complexes leading to novel fragmentation pathways of fluoride adducts of pregnenolone acetate, and bicarbonate adducts of d(4)-pregnenolone, are also discussed.

Intracellular trafficking pathways for nuclear delivery of plasmid DNA complexed with highly efficient endosome escape polymers.

PubMed

Gillard, Marianne; Jia, Zhongfan; Hou, Jeff Jia Cheng; Song, Michael; Gray, Peter P; Munro, Trent P; Monteiro, Michael J

2014-10-13

Understanding the pathways for nuclear entry could see vast improvements in polymer design for the delivery of genetic materials to cells. Here, we use a novel diblock copolymer complexed with plasmid DNA (pDNA) to determine both its cellular entry and nuclear pathways. The diblock copolymer (A-C3) is specifically designed to bind and protect pDNA, release it at a specific time, but more importantly, rapidly escape the endosome. The copolymer was taken up by HEK293 cells preferentially via the clathrin-mediated endocytosis (CME) pathway, and the pDNA entered the nucleus to produce high gene expression levels in all cells after 48 h, a similar observation to the commercially available polymer transfection agent, PEI Max. This demonstrates that the polymers must first escape the endosome and then mediate transport of pDNA to the nucleus for occurrence of gene expression. The amount of pDNA within the nucleus was found to be higher for our A-C3 polymer than PEI Max, with our polymer delivering 7 times more pDNA than PEI Max after 24 h. We further found that entry into the nucleus was primarily through the small nuclear pores and did not occur during mitosis when the nuclear envelope becomes compromised. The observation that the polymers are also found in the nucleus supports the hypothesis that the large pDNA/polymer complex (size ~200 nm) must dissociate prior to nucleus entry and that cationic and hydrophobic monomer units on the polymer may facilitate active transport of the pDNA through the nuclear pore.

Novel Fragmentation Pathways of Anionic Adducts of Steroids Formed by Electrospray Anion Attachment Involving Regioselective Attachment, Regiospecific Decompositions, Charge-Induced Pathways, and Ion-Dipole Complex Intermediates

NASA Astrophysics Data System (ADS)

Rannulu, Nalaka S.; Cole, Richard B.

2012-09-01

The analysis of several bifunctional neutral steroids, 5-α-pregnane diol (5-α-pregnane-3α-20βdiol), estradiol (3,17α-dihydroxy-1,3,5(10)-estratriene), progesterone (4-pregnene-3,20-dione), lupeol (3β-hydroxy-20(29)-lupene), pregnenolone (5-pregnen-3β-ol-20-one), and pregnenolone acetate (5-pregnen-3β-ol-20-one acetate) was accomplished by negative ion electrospray mass spectrometry (ESI-MS) employing adduct formation with various anions: fluoride, bicarbonate, acetate, and chloride. Fluoride yielded higher abundances of anionic adducts and more substantial abundances of deprotonated molecules compared with other investigated anions. Collision-induced dissociation (CID) of precursor [M + anion]- adducts of these steroids revealed that fluoride adduct [M + F]- precursors first lose HF to produce [M - H]- and then undergo consecutive decompositions to yield higher abundances of structurally-informative product ions than the other tested anions. In addition to charge-remote fragmentations, the majority of CID pathways of estradiol are deduced to occur via charge-induced fragmentation. Most interestingly, certain anions exhibit preferential attachment to a specific site on these bifunctional steroid molecules, which we are calling "regioselective anion attachment." Regioselective anion attachment is evidenced by subsequent regiospecific decomposition. Regioselective attachment of fluoride (and acetate) anions to low (and moderate) acidity functional groups of pregnenolone, respectively, is demonstrated using deuterated compounds. Moreover, the formation of unique intermediate ion-dipole complexes leading to novel fragmentation pathways of fluoride adducts of pregnenolone acetate, and bicarbonate adducts of d4-pregnenolone, are also discussed.

FOXM1 in sarcoma: role in cell cycle, pluripotency genes and stem cell pathways.

PubMed

Kelleher, Fergal C; O'Sullivan, Hazel

2016-07-05

FOXM1 is a pro-proliferative transcription factor that promotes cell cycle progression at the G1-S, and G2-M transitions. It is activated by phosphorylation usually mediated by successive cyclin - cyclin dependent kinase complexes, and is highly expressed in sarcoma. p53 down regulates FOXM1 and FOXM1 inhibition is also partly dependent on Rb and p21. Abnormalities of p53 or Rb are frequent in sporadic sarcomas with bone or soft tissue sarcoma, accounting for 36% of index cancers in the high penetrance TP53 germline disorder, Li-Fraumeni syndrome.FOXM1 stimulates transcription of pluripotency related genes including SOX2, KLF4, OCT4, and NANOG many of which are important in sarcoma, a disorder of mesenchymal stem cell/ partially committed progenitor cells. In a selected specific, SOX2 is uniformly expressed in synovial sarcoma. Embryonic pathways preferentially used in stem cell such as Hippo, Hedgehog, and Wnt dominate in FOXM1 stoichiometry to alter rates of FOXM1 production or degradation. In undifferentiated pleomorphic sarcoma, liposarcoma, and fibrosarcoma, dysregulation of the Hippo pathway increases expression of the effector co-transcriptional activator Yes-Associated Protein (YAP). A complex involving YAP and the transcription factor TEAD elevates FOXM1 in these sarcoma subtypes. In another scenario 80% of desmoid tumors have nuclear localization of β-catenin, the Wnt pathway effector molecule. Thiazole antibiotics inhibit FOXM1 and because they have an auto-regulator loop FOXM1 expression is also inhibited. Current systemic treatment of sarcoma is of limited efficacy and inhibiting FOXM1 represents a potential new strategy.

Age-related changes in ATP-producing pathways in human skeletal muscle in vivo.

PubMed

Lanza, Ian R; Befroy, Douglas E; Kent-Braun, Jane A

2005-11-01

Energy for muscle contractions is supplied by ATP generated from 1) the net hydrolysis of phosphocreatine (PCr) through the creatine kinase reaction, 2) oxidative phosphorylation, and 3) anaerobic glycolysis. The effect of old age on these pathways is unclear. The purpose of this study was to examine whether age may affect ATP synthesis rates from these pathways during maximal voluntary isometric contractions (MVIC). Phosphorus magnetic resonance spectroscopy was used to assess high-energy phosphate metabolite concentrations in skeletal muscle of eight young (20-35 yr) and eight older (65-80 yr) men. Oxidative capacity was assessed from PCr recovery after a 16-s MVIC. We determined the contribution of each pathway to total ATP synthesis during a 60-s MVIC. Oxidative capacity was similar across age groups. Similar rates of ATP synthesis from PCr hydrolysis and oxidative phosphorylation were observed in young and older men during the 60-s MVIC. Glycolytic flux was higher in young than older men during the 60-s contraction (P < 0.001). When expressed relative to the overall ATP synthesis rate, older men relied on oxidative phosphorylation more than young men (P = 0.014) and derived a smaller proportion of ATP from anaerobic glycolysis (P < 0.001). These data demonstrate that although oxidative capacity was unaltered with age, peak glycolytic flux and overall ATP production from anaerobic glycolysis were lower in older men during a high-intensity contraction. Whether this represents an age-related limitation in glycolytic metabolism or a preferential reliance on oxidative ATP production remains to be determined.

Interplay of pathogenic forms of human tau with different autophagic pathways.

PubMed

Caballero, Benjamin; Wang, Yipeng; Diaz, Antonio; Tasset, Inmaculada; Juste, Yves Robert; Stiller, Barbara; Mandelkow, Eva-Maria; Mandelkow, Eckhard; Cuervo, Ana Maria

2018-02-01

Loss of neuronal proteostasis, a common feature of the aging brain, is accelerated in neurodegenerative disorders, including different types of tauopathies. Aberrant turnover of tau, a microtubule-stabilizing protein, contributes to its accumulation and subsequent toxicity in tauopathy patients' brains. A direct toxic effect of pathogenic forms of tau on the proteolytic systems that normally contribute to their turnover has been proposed. In this study, we analyzed the contribution of three different types of autophagy, macroautophagy, chaperone-mediated autophagy, and endosomal microautophagy to the degradation of tau protein variants and tau mutations associated with this age-related disease. We have found that the pathogenic P301L mutation inhibits degradation of tau by any of the three autophagic pathways, whereas the risk-associated tau mutation A152T reroutes tau for degradation through a different autophagy pathway. We also found defective autophagic degradation of tau when using mutations that mimic common posttranslational modifications in tau or known to promote its aggregation. Interestingly, although most mutations markedly reduced degradation of tau through autophagy, the step of this process preferentially affected varies depending on the type of tau mutation. Overall, our studies unveil a complex interplay between the multiple modifications of tau and selective forms of autophagy that may determine its physiological degradation and its faulty clearance in the disease context. © 2017 The Authors. Aging Cell published by the Anatomical Society and John Wiley & Sons Ltd.

Ku counteracts mobilization of PARP1 and MRN in chromatin damaged with DNA double-strand breaks

PubMed Central

Cheng, Qiao; Barboule, Nadia; Frit, Philippe; Gomez, Dennis; Bombarde, Oriane; Couderc, Bettina; Ren, Guo-Sheng; Salles, Bernard; Calsou, Patrick

2011-01-01

In mammalian cells, the main pathway for DNA double-strand breaks (DSBs) repair is classical non-homologous end joining (C-NHEJ). An alternative or back-up NHEJ (B-NHEJ) pathway has emerged which operates preferentially under C-NHEJ defective conditions. Although B-NHEJ appears particularly relevant to genomic instability associated with cancer, its components and regulation are still largely unknown. To get insights into this pathway, we have knocked-down Ku, the main contributor to C-NHEJ. Thus, models of human cell lines have been engineered in which the expression of Ku70/80 heterodimer can be significantly lowered by the conditional induction of a shRNA against Ku70. On Ku reduction in cells, resulting NHEJ competent protein extracts showed a shift from C- to B-NHEJ that could be reversed by addition of purified Ku protein. Using a cellular fractionation protocol after treatment with a strong DSBs inducer followed by western blotting or immunostaining, we established that, among C-NHEJ factors, Ku is the main counteracting factor against mobilization of PARP1 and the MRN complex to damaged chromatin. In addition, Ku limits PAR synthesis and single-stranded DNA production in response to DSBs. These data support the involvement of PARP1 and the MRN proteins in the B-NHEJ route for the repair of DNA DSBs. PMID:21880593

Delayed Luminance and Chromatic Contrast Sensitivity in Infants with Spontaneously Regressed Retinopathy of Prematurity

PubMed Central

Bosworth, Rain; Robbins, Shira L.; Granet, David B.; Dobkins, Karen

2013-01-01

Background The current study assessed whether contrast sensitivity is affected in preterm infants with a history of spontaneously regressed retinopathy of prematurity (ROP, Stages 1–3). Specifically, we employed luminance (light/dark) and chromatic (red/green) stimuli, which are mediated by the magnocellular (M) and parvocellular (P) subcortical pathways, respectively. Methods Contrast sensitivity (CS) was measured using forced choice preferential looking testing in 21 infants with a history of ROP and 41 control preterm infants who were born prematurely but did not develop ROP, tested between 8 and 47 weeks (2–11 months) postterm age. Infants were presented with chromatic and luminance drifting sinusoidal gratings, which appeared randomly on the left or right side of the monitor on each trial. The contrast of the stimuli varied across trials and was defined in terms of root mean squared cone contrast for long- and medium-wavelength cones. Results Between 8 and 25 weeks postterm, ROP infants had significantly worse CS, and there was a trend for greater impairment for Luminance than Chromatic CS. This delay was not seen at older ages between 26 and 47 weeks postterm. Conclusions These findings are consistent with the concept that early maturation of the M pathway is vulnerable to biological insult, as in the case of ROP, to a greater extent than is the P pathway. PMID:23744448

Targeting superoxide dismutase to endothelial caveolae profoundly alleviates inflammation caused by endotoxin.

PubMed

Shuvaev, Vladimir V; Kiseleva, Raisa Yu; Arguiri, Evguenia; Villa, Carlos H; Muro, Silvia; Christofidou-Solomidou, Melpo; Stan, Radu V; Muzykantov, Vladimir R

2018-02-28

Inflammatory mediators binding to Toll-Like receptors (TLR) induce an influx of superoxide anion in the ensuing endosomes. In endothelial cells, endosomal surplus of superoxide causes pro-inflammatory activation and TLR4 agonists act preferentially via caveolae-derived endosomes. To test the hypothesis that SOD delivery to caveolae may specifically inhibit this pathological pathway, we conjugated SOD with antibodies (Ab/SOD, size ~10nm) to plasmalemmal vesicle-associated protein (Plvap) that is specifically localized to endothelial caveolae in vivo and compared its effects to non-caveolar target CD31/PECAM-1. Plvap Ab/SOD bound to endothelial cells in culture with much lower efficacy than CD31 Ab/SOD, yet blocked the effects of LPS signaling with higher efficiency than CD31 Ab/SOD. Disruption of cholesterol-rich membrane domains by filipin inhibits Plvap Ab/SOD endocytosis and LPS signaling, implicating the caveolae-dependent pathway(s) in both processes. Both Ab/SOD conjugates targeted to Plvap and CD31 accumulated in the lungs after IV injection in mice, but the former more profoundly inhibited LPS-induced pulmonary inflammation and elevation of plasma level of interferon-beta and -gamma and interleukin-27. Taken together, these results indicate that targeted delivery of SOD to specific cellular compartments may offer effective, mechanistically precise interception of pro-inflammatory signaling mediated by reactive oxygen species. Copyright © 2018 Elsevier B.V. All rights reserved.

Molecular profiling of ALDH1+ colorectal cancer stem cells reveals preferential activation of MAPK, FAK, and oxidative stress pro-survival signalling pathways.

PubMed

Vishnubalaji, Radhakrishnan; Manikandan, Muthurangan; Fahad, Mohamed; Hamam, Rimi; Alfayez, Musaad; Kassem, Moustapha; Aldahmash, Abdullah; Alajez, Nehad M

2018-03-02

Tumour heterogeneity leads to variable clinical response and inaccurate diagnostic and prognostic assessment. Cancer stem cells (CSCs) represent a subpopulation responsible for invasion, metastasis, therapeutic resistance, and recurrence in many human cancer types. However, the true identity of colorectal cancer (CRC) SCs remains elusive. Here, we aimed to characterize and define the gene expression portrait of CSCs in CRC-model SW403 cells. We found that ALDH + positive cells are clonogenic and highly proliferative; their global gene expression profiling-based molecular signature revealed gene enrichment related to DNA damage, MAPK, FAK, oxidative stress response, and Wnt signalling. ALDH + cells showed enhanced ROS stress resistance, whereas MAPK/FAK pathway pharmacologic inhibition limited their survival. Conversely, 5-fluorouracil increased the ALDH + cell fraction among the SW403, HCT116 and SW620 CRC models. Notably, analysis of ALDH1A1 and POU5F1 expression levels in cohorts of 462 or 420 patients for overall (OS) or disease-free (DFS) survival, respectively, obtained from the Cancer Genome Atlas CRC dataset, revealed strong association between elevated expression and poor OS ( p = 0.006) and poor DFS ( p = 0.05), thus implicating ALDH1A1 and POU5F1 in CRC prognosis. Our data reveal distinct molecular signature of ALDH + CSCs in CRC and suggest pathways relevant for successful targeted therapies and management of CRC.

Investigating low flow process controls, through complex modelling, in a UK chalk catchment

NASA Astrophysics Data System (ADS)

Lubega Musuuza, Jude; Wagener, Thorsten; Coxon, Gemma; Freer, Jim; Woods, Ross; Howden, Nicholas

2017-04-01

The typical streamflow response of Chalk catchments is dominated by groundwater contributions due the high degree of groundwater recharge through preferential flow pathways. The groundwater store attenuates the precipitation signal, which causes a delay between the corresponding high and low extremes in the precipitation and the stream flow signals. Streamflow responses can therefore be quite out of phase with the precipitation input to a Chalk catchment. Therefore characterising such catchment systems, including modelling approaches, clearly need to reproduce these percolation and groundwater dominated pathways to capture these dominant flow pathways. The simulation of low flow conditions for chalk catchments in numerical models is especially difficult due to the complex interactions between various processes that may not be adequately represented or resolved in the models. Periods of low stream flows are particularly important due to competing water uses in the summer, including agriculture and water supply. In this study we apply and evaluate the physically-based Pennstate Integrated Hydrologic Model (PIHM) to the River Kennet, a sub-catchment of the Thames Basin, to demonstrate how the simulations of a chalk catchment are improved by a physically-based system representation. We also use an ensemble of simulations to investigate the sensitivity of various hydrologic signatures (relevant to low flows and droughts) to the different parameters in the model, thereby inferring the levels of control exerted by the processes that the parameters represent.

Separation technique provides rapid quantitative determination of cesium-137 in irradiated nuclear fuel

NASA Technical Reports Server (NTRS)

Ellenburg, E. J.; Mc Cown, J. J.

1967-01-01

Potassium cobalt ferrocyanide is used to determine cesium-137 activity in irradiated fuel samples. It preferentially removes cesium from an acid solution of the fuel material. The residue is filtered and analyzed with a gamma spectrometer.

Preferential production and transport of grass-derived pyrogenic carbon in NE-Australian savanna ecosystems

NASA Astrophysics Data System (ADS)

Saiz, Gustavo; Goodrick, Iain; Wurster, Christopher; Nelson, Paul N.; Wynn, Jonathan; Bird, Michael

2017-12-01

Understanding the main factors driving fire regimes in grasslands and savannas is critical to better manage their biodiversity and functions. Moreover, improving our knowledge on pyrogenic carbon (PyC) dynamics, including formation, transport and deposition, is fundamental to better understand a significant slow-cycling component of the global carbon cycle, particularly as these ecosystems account for a substantial proportion of the area globally burnt. However, a thorough assessment of past fire regimes in grass-dominated ecosystems is problematic due to challenges in interpreting the charcoal record of sediments. It is therefore critical to adopt appropriate sampling and analytical methods to allow the acquisition of reliable data and information on savanna fire dynamics. This study uses hydrogen pyrolysis (HyPy) to quantify PyC abundance and stable isotope composition (δ13C) in recent sediments across 38 micro-catchments covering a wide range of mixed C3/C4 vegetation in north Queensland, Australia. We exploited the contrasting δ13C values of grasses (i.e. C4; δ13C >-15‰) and woody vegetation (i.e. C3; δ13C <-24‰) to assess the preferential production and transport of grass-derived PyC in savanna ecosystems. Analyses were conducted on bulk and size-fractionated samples to determine the fractions into which PyC preferentially accumulates. Our data show that the δ13C value of PyC in the sediments is decoupled from the δ13C value of total organic carbon, which suggests that a significant component of PyC may be derived from incomplete grass combustion, even when the proportion of C4 grass biomass in the catchment was relatively small. Furthermore, we conducted 16 experimental burns that indicate that there is a comminution of PyC produced in-situ to smaller particles, which facilitates the transport of this material, potentially affecting its preservation potential. Savanna fires preferentially burn the grass understory rather than large trees, leading to a bias toward the finer C4–derived PyC in the sedimentary record. This in turn, provides further evidence for the preferential production and transport of C4-derived PyC in mixed ecosystems where grass and woody vegetation coexist. Moreover, our isotopic approach provides independent validation of findings derived from conventional charcoal counting techniques concerning the appropriateness of adopting a relatively small particle size threshold.

Transit time distributions to assess present and future contamination risk of karst aquifers over Europe and the Mediterranean

NASA Astrophysics Data System (ADS)

Hartmann, Andreas; Gleeson, Tom; Wada, Yoshihide; Wagener, Thorsten

2016-04-01

Karst develops through the dissolution of carbonate rock. Karst groundwater in Europe is a major source of fresh water contributing up to half of the total drinking water supply in some countries. Climate model projections suggest that in the next 100 years, karst regions will experience a strong increase in temperature and a serious decrease of precipitation - especially in the Mediterranean region. Previous work showed that the karstic preferential recharge processes result in enhanced recharge rates and future climate sensitivity. But as there is fast water flow form the surface to the aquifer, there is also an enhanced risk of groundwater contamination. In this study we will assess the contamination risk of karst aquifers over Europe and the Mediterranean using simulated transit time distributions. Using a new type of semi-distributed model that considers the spatial heterogeneity of the karst system by distribution functions we simulated a range of spatially variable pathways of karstic groundwater recharge. The model is driven by the bias-corrected 5 GCMs of the ISI-MIP project (RCP8.5). Transit time distributions are calculated by virtual tracer experiments. These are repeated several times in the present (1991-2010) and the future (2080-2099). We can show that regions with larger fractions of preferential recharge show higher risks of contamination and that spatial patterns of contamination risk change towards the future.

Solubilization of aromatic and hydrophobic moieties by arginine in aqueous solutions

NASA Astrophysics Data System (ADS)

Li, Jianguo; Garg, Manju; Shah, Dhawal; Rajagopalan, Raj

2010-08-01

Experiments hold intriguing, circumstantial clues to the mechanisms behind arginine-mediated solubilization of small organic drugs and suppression of protein aggregation driven by hydrophobic or aromatic associations, but how exactly arginine's molecular structure and interactions contribute to its function remains unclear since attention has focused so far on the thermodynamics of the preferential exclusion or binding of arginine. Here, we examine, through molecular dynamics simulations, how arginine solubilizes nanoscale particles with hydrophobic surfaces or aromatic-ring-type surface interactions. We show that preferential, hydrophobic, and dispersion interactions of arginine's guanidinium group with the particles lead to a surfactant-like behavior of arginine around the particles and to a solvation layer with a protective polar mask creating a hydrophilic shell. Additionally, arginine-arginine association around the solvation layer further prevents aggregative contacts. The results shed some light on the mechanistic basis of arginine's function as a suppressant of protein aggregation, although the complex energy landscapes and kinetic pathways of aggregation are protein-dependent and pose formidable challenges to developing comprehensive mechanistic pictures. Our results suggest arginine's mode of interaction with hydrophobic patches and aromatic residues could reduce aggregation-prone intermediate states of proteins and shield protein-protein aggregative contacts. The approach used here offers a systematic way of exploring implications of other amino acid/excipient interactions by studying interactions of the excipient with particles grafted with amino acids.

Alternative Splicing Profile and Sex-Preferential Gene Expression in the Female and Male Pacific Abalone Haliotis discus hannai.

PubMed

Kim, Mi Ae; Rhee, Jae-Sung; Kim, Tae Ha; Lee, Jung Sick; Choi, Ah-Young; Choi, Beom-Soon; Choi, Ik-Young; Sohn, Young Chang

2017-03-09

In order to characterize the female or male transcriptome of the Pacific abalone and further increase genomic resources, we sequenced the mRNA of full-length complementary DNA (cDNA) libraries derived from pooled tissues of female and male Haliotis discus hannai by employing the Iso-Seq protocol of the PacBio RSII platform. We successfully assembled whole full-length cDNA sequences and constructed a transcriptome database that included isoform information. After clustering, a total of 15,110 and 12,145 genes that coded for proteins were identified in female and male abalones, respectively. A total of 13,057 putative orthologs were retained from each transcriptome in abalones. Overall Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analyzed in each database showed a similar composition between sexes. In addition, a total of 519 and 391 isoforms were genome-widely identified with at least two isoforms from female and male transcriptome databases. We found that the number of isoforms and their alternatively spliced patterns are variable and sex-dependent. This information represents the first significant contribution to sex-preferential genomic resources of the Pacific abalone. The availability of whole female and male transcriptome database and their isoform information will be useful to improve our understanding of molecular responses and also for the analysis of population dynamics in the Pacific abalone.

Alternative Splicing Profile and Sex-Preferential Gene Expression in the Female and Male Pacific Abalone Haliotis discus hannai

PubMed Central

Kim, Mi Ae; Rhee, Jae-Sung; Kim, Tae Ha; Lee, Jung Sick; Choi, Ah-Young; Choi, Beom-Soon; Choi, Ik-Young; Sohn, Young Chang

2017-01-01

In order to characterize the female or male transcriptome of the Pacific abalone and further increase genomic resources, we sequenced the mRNA of full-length complementary DNA (cDNA) libraries derived from pooled tissues of female and male Haliotis discus hannai by employing the Iso-Seq protocol of the PacBio RSII platform. We successfully assembled whole full-length cDNA sequences and constructed a transcriptome database that included isoform information. After clustering, a total of 15,110 and 12,145 genes that coded for proteins were identified in female and male abalones, respectively. A total of 13,057 putative orthologs were retained from each transcriptome in abalones. Overall Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analyzed in each database showed a similar composition between sexes. In addition, a total of 519 and 391 isoforms were genome-widely identified with at least two isoforms from female and male transcriptome databases. We found that the number of isoforms and their alternatively spliced patterns are variable and sex-dependent. This information represents the first significant contribution to sex-preferential genomic resources of the Pacific abalone. The availability of whole female and male transcriptome database and their isoform information will be useful to improve our understanding of molecular responses and also for the analysis of population dynamics in the Pacific abalone. PMID:28282934

The Chlamydial Inclusion Preferentially Intercepts Basolaterally Directed Sphingomyelin-Containing Exocytic Vacuoles

PubMed Central

Moore, Elizabeth R.; Fischer, Elizabeth R.; Mead, David J.; Hackstadt, Ted

2010-01-01

Chlamydiae replicate intracellularly within a unique vacuole termed the inclusion. The inclusion circumvents classical endosomal/lysosomal pathways but actively intercepts a subset of Golgi-derived exocytic vesicles containing sphingomyelin (SM) and cholesterol. To further examine this interaction, we developed a polarized epithelial cell model to study vectoral trafficking of lipids and proteins to the inclusion. We examined seven epithelial cell lines for their ability to form single monolayers of polarized cells and support chlamydial development. Of these cell lines, polarized colonic mucosal C2BBe1 cells were readily infected with Chlamydia trachomatis and remained polarized throughout infection. Trafficking of (6-((N-(7-nitrobenz-2-oxa-1, 3-diazol-4-yl) amino)hexanoyl)sphingosine) (NBD-C6-ceramide) and its metabolic derivatives, NBD-glucosylceramide (GlcCer) and NBD-SM, was analyzed. SM was retained within L2-infected cells relative to mock-infected cells, correlating with a disruption of basolateral SM trafficking. There was no net retention of GlcCer within L2-infected cells and purification of C. trachomatis elementary bodies from polarized C2BBe1 cells confirmed that bacteria retained only SM. The chlamydial inclusion thus appears to preferentially intercept basolaterally-directed SM-containing exocytic vesicles, suggesting a divergence in SM and GlcCer trafficking. The observed changes in lipid trafficking were a chlamydia-specific effect because Coxiella burnetii-infected cells revealed no changes in GlcCer or SM polarized trafficking. PMID:18778406