qSR: a quantitative super-resolution analysis tool reveals the cell-cycle dependent organization of RNA Polymerase I in live human cells.

PubMed

Andrews, J O; Conway, W; Cho, W -K; Narayanan, A; Spille, J -H; Jayanth, N; Inoue, T; Mullen, S; Thaler, J; Cissé, I I

2018-05-09

We present qSR, an analytical tool for the quantitative analysis of single molecule based super-resolution data. The software is created as an open-source platform integrating multiple algorithms for rigorous spatial and temporal characterizations of protein clusters in super-resolution data of living cells. First, we illustrate qSR using a sample live cell data of RNA Polymerase II (Pol II) as an example of highly dynamic sub-diffractive clusters. Then we utilize qSR to investigate the organization and dynamics of endogenous RNA Polymerase I (Pol I) in live human cells, throughout the cell cycle. Our analysis reveals a previously uncharacterized transient clustering of Pol I. Both stable and transient populations of Pol I clusters co-exist in individual living cells, and their relative fraction vary during cell cycle, in a manner correlating with global gene expression. Thus, qSR serves to facilitate the study of protein organization and dynamics with very high spatial and temporal resolutions directly in live cell.

The production of monokaryotic hyphae by Cryptococcus neoformans can be induced by high temperature arrest of the cell cycle and is independent of same-sex mating.

PubMed

Fu, Jianmin; Morris, Ian R; Wickes, Brian L

2013-01-01

Cryptococcus neoformans is a heterothallic fungal pathogen of humans and animals. Although the fungus grows primarily as a yeast, hyphae are produced during the sexual phase and during a process called monokaryotic fruiting, which is also believed to involve sexual reproduction, but between cells of the same mating type. Here we report a novel monokaryotic fruiting mechanism that is dependent on the cell cycle and occurs in haploid cells in the absence of sexual reproduction. Cells grown at 37°C were found to rapidly produce hyphae (∼4 hrs) and at high frequency (∼40% of the population) after inoculation onto hyphae-inducing agar. Microscopic examination of the 37°C seed culture revealed a mixture of normal-sized and enlarged cells. Micromanipulation of single cells demonstrated that only enlarged cells were able to produce hyphae and genetic analysis confirmed that hyphae did not arise from α-α mating or endoduplication. Cell cycle analysis revealed that cells grown at 37°C had an increased population of cells in G2 arrest, with the proportion correlated with the frequency of monokaryotic fruiting. Cell sorting experiments demonstrated that enlarged cells were only found in the G2-arrested population and only this population contained cells able to produce hyphae. Treatment of cells at low temperature with the G2 cell cycle arrest agent, nocodazole, induced hyphal growth, confirming the role of the cell cycle in this process. Taken together, these results reveal a mating-independent mechanism for monokaryotic fruiting, which is dependent on the cell cycle for induction of hyphal competency.

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

Martinotti, Simona; Ranzato, Elia, E-mail: ranzato@unipmn.it; Parodi, Monica

Malignant mesothelioma (MMe) is a poor-prognosis tumor in need of innovative therapies. In a previous in vivo study, we showed synergistic anti-MMe properties of the ascorbate/epigallocatechin-3-gallate/gemcitabine combination. We have now focused on the mechanism of action, showing the induction of apoptosis and cell cycle arrest through measurements of caspase 3, intracellular Ca{sup 2+}, annexin V, and DNA content. StellArray™ PCR technology and Western immunoblotting revealed DAPK2-dependent apoptosis, upregulation of cell cycle promoters, downregulation of cell cycle checkpoints and repression of NFκB expression. The complex of data indicates that the mixture is synergistic in inducing cell cycle deregulation and non-inflammatory apoptosis,more » suggesting its possible use in MMe treatment. - Highlights: • Ascorbate/epigallocathechin-gallate/gemcitabine has been tested on mesothelioma cells • A synergistic mechanism has been shown for cell cycle arrest and apoptosis • PCR-array analysis has revealed the de-regulation of apoptosis and cell cycle genes • Maximum upregulation has been found for the Death-Associated Protein Kinase-2 gene • Data suggest that the mixture could be used as a clinical treatment.« less

Discovery and Enumeration of Organic-Chemical and Biomimetic Reaction Cycles within the Network of Chemistry.

PubMed

Bajczyk, Michał D; Dittwald, Piotr; Wołos, Agnieszka; Szymkuć, Sara; Grzybowski, Bartosz A

2018-02-23

Analysis of the chemical-organic knowledge represented as a giant network reveals that it contains millions of reaction sequences closing into cycles. Without realizing it, independent chemists working at different times have jointly created examples of cyclic sequences that allow for the recovery of useful reagents and for the autoamplification of synthetically important molecules, those that mimic biological cycles, and those that can be operated one-pot. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Modelling health and output at business cycle horizons for the USA.

PubMed

Narayan, Paresh Kumar

2010-07-01

In this paper we employ a theoretical framework - a simple macro model augmented with health - that draws guidance from the Keynesian view of business cycles to examine the relative importance of permanent and transitory shocks in explaining variations in health expenditure and output at business cycle horizons for the USA. The variance decomposition analysis of shocks reveals that at business cycle horizons permanent shocks explain the bulk of the variations in output, while transitory shocks explain the bulk of the variations in health expenditures. We undertake a shock decomposition analysis for private health expenditures versus public health expenditures and interestingly find that while transitory shocks are more important for private sector expenditures, permanent shocks dominate public health expenditures. Copyright (c) 2009 John Wiley & Sons, Ltd.

Preservice Teachers' Use of the Technology Integration Planning Cycle to Integrate iPads into Literacy Instruction

ERIC Educational Resources Information Center

Hutchison, Amy; Colwell, Jamie

2016-01-01

The purpose of this case study was to examine preservice teachers' use of the Technology Integration Planning Cycle (TIPC; Hutchison & Woodward, 2014) to integrate iPads into literacy instruction. Analysis revealed two findings related to using the TIPC to plan instruction: (a) Though the TIPC provides a structured approach to planning that…

Cluster analysis of intradiurnal holm oak pollen cycles at peri-urban and rural sampling sites in southwestern Spain

NASA Astrophysics Data System (ADS)

Hernández-Ceballos, M. A.; García-Mozo, H.; Galán, C.

2015-08-01

The impact of regional and local weather and of local topography on intradiurnal variations in airborne pollen levels was assessed by analysing bi-hourly holm oak ( Quercus ilex subsp. ballota (Desf.) Samp.) pollen counts at two sampling stations located 40 km apart, in southwestern Spain (Cordoba city and El Cabril nature reserve) over the period 2010-2011. Pollen grains were captured using Hirst-type volumetric spore traps. Analysis of regional weather conditions was based on the computation of backward trajectories using the HYSPLIT model. Sampling days were selected on the basis of phenological data; rainy days were eliminated, as were days lying outside a given range of percentiles (P95-P5). Analysis of cycles for the study period, as a whole, revealed differences between sampling sites, with peak bi-hourly pollen counts at night in Cordoba and at midday in El Cabril. Differences were also noted in the influence of surface weather conditions (temperature, relative humidity and wind). Cluster analysis of diurnal holm oak pollen cycles revealed the existence of five clusters at each sampling site. Analysis of backward trajectories highlighted specific regional air-flow patterns associated with each site. Findings indicated the contribution of both nearby and distant pollen sources to diurnal cycles. The combined use of cluster analysis and meteorological analysis proved highly suitable for charting the impact of local weather conditions on airborne pollen-count patterns. This method, and the specific tools used here, could be used not only to study diurnal variations in counts for other pollen types and in other biogeographical settings, but also in a number of other research fields involving airborne particle transport modelling, e.g. radionuclide transport in emergency preparedness exercises.

Cluster analysis of intradiurnal holm oak pollen cycles at peri-urban and rural sampling sites in southwestern Spain.

PubMed

Hernández-Ceballos, M A; García-Mozo, H; Galán, C

2015-08-01

The impact of regional and local weather and of local topography on intradiurnal variations in airborne pollen levels was assessed by analysing bi-hourly holm oak (Quercus ilex subsp. ballota (Desf.) Samp.) pollen counts at two sampling stations located 40 km apart, in southwestern Spain (Cordoba city and El Cabril nature reserve) over the period 2010-2011. Pollen grains were captured using Hirst-type volumetric spore traps. Analysis of regional weather conditions was based on the computation of backward trajectories using the HYSPLIT model. Sampling days were selected on the basis of phenological data; rainy days were eliminated, as were days lying outside a given range of percentiles (P95-P5). Analysis of cycles for the study period, as a whole, revealed differences between sampling sites, with peak bi-hourly pollen counts at night in Cordoba and at midday in El Cabril. Differences were also noted in the influence of surface weather conditions (temperature, relative humidity and wind). Cluster analysis of diurnal holm oak pollen cycles revealed the existence of five clusters at each sampling site. Analysis of backward trajectories highlighted specific regional air-flow patterns associated with each site. Findings indicated the contribution of both nearby and distant pollen sources to diurnal cycles. The combined use of cluster analysis and meteorological analysis proved highly suitable for charting the impact of local weather conditions on airborne pollen-count patterns. This method, and the specific tools used here, could be used not only to study diurnal variations in counts for other pollen types and in other biogeographical settings, but also in a number of other research fields involving airborne particle transport modelling, e.g. radionuclide transport in emergency preparedness exercises.

Metatranscriptomic analysis of a high-sulfide aquatic spring reveals insights into sulfur cycling and unexpected aerobic metabolism

PubMed Central

Elshahed, Mostafa S.; Najar, Fares Z.; Krumholz, Lee R.

2015-01-01

Zodletone spring is a sulfide-rich spring in southwestern Oklahoma characterized by shallow, microoxic, light-exposed spring water overlaying anoxic sediments. Previously, culture-independent 16S rRNA gene based diversity surveys have revealed that Zodletone spring source sediments harbor a highly diverse microbial community, with multiple lineages putatively involved in various sulfur-cycling processes. Here, we conducted a metatranscriptomic survey of microbial populations in Zodletone spring source sediments to characterize the relative prevalence and importance of putative phototrophic, chemolithotrophic, and heterotrophic microorganisms in the sulfur cycle, the identity of lineages actively involved in various sulfur cycling processes, and the interaction between sulfur cycling and other geochemical processes at the spring source. Sediment samples at the spring’s source were taken at three different times within a 24-h period for geochemical analyses and RNA sequencing. In depth mining of datasets for sulfur cycling transcripts revealed major sulfur cycling pathways and taxa involved, including an unexpected potential role of Actinobacteria in sulfide oxidation and thiosulfate transformation. Surprisingly, transcripts coding for the cyanobacterial Photosystem II D1 protein, methane monooxygenase, and terminal cytochrome oxidases were encountered, indicating that genes for oxygen production and aerobic modes of metabolism are actively being transcribed, despite below-detectable levels (<1 µM) of oxygen in source sediment. Results highlight transcripts involved in sulfur, methane, and oxygen cycles, propose that oxygenic photosynthesis could support aerobic methane and sulfide oxidation in anoxic sediments exposed to sunlight, and provide a viewpoint of microbial metabolic lifestyles under conditions similar to those seen during late Archaean and Proterozoic eons. PMID:26417542

Metatranscriptomic analysis of a high-sulfide aquatic spring reveals insights into sulfur cycling and unexpected aerobic metabolism.

PubMed

Spain, Anne M; Elshahed, Mostafa S; Najar, Fares Z; Krumholz, Lee R

2015-01-01

Zodletone spring is a sulfide-rich spring in southwestern Oklahoma characterized by shallow, microoxic, light-exposed spring water overlaying anoxic sediments. Previously, culture-independent 16S rRNA gene based diversity surveys have revealed that Zodletone spring source sediments harbor a highly diverse microbial community, with multiple lineages putatively involved in various sulfur-cycling processes. Here, we conducted a metatranscriptomic survey of microbial populations in Zodletone spring source sediments to characterize the relative prevalence and importance of putative phototrophic, chemolithotrophic, and heterotrophic microorganisms in the sulfur cycle, the identity of lineages actively involved in various sulfur cycling processes, and the interaction between sulfur cycling and other geochemical processes at the spring source. Sediment samples at the spring's source were taken at three different times within a 24-h period for geochemical analyses and RNA sequencing. In depth mining of datasets for sulfur cycling transcripts revealed major sulfur cycling pathways and taxa involved, including an unexpected potential role of Actinobacteria in sulfide oxidation and thiosulfate transformation. Surprisingly, transcripts coding for the cyanobacterial Photosystem II D1 protein, methane monooxygenase, and terminal cytochrome oxidases were encountered, indicating that genes for oxygen production and aerobic modes of metabolism are actively being transcribed, despite below-detectable levels (<1 µM) of oxygen in source sediment. Results highlight transcripts involved in sulfur, methane, and oxygen cycles, propose that oxygenic photosynthesis could support aerobic methane and sulfide oxidation in anoxic sediments exposed to sunlight, and provide a viewpoint of microbial metabolic lifestyles under conditions similar to those seen during late Archaean and Proterozoic eons.

Deciphering life history transcriptomes in different environments

PubMed Central

Etges, William J.; Trotter, Meredith V.; de Oliveira, Cássia C.; Rajpurohit, Subhash; Gibbs, Allen G.; Tuljapurkar, Shripad

2014-01-01

We compared whole transcriptome variation in six preadult stages and seven adult female ages in two populations of cactophilic Drosophila mojavensis reared on two host plants in order to understand how differences in gene expression influence standing life history variation. We used Singular Value Decomposition (SVD) to identify dominant trajectories of life cycle gene expression variation, performed pair-wise comparisons of stage and age differences in gene expression across the life cycle, identified when genes exhibited maximum levels of life cycle gene expression, and assessed population and host cactus effects on gene expression. Life cycle SVD analysis returned four significant components of transcriptional variation, revealing functional enrichment of genes responsible for growth, metabolic function, sensory perception, neural function, translation and aging. Host cactus effects on female gene expression revealed population and stage specific differences, including significant host plant effects on larval metabolism and development, as well as adult neurotransmitter binding and courtship behavior gene expression levels. In 3 - 6 day old virgin females, significant up-regulation of genes associated with meiosis and oogenesis was accompanied by down-regulation of genes associated with somatic maintenance, evidence for a life history tradeoff. The transcriptome of D. mojavensis reared in natural environments throughout its life cycle revealed core developmental transitions and genome wide influences on life history variation in natural populations. PMID:25442828

Quality Assessment of College Admissions Processes.

ERIC Educational Resources Information Center

Fisher, Caroline; Weymann, Elizabeth; Todd, Amy

2000-01-01

This study evaluated the admissions process for a Master's in Business Administration Program using such quality improvement techniques as customer surveys, benchmarking, and gap analysis. Analysis revealed that student dissatisfaction with the admissions process may be a factor influencing declining enrollment. Cycle time and number of student…

LeuT conformational sampling utilizing accelerated molecular dynamics and principal component analysis.

PubMed

Thomas, James R; Gedeon, Patrick C; Grant, Barry J; Madura, Jeffry D

2012-07-03

Monoamine transporters (MATs) function by coupling ion gradients to the transport of dopamine, norepinephrine, or serotonin. Despite their importance in regulating neurotransmission, the exact conformational mechanism by which MATs function remains elusive. To this end, we have performed seven 250 ns accelerated molecular dynamics simulations of the leucine transporter, a model for neurotransmitter MATs. By varying the presence of binding-pocket leucine substrate and sodium ions, we have sampled plausible conformational states representative of the substrate transport cycle. The resulting trajectories were analyzed using principal component analysis of transmembrane helices 1b and 6a. This analysis revealed seven unique structures: two of the obtained conformations are similar to the currently published crystallographic structures, one conformation is similar to a proposed open inward structure, and four conformations represent novel structures of potential importance to the transport cycle. Further analysis reveals that the presence of binding-pocket sodium ions is necessary to stabilize the locked-occluded and open-inward conformations. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Effect of excess lithium in LiMn2O4 and Li1.15Mn1.85O4 electrodes revealed by quantitative analysis of soft X-ray absorption spectroscopy

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

Zhuo, Zengqing; Olalde-Velasco, Paul.; Chin, Timothy

We performed a comparative study of the soft x-ray absorption spectroscopy of the LiMn2O4 and Li1.15Mn1.85O4 electrode materials with a quantitative analysis of the Mn oxidation states. The revealed redox evolution of Mn upon the electrochemical cycling clarifies the effect of the excess Li in the materials, which naturally explains the different electrochemical performance. The spectral analysis perfectly agrees with the different initial cycling capacities of the two materials. The results show unambiguously that Mn3+ starts to dominate the electrode surface after only one cycle. More importantly, the data show that, while LiMn2O4 electrodes follow the nominal Mn redox evolution,more » the formation of Mn3+ on the electrode surface is largely retarded for the Li1.15Mn1.85O4 during most of the electrochemical process. Such a different surface Mn redox behavior leads to differences in the detrimental effects of Mn2+ formation on the surface, which is observed directly after only two cycles. Our results provide strong evidence that a key effect of the (bulk) excess Li doping is actually due to processes on the electrode surfaces.« less

Effect of excess lithium in LiMn2O4 and Li1.15Mn1.85O4 electrodes revealed by quantitative analysis of soft X-ray absorption spectroscopy

DOE PAGES

Zhuo, Zengqing; Olalde-Velasco, Paul.; Chin, Timothy; ...

2017-02-27

We performed a comparative study of the soft x-ray absorption spectroscopy of the LiMn2O4 and Li1.15Mn1.85O4 electrode materials with a quantitative analysis of the Mn oxidation states. The revealed redox evolution of Mn upon the electrochemical cycling clarifies the effect of the excess Li in the materials, which naturally explains the different electrochemical performance. The spectral analysis perfectly agrees with the different initial cycling capacities of the two materials. The results show unambiguously that Mn3+ starts to dominate the electrode surface after only one cycle. More importantly, the data show that, while LiMn2O4 electrodes follow the nominal Mn redox evolution,more » the formation of Mn3+ on the electrode surface is largely retarded for the Li1.15Mn1.85O4 during most of the electrochemical process. Such a different surface Mn redox behavior leads to differences in the detrimental effects of Mn2+ formation on the surface, which is observed directly after only two cycles. Our results provide strong evidence that a key effect of the (bulk) excess Li doping is actually due to processes on the electrode surfaces.« less

A TRMM-Calibrated Infrared Technique for Convective and Stratiform Rainfall: Analysis and Validation

NASA Technical Reports Server (NTRS)

Negri, Andrew; Starr, David OC. (Technical Monitor)

2001-01-01

A satellite infrared technique with passive microwave calibration has been developed for estimating convective and stratiform rainfall. The Convective-Stratiform Technique, calibrated by coincident, physically retrieved rain rates from the TRMM Microwave Imager (TMI), has been applied to 30 min interval GOES infrared data and aggregated over seasonal and yearly periods over northern South America. The diurnal cycle of rainfall, as well as the division between convective and stratiform rainfall is presented. For the period Jan-April 1999, analysis revealed significant effects of local circulations (river breeze, land/sea breeze, mountain/valley) on both the total rainfall and it's diurnal cycle. Results compared well (a one-hour lag) with the diurnal cycle derived from TOGA radar-estimated rainfall in Rondonia. The satellite estimates revealed that the convective rain constituted 24% of the rain area while accounting for 67% of the rain volume. Estimates of the diurnal cycle (both total rainfall and convective/stratiform) for an area encompassing the Amazon Basin (3 x 10(exp 6) sq km) were in phase with those from the TRMM Precipitation Radar, despite the latter's limited sampling. Results will be presented comparing the yearly (2000) diurnal cycle for large regions (including the Amazon Basin), and an intercomparison of January-March estimates for three years, (1999-2001). We hope to demonstrate the utility of using the TRMM PR observations as verification for infrared estimates of the diurnal cycle, and as verification of the apportionment of rainfall into convective and stratiform components.

A TRMM-Calibrated Infrared Technique for Convective and Stratiform Rainfall: Analysis and Validation

NASA Technical Reports Server (NTRS)

Negri, Andrew; Starr, David OC. (Technical Monitor)

2001-01-01

A satellite infrared technique with passive microwave calibration has been developed for estimating convective and stratiform. rainfall. The Convective-Stratiform Technique, calibrated by coincident, physically retrieved rain rates from the TRMM Microwave Imager (TMI), has been applied to 30 min interval GOES infrared data and aggregated over seasonal and yearly periods over northern South America. The diurnal cycle of rainfall, as well as the division between convective and stratiform rainfall is presented. For the period Jan-April 1999, analysis revealed significant effects of local circulations (river breeze, land/sea breeze, mountain/valley) on both the total rainfall and it's diurnal cycle. Results compared well (a one-hour lag) with the diurnal cycle derived from TOGA radar-estimated rainfall in Rondonia. The satellite estimates revealed that the convective rain constituted 24% of the rain area while accounting for 67% of the rain volume. Estimates of the diurnal cycle (both total rainfall and convective/stratiform) for an area encompassing the Amazon Basin (3 x 10(exp 6) square km) were in phase with those from the TRMM Precipitation Radar, despite the latter's limited sampling. Results will be presented comparing the yearly (2000) diurnal cycle for large regions (including the Amazon Basin), and an intercomparison of January-March estimates for three years, 1999-2001. We hope to demonstrate the utility of using the TRMM PR observations as verification for infrared estimates of the diurnal cycle, and as verification of the apportionment of rainfall into convective and stratiform components.

Post mortem analysis of fatigue mechanisms in LiNi0.8Co0.15Al0.05O2 - LiNi0.5Co0.2Mn0.3O2 - LiMn2O4/graphite lithium ion batteries

NASA Astrophysics Data System (ADS)

Lang, Michael; Darma, Mariyam Susana Dewi; Kleiner, Karin; Riekehr, Lars; Mereacre, Liuda; Ávila Pérez, Marta; Liebau, Verena; Ehrenberg, Helmut

2016-09-01

The fatigue of commercial lithium ion batteries after long-term cycling at two different temperatures and cycling rates is investigated. The cells are opened after cycling and post-mortem analysis are conducted. Two main contributions to the capacity loss of the batteries are revealed. The loss of active lithium leads to a relative shift between anodes and cathodes potentials. A growth of the solid electrolyte interface (SEI) on the anode is determined as well as the formation of lithium fluoride species as an electrolyte decomposition product. Those effects are reinforced by increasing cycling rates from 1C/2C (charge/discharge) to 2C/3C as well as by increasing cycling temperatures from 25 °C to 40 °C. The other contribution to the capacity loss originates from a fatigue of the blended cathodes consisting of LiNi0.5Co0.2Mn0.3O2 (NCM), LiNi0.8Co0.15Al0.05O2 (NCA) and LiMn2O4 (LMO). Phase-specific capacity losses and fatigue mechanisms are identified. The layered oxides tend to form microcracks and reveal changes of the surface structure leading to a worsening of the lithium kinetics. The cathode exhibits a loss of manganese at 40 °C cycling temperature. Cycling at 40 °C instead of 25 °C has the major impact on cathodes capacity loss, while cycling at 2C/3C rates barely influences it.

Distinguishing between stochasticity and determinism: Examples from cell cycle duration variability.

PubMed

Pearl Mizrahi, Sivan; Sandler, Oded; Lande-Diner, Laura; Balaban, Nathalie Q; Simon, Itamar

2016-01-01

We describe a recent approach for distinguishing between stochastic and deterministic sources of variability, focusing on the mammalian cell cycle. Variability between cells is often attributed to stochastic noise, although it may be generated by deterministic components. Interestingly, lineage information can be used to distinguish between variability and determinism. Analysis of correlations within a lineage of the mammalian cell cycle duration revealed its deterministic nature. Here, we discuss the sources of such variability and the possibility that the underlying deterministic process is due to the circadian clock. Finally, we discuss the "kicked cell cycle" model and its implication on the study of the cell cycle in healthy and cancerous tissues. © 2015 WILEY Periodicals, Inc.

Axial displacement of external and internal implant-abutment connection evaluated by linear mixed model analysis.

PubMed

Seol, Hyon-Woo; Heo, Seong-Joo; Koak, Jai-Young; Kim, Seong-Kyun; Kim, Shin-Koo

2015-01-01

To analyze the axial displacement of external and internal implant-abutment connection after cyclic loading. Three groups of external abutments (Ext group), an internal tapered one-piece-type abutment (Int-1 group), and an internal tapered two-piece-type abutment (Int-2 group) were prepared. Cyclic loading was applied to implant-abutment assemblies at 150 N with a frequency of 3 Hz. The amount of axial displacement, the Periotest values (PTVs), and the removal torque values(RTVs) were measured. Both a repeated measures analysis of variance and pattern analysis based on the linear mixed model were used for statistical analysis. Scanning electron microscopy (SEM) was used to evaluate the surface of the implant-abutment connection. The mean axial displacements after 1,000,000 cycles were 0.6 μm in the Ext group, 3.7 μm in the Int-1 group, and 9.0 μm in the Int-2 group. Pattern analysis revealed a breakpoint at 171 cycles. The Ext group showed no declining pattern, and the Int-1 group showed no declining pattern after the breakpoint (171 cycles). However, the Int-2 group experienced continuous axial displacement. After cyclic loading, the PTV decreased in the Int-2 group, and the RTV decreased in all groups. SEM imaging revealed surface wear in all groups. Axial displacement and surface wear occurred in all groups. The PTVs remained stable, but the RTVs decreased after cyclic loading. Based on linear mixed model analysis, the Ext and Int-1 groups' axial displacements plateaued after little cyclic loading. The Int-2 group's rate of axial displacement slowed after 100,000 cycles.

RIEGER-TYPE PERIODICITY DURING SOLAR CYCLES 14–24: ESTIMATION OF DYNAMO MAGNETIC FIELD STRENGTH IN THE SOLAR INTERIOR

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

Gurgenashvili, Eka; Zaqarashvili, Teimuraz V.; Kukhianidze, Vasil

2016-07-20

Solar activity undergoes a variation over timescales of several months known as Rieger-type periodicity, which usually occurs near maxima of sunspot cycles. An early analysis showed that the periodicity appears only in some cycles and is absent in other cycles. But the appearance/absence during different cycles has not been explained. We performed a wavelet analysis of sunspot data from the Greenwich Royal Observatory and the Royal Observatory of Belgium during cycles 14–24. We found that the Rieger-type periods occur in all cycles, but they are cycle dependent: shorter periods occur during stronger cycles. Our analysis revealed a periodicity of 185–195more » days during the weak cycles 14–15 and 24 and a periodicity of 155–165 days during the stronger cycles 16–23. We derived the dispersion relation of the spherical harmonics of the magnetic Rossby waves in the presence of differential rotation and a toroidal magnetic field in the dynamo layer near the base of the convection zone. This showed that the harmonics of fast Rossby waves with m = 1 and n = 4, where m ( n ) indicates the toroidal (poloidal) wavenumbers, perfectly fit with the observed periodicity. The variation of the toroidal field strength from weaker to stronger cycles may lead to the different periods found in those cycles, which explains the observed enigmatic feature of the Rieger-type periodicity. Finally, we used the observed periodicity to estimate the dynamo field strength during cycles 14–24. Our estimations suggest a field strength of ∼40 kG for the stronger cycles and ∼20 kG for the weaker cycles.« less

Transition metal redox and Mn disproportional reaction in LiMn0.5Fe0.5PO4 electrodes cycled with aqueous electrolyte

NASA Astrophysics Data System (ADS)

Zhuo, Zengqing; Hu, Jiangtao; Duan, Yandong; Yang, Wanli; Pan, Feng

2016-07-01

We performed soft x-ray absorption spectroscopy (sXAS) and a quantitative analysis of the transition metal redox in the LiMn0.5Fe0.5PO4 electrodes upon electrochemical cycling. In order to circumvent the complication of the surface reactions with organic electrolyte at high potential, the LiMn0.5Fe0.5PO4 electrodes are cycled with aqueous electrolyte. The analysis of the transitional metal L-edge spectra allows a quantitative determination of the redox evolution of Mn and Fe during the electrochemical cycling. The sXAS analysis reveals the evolving Mn oxidation states in LiMn0.5Fe0.5PO4. We found that electrochemically inactive Mn2+ is formed on the electrode surface during cycling. Additionally, the signal indicates about 20% concentration of Mn4+ at the charged state, providing a strong experimental evidence of the disproportional reaction of Mn3+ to Mn2+ and Mn4+ on the surface of the charged LiMn0.5Fe0.5PO4 electrodes.

Skin Cancer, Irradiation, and Sunspots: The Solar Cycle Effect

PubMed Central

Zurbenko, Igor

2014-01-01

Skin cancer is diagnosed in more than 2 million individuals annually in the United States. It is strongly associated with ultraviolet exposure, with melanoma risk doubling after five or more sunburns. Solar activity, characterized by features such as irradiance and sunspots, undergoes an 11-year solar cycle. This fingerprint frequency accounts for relatively small variation on Earth when compared to other uncorrelated time scales such as daily and seasonal cycles. Kolmogorov-Zurbenko filters, applied to the solar cycle and skin cancer data, separate the components of different time scales to detect weaker long term signals and investigate the relationships between long term trends. Analyses of crosscorrelations reveal epidemiologically consistent latencies between variables which can then be used for regression analysis to calculate a coefficient of influence. This method reveals that strong numerical associations, with correlations >0.5, exist between these small but distinct long term trends in the solar cycle and skin cancer. This improves modeling skin cancer trends on long time scales despite the stronger variation in other time scales and the destructive presence of noise. PMID:25126567

Molten salt synthesis and characterization of Li4Ti5-xMnxO12 (x = 0.0, 0.05 and 0.1) as anodes for Li-ion batteries

NASA Astrophysics Data System (ADS)

Nithya, V. D.; Kalai Selvan, R.; Vediappan, Kumaran; Sharmila, S.; Lee, Chang Woo

2012-11-01

Sub-micrometer sized Li4Ti5-xMnxO12 (x = 0.0, 0.05 and 0.1) particles were synthesized by a single step molten salt method using LiCl-KCl as a flux. The synthesized material was structurally characterized by X-ray diffraction (XRD) and Fourier transform infrared (FTIR) spectra. The XRD analysis revealed the particles to be highly crystalline and have a face-centered cubic spinel structure. The presence of possible functional group was confirmed through FTIR analysis. The FE-SEM images showed the particles to be polyhedral in shape with uniform size distribution. It was also revealed that there was a particle size reduction with the effect of Mn4+ dopant ions. The electrochemical studies performed using cyclic voltammogram (CV), charge-discharge, and electrochemical impedance analysis (EIS) indicate that Li4Ti4.9Mn0.1O4 possesses a better discharge capacity (305 mAh/g), cycling stability, and charge carrier conductivity than both Li4Ti4.95Mn0.05O12 (265 mAh/g) and Li4Ti5O12 (240 mAh/g). The cycling stability reveals that the acceptable capacity fading was observed even after 20th cycle. The results of electrochemical studies infer that Li4Ti4.9Mn0.1O4 could be utilized as a suitable anode material for Li-ion batteries.

The observed life cycle of a baroclinic instability

NASA Technical Reports Server (NTRS)

Randel, W. J.; Stanford, J. L.

1985-01-01

Medium-scale waves (zonal wavenumbers 4-7) frequently dominate Southern Hemisphere summer circulation patterns. Randel and Stanford have studied the dynamics of these features, demonstrating that the medium-scale waves result from baroclinic excitation and exhibit well-defined life cycles. This study details the evolution of the medium-scale waves during a particular life cycle. The specific case chosen exhibits a high degree of zonal symmetry, prompting study based upon zonally averaged diagnostics. An analysis of the medium-scale wave energetics reveals a well-defined life cycle of baroclinic growth, maturity, and barotropic decay. Eliassen-Palm flux diagrams detail the daily wave structure and its interaction with the zonally-averaged flow.

Oscillating in synchrony with a metronome: serial dependence, limit cycle dynamics, and modeling.

PubMed

Torre, Kjerstin; Balasubramaniam, Ramesh; Delignières, Didier

2010-07-01

We analyzed serial dependencies in periods and asynchronies collected during oscillations performed in synchrony with a metronome. Results showed that asynchronies contain 1/f fluctuations, and the series of periods contain antipersistent dependence. The analysis of the phase portrait revealed a specific asymmetry induced by synchronization. We propose a hybrid limit cycle model including a cycle-dependent stiffness parameter provided with fractal properties, and a parametric driving function based on velocity. This model accounts for most experimentally evidenced statistical features, including serial dependence and limit cycle dynamics. We discuss the results and modeling choices within the framework of event-based and emergent timing.

Transcriptional response to petiole heat girdling in cassava.

PubMed

Zhang, Yang; Ding, Zehong; Ma, Fangfang; Chauhan, Raj Deepika; Allen, Doug K; Brutnell, Thomas P; Wang, Wenquan; Peng, Ming; Li, Pinghua

2015-02-12

To examine the interactions of starch and sugar metabolism on photosynthesis in cassava, a heat-girdling treatment was applied to petioles of cassava leaves at the end of the light cycle to inhibit starch remobilization during the night. The inhibition of starch remobilization caused significant starch accumulation at the beginning of the light cycle, inhibited photosynthesis, and affected intracellular sugar levels. RNA-seq analysis of heat-treated and control plants revealed significantly decreased expression of genes related to photosynthesis, as well as N-metabolism and chlorophyll biosynthesis. However, expression of genes encoding TCA cycle enzymes and mitochondria electron transport components, and flavonoid biosynthetic pathway enzymes were induced. These studies reveal a dynamic transcriptional response to perturbation of sink demand in a single leaf, and provide useful information for understanding the regulations of cassava under sink or source limitation.

Transcriptional response to petiole heat girdling in cassava

PubMed Central

Zhang, Yang; Ding, Zehong; Ma, Fangfang; Chauhan, Raj Deepika; Allen, Doug K.; Brutnell, Thomas P.; Wang, Wenquan; Peng, Ming; Li, Pinghua

2015-01-01

To examine the interactions of starch and sugar metabolism on photosynthesis in cassava, a heat-girdling treatment was applied to petioles of cassava leaves at the end of the light cycle to inhibit starch remobilization during the night. The inhibition of starch remobilization caused significant starch accumulation at the beginning of the light cycle, inhibited photosynthesis, and affected intracellular sugar levels. RNA-seq analysis of heat-treated and control plants revealed significantly decreased expression of genes related to photosynthesis, as well as N-metabolism and chlorophyll biosynthesis. However, expression of genes encoding TCA cycle enzymes and mitochondria electron transport components, and flavonoid biosynthetic pathway enzymes were induced. These studies reveal a dynamic transcriptional response to perturbation of sink demand in a single leaf, and provide useful information for understanding the regulations of cassava under sink or source limitation. PMID:25672661

Impacts of mesoscale eddies in the South China Sea on biogeochemical cycles

NASA Astrophysics Data System (ADS)

Guo, Mingxian; Chai, Fei; Xiu, Peng; Li, Shiyu; Rao, Shivanesh

2015-09-01

Biogeochemical cycles associated with mesoscale eddies in the South China Sea (SCS) were investigated. The study was based on a coupled physical-biogeochemical Pacific Ocean model (Regional Ocean Model System-Carbon, Silicate, and Nitrogen Ecosystem, ROMS-CoSiNE) simulation for the period from 1991 to 2008. A total of 568 mesoscale eddies with lifetime longer than 30 days were used in the analysis. Composite analysis revealed that the cyclonic eddies were associated with abundance of nutrients, phytoplankton, and zooplankton while the anticyclonic eddies depressed biogeochemical cycles, which are generally controlled by the eddy pumping mechanism. In addition, diatoms were dominant in phytoplankton species due to the abundance of silicate. Dipole structures of vertical fluxes with net upward motion in cyclonic eddies and net downward motion in anticyclonic eddies were revealed. During the lifetime of an eddy, the evolutions of physical, biological, and chemical structures were not linearly coupled at the eddy core where plankton grew, and composition of the community depended not only on the physical and chemical processes but also on the adjustments by the predator-prey relationship.

Rapid Assessment of Genotoxicity by Flow Cytometric Detection of Cell Cycle Alterations.

PubMed

Bihari, Nevenka

2017-01-01

Flow cytometry is a convenient method for the determination of genotoxic effects of environmental pollution and can reveal genotoxic compounds in unknown environmental mixtures. It is especially suitable for the analyses of large numbers of samples during monitoring programs. The speed of detection is one of the advantages of this technique which permits the acquisition of 10 4 -10 5 cells per sample in 5 min. This method can rapidly detect cell cycle alterations resulting from DNA damage. The outcome of such an analysis is a diagram of DNA content across the cell cycle which indicates cell proliferation, G 2 arrests, G 1 delays, apoptosis, and ploidy.Here, we present the flow cytometric procedure for rapid assessment of genotoxicity via detection of cell cycle alterations. The described protocol simplifies the analysis of genotoxic effects in marine environments and is suitable for monitoring purposes. It uses marine mussel cells in the analysis and can be adapted to investigations on a broad range of marine invertebrates.

Differences in environmental preferences towards cycling for transport among adults: a latent class analysis.

PubMed

Mertens, Lieze; Van Cauwenberg, Jelle; Ghekiere, Ariane; De Bourdeaudhuij, Ilse; Deforche, Benedicte; Van de Weghe, Nico; Van Dyck, Delfien

2016-08-12

Increasing cycling for transport can contribute to improve public health among adults. Micro-environmental factors (i.e. small-scaled street-setting features) may play an important role in affecting the street's appeal to cycle for transport. Understanding about the interplay between individuals and their physical environment is important to establish tailored environmental interventions. Therefore, the current study aimed to examine whether specific subgroups exist based on similarities in micro-environmental preferences to cycle for transport. Responses of 1950 middle-aged adults (45-65 years) on a series of choice tasks depicting potential cycling routes with manipulated photographs yielded three subgroups with different micro-environmental preferences using latent class analysis. Although latent class analysis revealed three different subgroups in the middle-aged adult population based on their environmental preferences, results indicated that cycle path type (i.e. a good separated cycle path) is the most important environmental factor for all participants and certainly for individuals who did not cycle for transport. Furthermore, only negligible differences were found between the importances of the other micro-environmental factors (i.e. traffic density, evenness of the cycle path, maintenance, vegetation and speed limits) regarding the two at risk subgroups and that providing a speed bump obviously has the least impact on the street's appeal to cycle for transport. Results from the current study indicate that only negligible differences were found between the three subgroups. Therefore, it might be suggested that tailored environmental interventions are not required in this research context.

Biofuels via Fast Pyrolysis of Perennial Grasses: A Life Cycle Evaluation of Energy Consumption and Greenhouse Gas Emissions.

PubMed

Zaimes, George G; Soratana, Kullapa; Harden, Cheyenne L; Landis, Amy E; Khanna, Vikas

2015-08-18

A well-to-wheel (WTW) life cycle assessment (LCA) model is developed to evaluate the environmental profile of producing liquid transportation fuels via fast pyrolysis of perennial grasses: switchgrass and miscanthus. The framework established in this study consists of (1) an agricultural model used to determine biomass growth rates, agrochemical application rates, and other key parameters in the production of miscanthus and switchgrass biofeedstock; (2) an ASPEN model utilized to simulate thermochemical conversion via fast pyrolysis and catalytic upgrading of bio-oil to renewable transportation fuel. Monte Carlo analysis is performed to determine statistical bounds for key sustainability and performance measures including life cycle greenhouse gas (GHG) emissions and Energy Return on Investment (EROI). The results of this work reveal that the EROI and GHG emissions (gCO2e/MJ-fuel) for fast pyrolysis derived fuels range from 1.52 to 2.56 and 22.5 to 61.0 respectively, over the host of scenarios evaluated. Further analysis reveals that the energetic performance and GHG reduction potential of fast pyrolysis-derived fuels are highly sensitive to the choice of coproduct scenario and LCA allocation scheme, and in select cases can change the life cycle carbon balance from meeting to exceeding the renewable fuel standard emissions reduction threshold for cellulosic biofuels.

Regulatory network analysis of Epstein-Barr virus identifies functional modules and hub genes involved in infectious mononucleosis.

PubMed

Poorebrahim, Mansour; Salarian, Ali; Najafi, Saeideh; Abazari, Mohammad Foad; Aleagha, Maryam Nouri; Dadras, Mohammad Nasr; Jazayeri, Seyed Mohammad; Ataei, Atousa; Poortahmasebi, Vahdat

2017-05-01

Epstein-Barr virus (EBV) is the most common cause of infectious mononucleosis (IM) and establishes lifetime infection associated with a variety of cancers and autoimmune diseases. The aim of this study was to develop an integrative gene regulatory network (GRN) approach and overlying gene expression data to identify the representative subnetworks for IM and EBV latent infection (LI). After identifying differentially expressed genes (DEGs) in both IM and LI gene expression profiles, functional annotations were applied using gene ontology (GO) and BiNGO tools, and construction of GRNs, topological analysis and identification of modules were carried out using several plugins of Cytoscape. In parallel, a human-EBV GRN was generated using the Hu-Vir database for further analyses. Our analysis revealed that the majority of DEGs in both IM and LI were involved in cell-cycle and DNA repair processes. However, these genes showed a significant negative correlation in the IM and LI states. Furthermore, cyclin-dependent kinase 2 (CDK2) - a hub gene with the highest centrality score - appeared to be the key player in cell cycle regulation in IM disease. The most significant functional modules in the IM and LI states were involved in the regulation of the cell cycle and apoptosis, respectively. Human-EBV network analysis revealed several direct targets of EBV proteins during IM disease. Our study provides an important first report on the response to IM/LI EBV infection in humans. An important aspect of our data was the upregulation of genes associated with cell cycle progression and proliferation.

Comparative cell cycle transcriptomics reveals synchronization of developmental transcription factor networks in cancer cells

PubMed Central

Johard, Helena; Mahdessian, Diana; Fedr, Radek; Marks, Carolyn; Medalová, Jiřina; Souček, Karel; Lundberg, Emma; Linnarsson, Sten; Bryja, Vítězslav; Sekyrova, Petra; Altun, Mikael; Andäng, Michael

2017-01-01

The cell cycle coordinates core functions such as replication and cell division. However, cell-cycle-regulated transcription in the control of non-core functions, such as cell identity maintenance through specific transcription factors (TFs) and signalling pathways remains unclear. Here, we provide a resource consisting of mapped transcriptomes in unsynchronized HeLa and U2OS cancer cells sorted for cell cycle phase by Fucci reporter expression. We developed a novel algorithm for data analysis that enables efficient visualization and data comparisons and identified cell cycle synchronization of Notch signalling and TFs associated with development. Furthermore, the cell cycle synchronizes with the circadian clock, providing a possible link between developmental transcriptional networks and the cell cycle. In conclusion we find that cell cycle synchronized transcriptional patterns are temporally compartmentalized and more complex than previously anticipated, involving genes, which control cell identity and development. PMID:29228002

The development and validation of a three-tier diagnostic test measuring pre-service elementary education and secondary science teachers' understanding of the water cycle

NASA Astrophysics Data System (ADS)

Schaffer, Dannah Lynn

The main goal of this research study was to develop and validate a three-tier diagnostic test to determine pre-service teachers' (PSTs) conceptual knowledge of the water cycle. For a three-tier diagnostic test, the first tier assesses content knowledge; in the second tier, a reason is selected for the content answer; and the third tier allows test-takers to select how confident they are in their answers for the first two tiers. The second goal of this study was to diagnose any alternative conceptions PSTs might have about the water cycle. The Water Cycle Diagnostic Test (WCDT) was developed using the theoretical framework by Treagust (1986, 1988, and 1995), and in similar studies that developed diagnostic tests (e.g., Calean & Subramaniam, 2010a; Odom & Barrow, 2007; Pesman & Eryilmaz, 2010). The final instrument consisted of 15 items along with a demographic survey that examined PSTs' weather-related experiences that may or may not have affected the PSTs' understanding of the water cycle. The WCDT was administered to 77 PSTs enrolled in science methods courses during the fall of 2012. Among the 77 participants, 37 of the PSTs were enrolled in elementary education (EPST) and 40 in secondary science (SPST). Using exploratory factor analysis, five categories were factored out for the WCDT: Phase Change of Water; Condensation and Storage; Clouds; Global Climate Change; and Movement through the Water Cycle. Analysis of the PSTs' responses demonstrated acceptable reliability (alpha = 0.62) for the instrument, and acceptable difficulty indices and discrimination indices for 12 of the items. Analysis indicated that the majority of the PSTs had a limited understanding of the water cycle. Of the PSTs sampled, SPSTs were significantly more confident in their answers' on the WCDT than the EPSTs. Completion of an undergraduate atmospheric science and/or meteorology course, as well as a higher interest in listening and/or viewing weather-related programs, resulted in PSTs having greater understanding and confidence in their answers on the WCDT. The analysis of the PSTs' responses revealed 49 potential alternative conceptions and areas where PSTs' lack of knowledge was revealed from the WCDT.

The long non-coding RNA GAS5 differentially regulates cell cycle arrest and apoptosis through activation of BRCA1 and p53 in human neuroblastoma

PubMed Central

Mazar, Joseph; Rosado, Amy; Shelley, John; Marchica, John; Westmoreland, Tamarah J

2017-01-01

The long non-coding RNA GAS5 has been shown to modulate cancer proliferation in numerous human cancer systems and has been correlated with successful patient outcome. Our examination of GAS5 in neuroblastoma has revealed robust expression in both MYCN-amplified and non-amplified cell lines. Knockdown of GAS5 In vitro resulted in defects in cell proliferation, apoptosis, and induced cell cycle arrest. Further analysis of GAS5 clones revealed multiple novel splice variants, two of which inversely modulated with MYCN status. Complementation studies of the variants post-knockdown of GAS5 indicated alternate phenotypes, with one variant (FL) considerably enhancing cell proliferation by rescuing cell cycle arrest and the other (C2) driving apoptosis, suggesting a unique role for each in neuroblastoma cancer physiology. Global sequencing and ELISA arrays revealed that the loss of GAS5 induced p53, BRCA1, and GADD45A, which appeared to modulate cell cycle arrest in concert. Complementation with only the FL GAS5 clone could rescue cell cycle arrest, stabilizing HDM2, and leading to the loss of p53. Together, these data offer novel therapeutic targets in the form of lncRNA splice variants for separate challenges against cancer growth and cell death. PMID:28035057

Astronomical cycle origin of bedded chert: A middle Triassic bedded chert sequence, Inuyama, Japan

NASA Astrophysics Data System (ADS)

Ikeda, Masayuki; Tada, Ryuji; Sakuma, Hironobu

2010-09-01

Astronomical forcing is one of the main drivers of climate change, and astronomical cyclicity recorded in sediments provides a clue to understand the dynamics of the global climate system. Bedded cherts consist of rhythmic alternations of chert and shale beds. Although previous studies have hypothesized that the origin of bedded chert is related to astronomical cycles (e.g. Fischer, 1976; Hori et al., 1993), conclusive proof remains elusive. To explore this possibility, we established a continuous, high-resolution lithostratigraphy of middle Triassic bedded chert in Central Japan. The average duration of each chert-shale couplet is 20 kyr, similar to that of the precession cycle. Spectral analysis of a bed number series of thickness variations in chert beds was performed assuming that each chert-shale couplet represents a 20-kyr precession cycle. The results reveal cycles involving approximately 200, 20, 5, and 2-3 beds, corresponding to periodicities of approximately 4000, 400, 100, and 40-60 kyr, respectively. By further assuming that the 20-bed cycle represents a 405-kyr eccentricity cycle of constant and stable periodicity, we converted the bed number series to a time series. Spectral analysis of the time series revealed distinct periodicities of 3600, 117, 97, and 38 kyr, in addition to 405 kyr. Besides 3600 kyr, these periodicities agree well with the 120, 95, and 37 kyr periodicities for eccentricity cycles and the obliquity cycle during the Triassic. Moreover, we detected amplitude modulation of the approximately 100-kyr cycle of thickness variations in chert beds with a 405-kyr periodicity, which may correspond to amplitude modulation of 100-kyr climatic precession cycle with the 405-kyr periodicity. The approximately 3600-kyr periodicity described above and 1800-kyr periodicity manifested as the amplitude modulation of the 405-kyr cycle are correlated to present-day long-term eccentricity cycles of 2400 and 4800 kyr evolved by chaotic behavior of solar planets. Collectively, these similarities in the periodicities of dominant cycles, their hierarchy, and the nature of amplitude modulation of cycles in chert bed thickness with those of astronomical cycles strongly support the hypothesis that the sedimentary rhythm of bedded chert is paced by astronomical cycles, thereby indicating the potential of bedded chert as a template for a Mesozoic cyclostratigraphy.

CCS52A2/FZR1, a cell cycle regulator, is an essential factor for shoot apical meristem maintenance in Arabidopsis thaliana.

PubMed

Liu, Yajie; Ye, Wei; Li, Beibei; Zhou, Xiaojing; Cui, Yuhai; Running, Mark P; Liu, Kede

2012-08-08

Cell division and cell fate decisions regulate organ formation and function in plant growth and development. It is still unclear how specific meristematic regulatory networks operate with the cell cycle machinery to translate stem cell identity and maintenance into cellular behavior. In this study, we address these questions by analysis of a shoot apex defective mutant, namely xcm9. Phenotypic analysis of the xcm9 mutant reveals concomitant premature termination of floral shoots with frequent bifurcation of the shoot apices, stems, and flowers. Microscopic observations show irregular cell organization in shoot apical meristems of xcm9. Positional cloning revealed that xcm9 is a loss of function allele of the CCS52A2/FZR1 gene, which has previously been implicated in root development. Expression analysis demonstrated that CCS52A2 maintains a higher transcriptional expression level in actively dividing tissue. Genetic studies indicated that the CCS52A2 gene functions together with WUSCHEL (WUS) and CLAVATA3 (CLV3) in regulating the development of the shoot meristem, and also contributes to this regulation together with the chromatin remodeling pathway. In addition, fewer xcm9 cells express CYCLIN B1:1, showing that cell cycle progression is disrupted in the mutant. We propose that the CCS52A2 gene is a mediator that functions together with meristematic genes to regulate meristem organization, and cross-functions with chromatin regulators in cell cycle progression during shoot apical meristem development.

Integrative Analysis Reveals an Outcome-associated and Targetable Pattern of p53 and Cell Cycle Deregulation in Diffuse Large B-cell Lymphoma

PubMed Central

Monti, Stefano; Chapuy, Bjoern; Takeyama, Kunihiko; Rodig, Scott J; Hao, Yangsheng; Yeda, Kelly T.; Inguilizian, Haig; Mermel, Craig; Curie, Treeve; Dogan, Ahmed; Kutok, Jeffery L; Beroukim, Rameen; Neuberg, Donna; Habermann, Thomas; Getz, Gad; Kung, Andrew L; Golub, Todd R; Shipp, Margaret A

2013-01-01

Summary Diffuse large B-cell lymphoma (DLBCL) is a clinically and biologically heterogeneous disease with a high proliferation rate. By integrating copy number data with transcriptional profiles and performing pathway analysis in primary DLBCLs, we identified a comprehensive set of copy number alterations (CNAs) that decreased p53 activity and perturbed cell cycle regulation. Primary tumors either had multiple complementary alterations of p53 and cell cycle components or largely lacked these lesions. DLBCLs with p53 and cell cycle pathway CNAs had decreased abundance of p53 target transcripts and increased expression of E2F target genes and the Ki67 proliferation marker. CNAs of the CDKN2A-TP53-RB-E2F axis provide a structural basis for increased proliferation in DLBCL, predict outcome with current therapy and suggest targeted treatment approaches. PMID:22975378

Psychosocial Profile of Women with Premenstrual Syndrome and Healthy Controls: A Comparative Study.

PubMed

Kleinstäuber, Maria; Schmelzer, Katarina; Ditzen, Beate; Andersson, Gerhard; Hiller, Wolfgang; Weise, Cornelia

2016-12-01

According to modern bio-psychosocial theories of premenstrual syndrome (PMS), the aim of this study is to investigate systematically associations between selected psychosocial factors and premenstrual symptoms in different menstrual cycle phases. Several psychosocial variables were assessed, in a sample of German women with PMS (N = 90) and without premenstrual complaints (N = 48) during the follicular and luteal phase of the menstrual cycle. Presence of PMS was indicated by analysis of contemporary daily ratings of premenstrual symptom severity and impairment for one menstrual cycle. Regarding perceived chronic stress (ƞ 2  = 0.34), self-efficacy (ƞ 2  = 0.12), and two dimensions of self-silencing (0.06 ≤ ƞ 2  ≤ 0.11) analyses revealed only a significant effect of group. Regarding body dissatisfaction and somatosensory amplification, a significant effect of group (0.07 ≤ ƞ 2  ≤ 0.16) and additionally a group by menstrual cycle phase interaction (ƞ 2  = 0.06) was identified. Regarding relationship quality, a significant effect of menstrual cycle phase (ƞ 2  = 0.08) and a group by menstrual cycle phase interaction (ƞ 2  = 0.06) was demonstrated. In respect to sexual contentment, acceptance of premenstrual symptoms, and the remaining two dimensions of self-silencing statistical analyses revealed no effects at all. Linear multiple regression analysis revealed that 20 % of the variance in PMS symptom severity was explained by the psychosocial variables investigated. Body dissatisfaction (ß = 0.26, p = 0.018) and the divided self-dimension of self-silencing (ß = 0.35, p = 0.016) were significant correlates of PMS severity. Results of this study are consistent with previous research and additionally show patterns of associations between specific psychosocial factors and PMS in dependence of menstrual cycle phase that have not been researched before. The role of the psychosocial variables we investigated in regard to the development and maintenance of PMS should be clarified in future research.

Environmental impact assessment of european non-ferro mining industries through life-cycle assessment

NASA Astrophysics Data System (ADS)

Hisan Farjana, Shahjadi; Huda, Nazmul; Parvez Mahmud, M. A.

2018-05-01

European mining industries are the vast industrial sector which contributes largely on their economy which constitutes of ferro and non-ferro metals and minerals industries. The non-ferro metals extraction and processing industries require focus of attention due to sustainability concerns as their manufacturing processes are highly energy intensive and impacts globally on environment. This paper analyses major environmental effects caused by European metal industries based on the life-cycle impact analysis technologies. This research work is the first work in considering the comparative environmental impact analysis of European non-ferro metal industries which will reveal their technological similarities and dissimilarities to assess their environmental loads. The life-cycle inventory datasets are collected from the EcoInvent database while the analysis is done using the CML baseline and ReCipe endpoint method using SimaPro software version 8.4. The CML and ReCipe method are chosen because they are specialized impact assessment methods for European continent. The impact categories outlined for discussion here are human health, global warming and ecotoxicity. The analysis results reveal that the gold industry is vulnerable for the environment due to waste emission and similar result retained by silver mines a little bit. But copper, lead, manganese and zinc mining processes and industries are environment friendly in terms of metal extraction technologies and waste emissions.

Time-frequency analysis of human motion during rhythmic exercises.

PubMed

Omkar, S N; Vyas, Khushi; Vikranth, H N

2011-01-01

Biomechanical signals due to human movements during exercise are represented in time-frequency domain using Wigner Distribution Function (WDF). Analysis based on WDF reveals instantaneous spectral and power changes during a rhythmic exercise. Investigations were carried out on 11 healthy subjects who performed 5 cycles of sun salutation, with a body-mounted Inertial Measurement Unit (IMU) as a motion sensor. Variance of Instantaneous Frequency (I.F) and Instantaneous Power (I.P) for performance analysis of the subject is estimated using one-way ANOVA model. Results reveal that joint Time-Frequency analysis of biomechanical signals during motion facilitates a better understanding of grace and consistency during rhythmic exercise.

Carcinogens induce loss of the primary cilium in human renal proximal tubular epithelial cells independently of effects on the cell cycle

PubMed Central

Radford, Robert; Slattery, Craig; Jennings, Paul; Blacque, Oliver; Pfaller, Walter; Gmuender, Hans; Van Delft, Joost; Ryan, Michael P.

2012-01-01

The primary cilium is an immotile sensory and signaling organelle found on the majority of mammalian cell types. Of the multitude of roles that the primary cilium performs, perhaps some of the most important include maintenance of differentiation, quiescence, and cellular polarity. Given that the progression of cancer requires disruption of all of these processes, we have investigated the effects of several carcinogens on the primary cilium of the RPTEC/TERT1 human proximal tubular epithelial cell line. Using both scanning electron microscopy and immunofluorescent labeling of the ciliary markers acetylated tubulin and Arl13b, we confirmed that RPTEC/TERT1 cells express primary cilium upon reaching confluence. Treatment with the carcinogens ochratoxin A (OTA) and potassium bromate (KBrO3) caused a significant reduction in the number of ciliated cells, while exposure to nifedipine, a noncarcinogenic renal toxin, had no effect on primary cilium expression. Flow cytometric analysis of the effects of all three compounds on the cell cycle revealed that only KBrO3 resulted in an increase in the proportion of cells entering the cell cycle. Microarray analysis revealed dysregulation of multiple pathways affecting ciliogenesis and ciliary maintenance following OTA and KBrO3 exposure, which were unaffected by nifedipine exposure. The primary cilium represents a unique physical checkpoint with relevance to carcinogenesis. We have shown that the renal carcinogens OTA and KBrO3 cause significant deciliation in a model of the proximal tubule. With KBrO3, this was followed by reentry into the cell cycle; however, deciliation was not found to be associated with reentry into the cell cycle following OTA exposure. Transcriptomic analysis identified dysregulation of Wnt signaling and ciliary trafficking in response to OTA and KBrO3 exposure. PMID:22262483

Rare sugar D-allose induces specific up-regulation of TXNIP and subsequent G1 cell cycle arrest in hepatocellular carcinoma cells by stabilization of p27kip1.

PubMed

Yamaguchi, Fuminori; Takata, Maki; Kamitori, Kazuyo; Nonaka, Machiko; Dong, Youyi; Sui, Li; Tokuda, Masaaki

2008-02-01

'Rare sugars' are defined as monosaccharides that exist in nature but are only present in limited quantities. The development of mass production method of rare sugars revealed some interesting physiological effects of these on animal cells, but the mechanisms have not been well studied. We examined the effect of D-allose on the proliferation of cancer cells and the underlying molecular mechanism of the action. The HuH-7 hepatocellular carcinoma cells were treated with various monosaccharides for 48 h and D-allose was shown to inhibit cell growth by 40% in a dose-dependent manner. D-allose induced G1 cell cycle arrest but not apoptosis. The microarray analysis revealed that D-allose significantly up-regulated thioredoxin interacting protein (TXNIP) gene expression, which is often suppressed in tumor cells and western blot analysis confirmed its increase at protein level. The overexpression of TXNIP also induced G1 cell cycle arrest. Analysis of cell cycle regulatory genes showed p27kip1, a key regulator of G1/S cell cycle transition, to be increased at the protein but not the transcriptional level. Protein interaction between TXNIP and jab1, and p27kip1 and jab1, was observed, suggesting stabilization of p27kip1 protein by the competitive inhibition of jab1-mediated nuclear export of p27kip1 by TXNIP. In addition, increased interaction and nuclear localization of TXNIP and p27kip1 were apparent after D-allose treatment. Our findings surprisingly suggest that D-allose, a simple monosaccharide, may act as a novel anticancer agent via unique TXNIP induction and p27kip1 protein stabilization.

Transcriptome profiling and pathway analysis of hepatotoxicity induced by tris (2-ethylhexyl) trimellitate (TOTM) in mice.

PubMed

Chen, Xian-Hua; Ma, Li; Hu, Yi-Xiang; Wang, Dan-Xian; Fang, Li; Li, Xue-Lai; Zhao, Jin-Chuan; Yu, Hai-Rong; Ying, Hua-Zhong; Yu, Chen-Huan

2016-01-01

Tris (2-ethylhexyl) trimellitate (TOTM) is commonly used as an alternative plasticizer for medical devices. But very little information was available on its biological effects. In this study, we investigated toxicity effects of TOTM on hepatic differential gene expression analyzed by using high-throughput sequencing analysis for over-represented functions and phenotypically anchored to complementary histopathologic, and biochemical data in the liver of mice. Among 1668 candidate genes, 694 genes were up-regulated and 974 genes were down-regulated after TOTM exposure. Using Gene Ontology analysis, TOTM affected three processes: the cell cycle, metabolic process and oxidative activity. Furthermore, 11 key genes involved in the above processes were validated by real time PCR. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that these genes were involved in the cell cycle pathway, lipid metabolism and oxidative process. It revealed the transcriptome gene expression response to TOTM exposure in mouse, and these data could contribute to provide a clearer understanding of the molecular mechanisms of TOTM-induced hepatotoxicity in human. Copyright © 2015 Elsevier B.V. All rights reserved.

Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress.

PubMed

Priest, Henry D; Fox, Samuel E; Rowley, Erik R; Murray, Jessica R; Michael, Todd P; Mockler, Todd C

2014-01-01

Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules which were up-regulated by each abiotic stress fell into diverse and unique gene ontology GO categories. This study provides genomics resources and improves our understanding of abiotic stress responses of Brachypodium.

Correlation of the earth's rotation rate and the secular change of the geomagnetic field. [power spectra/harmonic analysis

NASA Technical Reports Server (NTRS)

Jin, R. S.

1975-01-01

Power spectral density analysis using Burg's maximum entropy method was applied to the geomagnetic dipole field and its rate of change for the years 1901 to 1969. Both spectra indicate relative maxima at 0.015 cycles/year and its harmonics. These maxima correspond approximately to 66, 33, 22, 17, 13, 11, and 9-year spectral lines. The application of the same analysis techniques to the length-of-day (l.o.d) fluctuations for the period 1865 to 1961 reveal similar spectral characteristics. Although peaks were observed at higher harmonics of the fundamental frequency, the 22-year and 11-year lines are not attributed unambiguously to the solar magnetic cycle and the solar cycle. It is suggested that the similarity in the l.o.d fluctuations and the dipole field variations is related to the motion within the earth's fluid core during the past one hundred years.

Early in-session cognitive-emotional problem-solving predicts 12-month outcomes in depression with personality disorder.

PubMed

McCarthy, Kye L; Mergenthaler, Erhard; Grenyer, Brin F S

2014-01-01

Therapist-patient verbalizations reveal complex cognitive-emotional linguistic data. How these variables contribute to change requires further research. Emotional-cognitive text analysis using the Ulm cycles model software was applied to transcripts of the third session of psychotherapy for 20 patients with depression and personality disorder. Results showed that connecting cycle sequences of problem-solving in the third hour predicted 12-month clinical outcomes. Therapist-patient dyads most improved spent significantly more time early in session in connecting cycles, whilst the least improved moved into connecting cycles late in session. For this particular sample, it was clear that positive emotional problem-solving in therapy was beneficial.

Stability of Catalyzed Magnesium Hydride Nanocrystalline During Hydrogen Cycling. Part II: Microstructure Evolution

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

Zhou, Chengshang; Fang, Zhigang Zak; Bowman, Robert C.

2015-10-01

In Part I, the cyclic stabilities of the kinetics of catalyzed MgH2 systems including MgH2–TiH2, MgH2–TiMn2, and MgH2–VTiCr were investigated, showing stable kinetics at 300 °C but deteriorations of the hydrogenation kinetics at temperatures below 150 °C. The present Part II describes the characterization of uncycled and cycled catalyzed MgH2 by X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and X-ray photoelectron spectroscopy (XPS) analysis. XRD analysis shows the crystallite sizes of the Mg and MgH2 significantly increased after the cycling. The mean crystallite sizes of the catalysts (TiH2 and VTiCr) increased moderately after the cycling. SEMmore » and TEM imaging were used to compare the microstructures of uncycled (as-milled) and cycled materials, revealing a drastic change of the microstructure after 100 cycles. In particular, results from energy-dispersive spectroscopy (EDS) mapping show that a change of distribution of the catalyst particles in the Mg and MgH2 phase occurred during the cycling.« less

Genome-Based Metabolic Mapping and 13C Flux Analysis Reveal Systematic Properties of an Oleaginous Microalga Chlorella protothecoides

DOE PAGES

Wu, Chao; Xiong, Wei; Dai, Junbiao; ...

2014-12-15

We report that integrated and genome-based flux balance analysis, metabolomics, and 13C-label profiling of phototrophic and heterotrophic metabolism in Chlorella protothecoides, an oleaginous green alga for biofuel. The green alga Chlorella protothecoides, capable of autotrophic and heterotrophic growth with rapid lipid synthesis, is a promising candidate for biofuel production. Based on the newly available genome knowledge of the alga, we reconstructed the compartmentalized metabolic network consisting of 272 metabolic reactions, 270 enzymes, and 461 encoding genes and simulated the growth in different cultivation conditions with flux balance analysis. Phenotype-phase plane analysis shows conditions achieving theoretical maximum of the biomass andmore » corresponding fatty acid-producing rate for phototrophic cells (the ratio of photon uptake rate to CO 2 uptake rate equals 8.4) and heterotrophic ones (the glucose uptake rate to O 2 consumption rate reaches 2.4), respectively. Isotope-assisted liquid chromatography-mass spectrometry/mass spectrometry reveals higher metabolite concentrations in the glycolytic pathway and the tricarboxylic acid cycle in heterotrophic cells compared with autotrophic cells. We also observed enhanced levels of ATP, nicotinamide adenine dinucleotide (phosphate), reduced, acetyl-Coenzyme A, and malonyl-Coenzyme A in heterotrophic cells consistently, consistent with a strong activity of lipid synthesis. To profile the flux map in experimental conditions, we applied nonstationary 13C metabolic flux analysis as a complementing strategy to flux balance analysis. We found that the result reveals negligible photorespiratory fluxes and a metabolically low active tricarboxylic acid cycle in phototrophic C. protothecoides. In comparison, high throughput of amphibolic reactions and the tricarboxylic acid cycle with no glyoxylate shunt activities were measured for heterotrophic cells. Lastly, taken together, the metabolic network modeling assisted by experimental metabolomics and 13C labeling better our understanding on global metabolism of oleaginous alga, paving the way to the systematic engineering of the microalga for biofuel production.« less

The Rho GTPase effector ROCK regulates cyclin A, cyclin D1, and p27Kip1 levels by distinct mechanisms.

PubMed

Croft, Daniel R; Olson, Michael F

2006-06-01

The members of the Rho GTPase family are well known for their regulation of actin cytoskeletal structures. In addition, they influence progression through the cell cycle. The RhoA and RhoC proteins regulate numerous effector proteins, with a central and vital signaling role mediated by the ROCK I and ROCK II serine/threonine kinases. The requirement for ROCK function in the proliferation of numerous cell types has been revealed by studies utilizing ROCK-selective inhibitors such as Y-27632. However, the mechanisms by which ROCK signaling promotes cell cycle progression have not been thoroughly characterized. Using a conditionally activated ROCK-estrogen receptor fusion protein, we found that ROCK activation is sufficient to stimulate G1/S cell cycle progression in NIH 3T3 mouse fibroblasts. Further analysis revealed that ROCK acts via independent pathways to alter the levels of cell cycle regulatory proteins: cyclin D1 and p21(Cip1) elevation via Ras and the mitogen-activated protein kinase pathway, increased cyclin A via LIM kinase 2, and reduction of p27(Kip1) protein levels. Therefore, the influence of ROCK on cell cycle regulatory proteins occurs by multiple independent mechanisms.

HMG versus rFSH for ovulation induction in developing countries: a cost-effectiveness analysis based on the results of a recent meta-analysis.

PubMed

Al-Inany, Hesham G; Abou-Setta, Ahmed M; Aboulghar, Mohamed A; Mansour, Ragaa T; Serour, Gamal I

2006-02-01

Both cost and effectiveness should be considered conjointly to aid judgments about drug choice. Therefore, based on the results of a recent published meta-analysis, a Markov model was developed to conduct a cost-effectiveness analysis for estimation of the cost of an ongoing pregnancy in IVF/intracytoplasmic sperm injection (ICSI) cycles. In addition, Monte Carlo micro-simulation was used to examine the potential impact of assumptions and other uncertainties represented in the model. The results of the study reveal that the estimated average cost of an ongoing pregnancy is 13,946 Egyptian pounds (EGP), and 18,721 EGP for a human menopausal gonadotrophin (HMG) and rFSH cycle respectively. On performing a sensitivity analysis on cycle costs, it was demonstrated that the rFSH price should be 0.61 EGP/IU to be as cost-effective as HMG at the price of 0.64 EGP/IU (i.e. around 60% reduction in its current price). The difference in cost between HMG and rFSH in over 100,000 cycles would result in an additional 4565 ongoing pregnancies if HMG was used. Therefore, HMG was clearly more cost-effective than rFSH. The decision to adopt a more expensive, cost-ineffective treatment could result in a lower number of cycles of IVF/ICSI treatment undertaken, especially in the case of most developing countries.

Nanoscale morphological and chemical changes of high voltage lithium-manganese rich NMC composite cathodes with cycling.

PubMed

Yang, Feifei; Liu, Yijin; Martha, Surendra K; Wu, Ziyu; Andrews, Joy C; Ice, Gene E; Pianetta, Piero; Nanda, Jagjit

2014-08-13

Understanding the evolution of chemical composition and morphology of battery materials during electrochemical cycling is fundamental to extending battery cycle life and ensuring safety. This is particularly true for the much debated high energy density (high voltage) lithium-manganese rich cathode material of composition Li(1 + x)M(1 - x)O2 (M = Mn, Co, Ni). In this study we combine full-field transmission X-ray microscopy (TXM) with X-ray absorption near edge structure (XANES) to spatially resolve changes in chemical phase, oxidation state, and morphology within a high voltage cathode having nominal composition Li1.2Mn0.525Ni0.175Co0.1O2. Nanoscale microscopy with chemical/elemental sensitivity provides direct quantitative visualization of the cathode, and insights into failure. Single-pixel (∼ 30 nm) TXM XANES revealed changes in Mn chemistry with cycling, possibly to a spinel conformation and likely including some Mn(II), starting at the particle surface and proceeding inward. Morphological analysis of the particles revealed, with high resolution and statistical sampling, that the majority of particles adopted nonspherical shapes after 200 cycles. Multiple-energy tomography showed a more homogeneous association of transition metals in the pristine particle, which segregate significantly with cycling. Depletion of transition metals at the cathode surface occurs after just one cycle, likely driven by electrochemical reactions at the surface.

Nanoscale Morphological and Chemical Changes of High Voltage Lithium–Manganese Rich NMC Composite Cathodes with Cycling

PubMed Central

2015-01-01

Understanding the evolution of chemical composition and morphology of battery materials during electrochemical cycling is fundamental to extending battery cycle life and ensuring safety. This is particularly true for the much debated high energy density (high voltage) lithium–manganese rich cathode material of composition Li1 + xM1 – xO2 (M = Mn, Co, Ni). In this study we combine full-field transmission X-ray microscopy (TXM) with X-ray absorption near edge structure (XANES) to spatially resolve changes in chemical phase, oxidation state, and morphology within a high voltage cathode having nominal composition Li1.2Mn0.525Ni0.175Co0.1O2. Nanoscale microscopy with chemical/elemental sensitivity provides direct quantitative visualization of the cathode, and insights into failure. Single-pixel (∼30 nm) TXM XANES revealed changes in Mn chemistry with cycling, possibly to a spinel conformation and likely including some Mn(II), starting at the particle surface and proceeding inward. Morphological analysis of the particles revealed, with high resolution and statistical sampling, that the majority of particles adopted nonspherical shapes after 200 cycles. Multiple-energy tomography showed a more homogeneous association of transition metals in the pristine particle, which segregate significantly with cycling. Depletion of transition metals at the cathode surface occurs after just one cycle, likely driven by electrochemical reactions at the surface. PMID:25054780

Cell cycle activation in p21 dependent pathway: An alternative mechanism of organophosphate induced dopaminergic neurodegeneration.

PubMed

Wani, Willayat Yousuf; Kandimalla, Ramesh J L; Sharma, Deep Raj; Kaushal, Alka; Ruban, Anand; Sunkaria, Aditya; Vallamkondu, Jayalakshmi; Chiarugi, Alberto; Reddy, P Hemachandra; Gill, Kiran Dip

2017-07-01

In the previous study, we demonstrated that dichlorvos induces oxidative stress in dopaminergic neuronal cells and subsequent caspase activation mediates apoptosis. In the present study, we evaluated the effect and mechanism of dichlorvos induced oxidative stress on cell cycle activation in NGF-differentiated PC12 cells. Dichlorvos exposure resulted in oxidative DNA damage along with activation of cell cycle machinery in differentiated PC12 cells. Dichlorvos exposed cells exhibited an increased expression of p53, cyclin-D1, pRb and decreased expression of p21suggesting a re-entry of differentiated cells into the cell cycle. Cell cycle analysis of dichlorvos exposed cells revealed a reduction of cells in the G 0 /G 1 phase of the cell cycle (25%), and a concomitant increase of cells in S phase (30%) and G2/M phase (43.3%) compared to control PC12 cells. Further, immunoblotting of cytochrome c, Bax, Bcl-2 and cleaved caspase-3 revealed that dichlorvos induces a caspase-dependent cell death in PC12 cells. These results suggest that Dichlorvos exposure has the potential to generate oxidative stress which evokes activation of cell cycle machinery leading to apoptotic cell death via cytochrome c release from mitochondria and subsequent caspase-3 activation in differentiated PC12 cells. Copyright © 2016 Elsevier B.V. All rights reserved.

Lower Extremity Muscle Activity during Cycling in Adolescents with and without Cerebral Palsy

PubMed Central

Lauer, Richard T.; Johnston, Therese E.; Smith, Brian T.; Lee, Samuel C.K.

2008-01-01

Background In individuals with cerebral palsy (CP), adaptation and plasticity in the neuromuscular system can lead to detrimental changes affecting gait. Cycling may be an effective method to improve mobility. The biomechanics of cycling in adolescents with CP have been studied, but further analysis of the frequency and amplitude characteristics of the electromyographic (EMG) signals can assist with interpretation of the cycling kinematics. Methods Data were analyzed from ten adolescents with typical development (TD) (mean = 14.9 SD = 1.4 years) and ten adolescents with CP (mean = 15.6 SD = 1.8 years) as they cycled at two different cadences. Analyses of the lower extremity EMG signals involved frequency and amplitude analysis across the cycling revolution. Findings Examination of cycling cadence revealed that adolescents with CP had altered EMG characteristics in comparison to adolescents with typical development across the entire crank revolution for all muscles. Analyses of individual muscles indicated both inappropriate muscle activation and weakness. Interpretation A more comprehensive analysis of EMG activity has the potential to provide insight into how a task is accomplished. In this study, the control of the several muscles, especially the rectus femoris, was significantly different in adolescents with cerebral palsy. This, combined with muscle weakness, may have contributed to the observed deviations in joint kinematics. Interventions that increase muscle strength with feedback to the nervous system about appropriate activation timing may be beneficial to allow individuals with CP to cycle more efficiently. PMID:18082920

Gait phenotypes in paediatric hereditary spastic paraplegia revealed by dynamic time warping analysis and random forests

PubMed Central

Martín-Gonzalo, Juan Andrés; Rodríguez-Andonaegui, Irene; López-López, Javier; Pascual-Pascual, Samuel Ignacio

2018-01-01

The Hereditary Spastic Paraplegias (HSP) are a group of heterogeneous disorders with a wide spectrum of underlying neural pathology, and hence HSP patients express a variety of gait abnormalities. Classification of these phenotypes may help in monitoring disease progression and personalizing therapies. This is currently managed by measuring values of some kinematic and spatio-temporal parameters at certain moments during the gait cycle, either in the doctor´s surgery room or after very precise measurements produced by instrumental gait analysis (IGA). These methods, however, do not provide information about the whole structure of the gait cycle. Classification of the similarities among time series of IGA measured values of sagittal joint positions throughout the whole gait cycle can be achieved by hierarchical clustering analysis based on multivariate dynamic time warping (DTW). Random forests can estimate which are the most important isolated parameters to predict the classification revealed by DTW, since clinicians need to refer to them in their daily practice. We acquired time series of pelvic, hip, knee, ankle and forefoot sagittal angular positions from 26 HSP and 33 healthy children with an optokinetic IGA system. DTW revealed six gait patterns with different degrees of impairment of walking speed, cadence and gait cycle distribution and related with patient’s age, sex, GMFCS stage, concurrence of polyneuropathy and abnormal visual evoked potentials or corpus callosum. The most important parameters to differentiate patterns were mean pelvic tilt and hip flexion at initial contact. Longer time of support, decreased values of hip extension and increased knee flexion at initial contact can differentiate the mildest, near to normal HSP gait phenotype and the normal healthy one. Increased values of knee flexion at initial contact and delayed peak of knee flexion are important factors to distinguish GMFCS stages I from II-III and concurrence of polyneuropathy. PMID:29518090

The influence of cycling temperature and cycling rate on the phase specific degradation of a positive electrode in lithium ion batteries: A post mortem analysis

NASA Astrophysics Data System (ADS)

Darma, Mariyam Susana Dewi; Lang, Michael; Kleiner, Karin; Mereacre, Liuda; Liebau, Verena; Fauth, Francois; Bergfeldt, Thomas; Ehrenberg, Helmut

2016-09-01

The influence of cycling temperatures and cycling rates on the cycling stability of the positive electrode (cathode) of commercial batteries are investigated. The cathode is a mixture of LiMn2O4 (LMO), LiNi0.5Co0.2Mn0.3O2 (NCM) and LiNi0.8Co0.15Al0.05O2 (NCA). It is found that increasing the cycling temperature from 25 °C to 40 °C is detrimental to the long term cycling stability of the cathode. Contrastingly, the improved cycling stability is observed for the cathodes cycled at higher charge/discharge rate (2C/3C instead of 1C/2C). The microstructure analysis by X-ray powder diffraction reveals that a significant capacity fading and an increased overvoltage is observed for NCM and NCA in all the fatigued cathodes. After high number of cycling (above 1500 cycles), NCM becomes partially inactive. In contrast to NCM and NCA, LMO shows a good cycling stability at 25 °C. A pronounced degradation of LMO is only observed for the fatigued cathodes cycled at 40 °C. The huge capacity losses of NCM and NCA are most likely because the blended cathodes were cycled up to 4.12 V vs. the graphite anode during the cycle-life test (corresponds to 4.16 V vs. Li+/Li); which is beyond the stability limit of the layered oxides below 4.05 V vs. Li+/Li.

Novel Analysis Software for Detecting and Classifying Ca2+ Transient Abnormalities in Stem Cell-Derived Cardiomyocytes

PubMed Central

Penttinen, Kirsi; Siirtola, Harri; Àvalos-Salguero, Jorge; Vainio, Tiina; Juhola, Martti; Aalto-Setälä, Katriina

2015-01-01

Comprehensive functioning of Ca2+ cycling is crucial for excitation–contraction coupling of cardiomyocytes (CMs). Abnormal Ca2+ cycling is linked to arrhythmogenesis, which is associated with cardiac disorders and heart failure. Accordingly, we have generated spontaneously beating CMs from induced pluripotent stem cells (iPSC) derived from patients with catecholaminergic polymorphic ventricular tachycardia (CPVT), which is an inherited and severe cardiac disease. Ca2+ cycling studies have revealed substantial abnormalities in these CMs. Ca2+ transient analysis performed manually lacks accepted analysis criteria, and has both low throughput and high variability. To overcome these issues, we have developed a software tool, AnomalyExplorer based on interactive visualization, to assist in the classification of Ca2+ transient patterns detected in CMs. Here, we demonstrate the usability and capability of the software, and we also compare the analysis efficiency to manual analysis. We show that AnomalyExplorer is suitable for detecting normal and abnormal Ca2+ transients; furthermore, this method provides more defined and consistent information regarding the Ca2+ abnormality patterns and cell line specific differences when compared to manual analysis. This tool will facilitate and speed up the analysis of CM Ca2+ transients, making it both more accurate and user-independent. AnomalyExplorer can be exploited in Ca2+ cycling analysis to study basic disease pathology and the effects of different drugs. PMID:26308621

Novel Analysis Software for Detecting and Classifying Ca2+ Transient Abnormalities in Stem Cell-Derived Cardiomyocytes.

PubMed

Penttinen, Kirsi; Siirtola, Harri; Àvalos-Salguero, Jorge; Vainio, Tiina; Juhola, Martti; Aalto-Setälä, Katriina

2015-01-01

Comprehensive functioning of Ca2+ cycling is crucial for excitation-contraction coupling of cardiomyocytes (CMs). Abnormal Ca2+ cycling is linked to arrhythmogenesis, which is associated with cardiac disorders and heart failure. Accordingly, we have generated spontaneously beating CMs from induced pluripotent stem cells (iPSC) derived from patients with catecholaminergic polymorphic ventricular tachycardia (CPVT), which is an inherited and severe cardiac disease. Ca2+ cycling studies have revealed substantial abnormalities in these CMs. Ca2+ transient analysis performed manually lacks accepted analysis criteria, and has both low throughput and high variability. To overcome these issues, we have developed a software tool, AnomalyExplorer based on interactive visualization, to assist in the classification of Ca2+ transient patterns detected in CMs. Here, we demonstrate the usability and capability of the software, and we also compare the analysis efficiency to manual analysis. We show that AnomalyExplorer is suitable for detecting normal and abnormal Ca2+ transients; furthermore, this method provides more defined and consistent information regarding the Ca2+ abnormality patterns and cell line specific differences when compared to manual analysis. This tool will facilitate and speed up the analysis of CM Ca2+ transients, making it both more accurate and user-independent. AnomalyExplorer can be exploited in Ca2+ cycling analysis to study basic disease pathology and the effects of different drugs.

MINA controls proliferation and tumorigenesis of glioblastoma by epigenetically regulating cyclins and CDKs via H3K9me3 demethylation.

PubMed

Huang, M-Y; Xuan, F; Liu, W; Cui, H-J

2017-01-19

It is generally known that histone demethylases regulate gene transcription by altering the methylate status on histones, but their roles in cancers and the underlying molecular mechanisms still remain unclear. MYC-induced nuclear antigen (MINA) is reported to be a histone demethylase and highly expressed in many cancers. Here, for the first time, we show that MINA is involved in glioblastoma carcinogenesis and reveal the probable mechanisms of it in cell-cycle control. Kaplan-Meier analysis of progression-free survival showed that high MINA expression was strongly correlated with poor outcome and advancing tumor stage. MINA knockdown significantly repressed the cell proliferation and tumorigenesis abilities of glioblastoma cells in vitro and in vivo that were rescued by overexpressing the full-length MINA afterwards. Microarray analysis after knockdown of MINA revealed that MINA probably regulated glioblastoma carcinogenesis through the predominant cell-cycle pathways. Further investigation showed that MINA deficiency led to a cell-cycle arrest in G1 and G2 phases. And among the downstream genes, we found that cyclins and cyclin-dependent kinases were directly activated by MINA via the demethylation of H3K9me3.

Mathematics in the Making: Mapping Verbal Discourse in Polya's "Let Us Teach Guessing" Lesson

ERIC Educational Resources Information Center

Truxaw, Mary P.; DeFranco, Thomas C.

2007-01-01

This paper describes a detailed analysis of verbal discourse within an exemplary mathematics lesson--that is, George Polya teaching in the Mathematics Association of America [MAA] video classic, "Let Us Teach Guessing" (1966). The results of the analysis reveal an inductive model of teaching that represents recursive cycles rather than linear…

Effect of autoclaving on the surfaces of TiN -coated and conventional nickel-titanium rotary instruments.

PubMed

Spagnuolo, G; Ametrano, G; D'Antò, V; Rengo, C; Simeone, M; Riccitiello, F; Amato, M

2012-12-01

To evaluate the effects of repeated autoclave sterilization cycles on surface topography of conventional nickel-titanium ( NiTi ) and titanium nitride ( TiN )-coated rotary instruments. A total of 60 NiTi rotary instruments, 30 ProTaper (Dentsply Maillefer) and 30 TiN -coated AlphaKite (Komet/Gebr. Brasseler), were analysed. Instruments were evaluated in the as-received condition and after 1, 5 and 10 sterilization cycles. After sterilization, the samples were observed using scanning electron microscope (SEM), and surface chemical analysis was performed on each instrument with energy dispersive X-ray spectroscopy (EDS). Moreover, the samples were analysed by atomic force microscopy (AFM), and roughness average (Ra) and the root mean square value (RMS) of the scanned surface profiles were recorded. Data were analysed by means of anova followed by Tukey's test. Scanning electron microscope observations revealed the presence of pitting and deep milling marks in all instruments. EDS analysis confirmed that both types of instruments were composed mainly of nickel and titanium, whilst AlphaKite had additional nitride. After multiple autoclave sterilization cycles, SEM examinations revealed an increase in surface alterations, and EDS values indicated changes in chemical surface composition in all instruments. Ra and RMS values of ProTaper significantly increased after 5 (P = 0.006) and 10 cycles (P = 0.002) with respect to the as-received instruments, whilst AlphaKite showed significant differences compared with the controls after 10 cycles (P = 0.03). Multiple autoclave sterilization cycles modified the surface topography and chemical composition of conventional and TiN -coated NiTi rotary instruments. © 2012 International Endodontic Journal.

Proliferation marker pKi-67 affects the cell cycle in a self-regulated manner.

PubMed

Schmidt, Mirko H H; Broll, Rainer; Bruch, Hans-Peter; Duchrow, Michael

2002-01-01

The proliferation marker pKi-67 is commonly used in research and pathology to detect proliferating cells. In a previous work, we found the protein to be associated with regulators of the cell cycle, controlling S-phase progression, as well as entry into and exit from mitosis. Here we investigate whether pKi-67 has a regulative effect on the cell cycle itself. For that purpose we cloned four fragments of pKi-67, together representing nearly the whole protein, and an N-terminal pKi-67 antisense oligonucleotide into a tetracycline inducible gene expression system. The sense fragments were C-terminally modified by addition of either a nuclear localization sequence (NLS) or a STOP codon to address the impact of their intracellular distribution. FACS based cell cycle analysis revealed that expression of nearly all pKi-67 domains and the antisense oligonucleotide led to a decreased amount of cells in S-phase and an increased number of cells in G(2)/M- and G(1)-phase. Subsequent analysis of the endogenous pKi-67 mRNA and protein levels revealed that the constructs with the most significant impact on the cell cycle were able to silence pKi-67 transcription as well. We conclude from the data that pKi-67 influences progression of S-phase and mitosis in a self-regulated manner and, therefore, effects the cell cycle checkpoints within both phases. Furthermore, we found pKi-67 mediates an anti-apoptotic effect on the cell and we verified that this marker, although it is a potential ribosomal catalyst, is not expressed in differentiated tissues with a high transcriptional activity. Copyright 2002 Wiley-Liss, Inc.

Constitutive expression of thymidylate synthase from LCDV-C induces a transformed phenotype in fish cells.

PubMed

Zhao, Zhe; Shi, Yan; Ke, Fei; Wei, Sun; Gui, Jianfang; Zhang, Qiya

2008-03-01

Thymidylate synthase (TS), an essential enzyme in DNA synthesis and repair, plays a key role in the events of cell cycle regulation and tumor formation. Here, an investigation was presented about subcellular location and biological function of viral TS from lymphocystis disease virus from China (LCDV-C) in fish cells. Fluorescence microscopy revealed that LCDV-C TS was predominantly localized in the cytoplasm in fish cells. Cell cycle analysis demonstrated that LCDV-C TS promoted cell cycle progression into S and G2/M phase in the constitutive expressed cells. As a result, the cells have a faster growth rate compared with the control cells as revealed by cell growth curves. For foci assay, the TS-expressed cells gave rise to foci 4-5 weeks after incubation. Microscopic examination of the TS-induced foci revealed multilayered growth and crisscross morphology characteristic of transformed cells. Moreover, LCDV-C TS predisposed the transfected cells to acquire an anchorage-independent phenotype and could grow in 0.3% soft agar. So the data reveal LCDV-C TS is sufficient to induce a transformed phenotype in fish cells in vitro and exhibits its potential ability in cell transformation. To our knowledge, it is the first report on viral TS sequences associated with transforming activity.

Menstrual cycle perturbation by organohalogens and elements in the Cree of James Bay, Canada.

PubMed

Wainman, Bruce C; Kesner, James S; Martin, Ian D; Meadows, Juliana W; Krieg, Edward F; Nieboer, Evert; Tsuji, Leonard J

2016-04-01

Persistent organohalogens (POHs) and metals have been linked to alterations in menstrual cycle function and fertility in humans. The Cree First Nations people living near James Bay in Ontario and Quebec, Canada, have elevated levels of POHs, mercury and lead compared to other Canadians. The present study examines the interrelationships between selected POHs and elements on menstrual cycle function in these Cree women. Menstrual cycle characteristics were derived from structured daily diaries and endocrine measurements from daily urine samples collected during one cycle for 42 women age 19-42. We measured 31 POHs in blood plasma and 18 elements in whole blood, for 31 of the participants. POHs and elements detected in ≥ 70% of the participants were transformed by principal component (PC) analysis to reduce the contaminant exposure data to fewer, uncorrelated PCA variables. Multiple regression analysis revealed that, after adjusting for confounders, PC-3 values showed significant negative association with cycle length, after adjusting for confounders (p = 0.002). PC-3 accounted for 9.2% of the variance and shows positive loadings for cadmium, selenium, and PBDE congeners 47 and 153, and a negative loading for copper. Sensitivity analysis of the model to quantify likely effect sizes showed a range of menstrual cycle length from 25.3 to 28.3 days using the lower and upper 95% confidence limits of mean measured contaminant concentrations to predict cycle length. Our observations support the hypothesis that the menstrual cycle function of these women may be altered by exposure to POHs and elements from their environment. Copyright © 2015. Published by Elsevier Ltd.

13C-flux analysis reveals NADPH-balancing transhydrogenation cycles in stationary phase of nitrogen-starving Bacillus subtilis.

PubMed

Rühl, Martin; Le Coq, Dominique; Aymerich, Stéphane; Sauer, Uwe

2012-08-10

In their natural habitat, microorganisms are typically confronted with nutritional limitations that restrict growth and force them to persevere in a stationary phase. Despite the importance of this phase, little is known about the metabolic state(s) that sustains it. Here, we investigate metabolically active but non-growing Bacillus subtilis during nitrogen starvation. In the absence of biomass formation as the major NADPH sink, the intracellular flux distribution in these resting B. subtilis reveals a large apparent catabolic NADPH overproduction of 5.0 ± 0.6 mmol g(-1)h(-1) that was partly caused by high pentose phosphate pathway fluxes. Combining transcriptome analysis, stationary (13)C-flux analysis in metabolic deletion mutants, (2)H-labeling experiments, and kinetic flux profiling, we demonstrate that about half of the catabolic excess NADPH is oxidized by two transhydrogenation cycles, i.e. isoenzyme pairs of dehydrogenases with different cofactor specificities that operate in reverse directions. These transhydrogenation cycles were constituted by the combined activities of the glyceraldehyde 3-phosphate dehydrogenases GapA/GapB and the malic enzymes MalS/YtsJ. At least an additional 6% of the overproduced NADPH is reoxidized by continuous cycling between ana- and catabolism of glutamate. Furthermore, in vitro enzyme data show that a not yet identified transhydrogenase could potentially reoxidize ∼20% of the overproduced NADPH. Overall, we demonstrate the interplay between several metabolic mechanisms that concertedly enable network-wide NADPH homeostasis under conditions of high catabolic NADPH production in the absence of cell growth in B. subtilis.

13C-flux Analysis Reveals NADPH-balancing Transhydrogenation Cycles in Stationary Phase of Nitrogen-starving Bacillus subtilis *

PubMed Central

Rühl, Martin; Le Coq, Dominique; Aymerich, Stéphane; Sauer, Uwe

2012-01-01

In their natural habitat, microorganisms are typically confronted with nutritional limitations that restrict growth and force them to persevere in a stationary phase. Despite the importance of this phase, little is known about the metabolic state(s) that sustains it. Here, we investigate metabolically active but non-growing Bacillus subtilis during nitrogen starvation. In the absence of biomass formation as the major NADPH sink, the intracellular flux distribution in these resting B. subtilis reveals a large apparent catabolic NADPH overproduction of 5.0 ± 0.6 mmol·g−1·h−1 that was partly caused by high pentose phosphate pathway fluxes. Combining transcriptome analysis, stationary 13C-flux analysis in metabolic deletion mutants, 2H-labeling experiments, and kinetic flux profiling, we demonstrate that about half of the catabolic excess NADPH is oxidized by two transhydrogenation cycles, i.e. isoenzyme pairs of dehydrogenases with different cofactor specificities that operate in reverse directions. These transhydrogenation cycles were constituted by the combined activities of the glyceraldehyde 3-phosphate dehydrogenases GapA/GapB and the malic enzymes MalS/YtsJ. At least an additional 6% of the overproduced NADPH is reoxidized by continuous cycling between ana- and catabolism of glutamate. Furthermore, in vitro enzyme data show that a not yet identified transhydrogenase could potentially reoxidize ∼20% of the overproduced NADPH. Overall, we demonstrate the interplay between several metabolic mechanisms that concertedly enable network-wide NADPH homeostasis under conditions of high catabolic NADPH production in the absence of cell growth in B. subtilis. PMID:22740702

The glutathione cycle: Glutathione metabolism beyond the γ-glutamyl cycle.

PubMed

Bachhawat, Anand Kumar; Yadav, Shambhu

2018-04-17

Glutathione was discovered in 1888, over 125 years ago. Since then, our understanding of various functions and metabolism of this important molecule has grown over these years. But it is only now, in the last decade, that a somewhat complete picture of its metabolism has emerged. Glutathione metabolism has till now been largely depicted and understood by the γ-glutamyl cycle that was proposed in 1970. However, new findings and knowledge particularly on the transport and degradation of glutathione have revealed that many aspects of the γ-glutamyl cycle are incorrect. Despite this, an integrated critical analysis of the cycle has never been undertaken and this has led to the cycle and its errors perpetuating in the literature. This review takes a careful look at the γ-glutamyl cycle and its shortcomings and presents a "glutathione cycle" that captures the current understanding of glutathione metabolism. © 2018 IUBMB Life, 2018. © 2018 International Union of Biochemistry and Molecular Biology.

Persulfidation proteome reveals the regulation of protein function by hydrogen sulfide in diverse biological processes in Arabidopsis.

PubMed

Aroca, Angeles; Benito, Juan M; Gotor, Cecilia; Romero, Luis C

2017-10-13

Hydrogen sulfide-mediated signaling pathways regulate many physiological and pathophysiological processes in mammalian and plant systems. The molecular mechanism by which hydrogen sulfide exerts its action involves the post-translational modification of cysteine residues to form a persulfidated thiol motif, a process called protein persulfidation. We have developed a comparative and quantitative proteomic analysis approach for the detection of endogenous persulfidated proteins in wild-type Arabidopsis and L-CYSTEINE DESULFHYDRASE 1 mutant leaves using the tag-switch method. The 2015 identified persulfidated proteins were isolated from plants grown under controlled conditions, and therefore, at least 5% of the entire Arabidopsis proteome may undergo persulfidation under baseline conditions. Bioinformatic analysis revealed that persulfidated cysteines participate in a wide range of biological functions, regulating important processes such as carbon metabolism, plant responses to abiotic and biotic stresses, plant growth and development, and RNA translation. Quantitative analysis in both genetic backgrounds reveals that protein persulfidation is mainly involved in primary metabolic pathways such as the tricarboxylic acid cycle, glycolysis, and the Calvin cycle, suggesting that this protein modification is a new regulatory component in these pathways. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Measuring risky adolescent cycling behaviour.

PubMed

Feenstra, Hans; Ruiter, Robert A C; Schepers, Jan; Peters, Gjalt-Jorn; Kok, Gerjo

2011-09-01

Adolescents are at a greater risk of being involved in traffic accidents than most other age groups, even before they start driving cars. This article aims to determine the factor structure of a self-report questionnaire measuring adolescent risky cycling behaviour, the ACBQ (Adolescent Cycling Behaviour Questionnaire). The questionnaire's structure was based on the widely used Driver Behaviour Questionnaire (DBQ). A sample of secondary school students (N = 1749; age range: 13-18 years) filled out the questionnaire. Factor analysis revealed a three-factor structure underlying the questionnaire, which was confirmed on two equally large portions of the entire sample. These three underlying factors were identified as errors, common violations and exceptional violations. The ACBQ is a useful instrument for measuring adolescents' risky cycling behaviour.

Gap cycling for SWIFT.

PubMed

Corum, Curtis A; Idiyatullin, Djaudat; Snyder, Carl J; Garwood, Michael

2015-02-01

SWIFT (SWeep Imaging with Fourier Transformation) is a non-Cartesian MRI method with unique features and capabilities. In SWIFT, radiofrequency (RF) excitation and reception are performed nearly simultaneously, by rapidly switching between transmit and receive during a frequency-swept RF pulse. Because both the transmitted pulse and data acquisition are simultaneously amplitude-modulated in SWIFT (in contrast to continuous RF excitation and uninterrupted data acquisition in more familiar MRI sequences), crosstalk between different frequency bands occurs in the data. This crosstalk leads to a "bulls-eye" artifact in SWIFT images. We present a method to cancel this interband crosstalk by cycling the pulse and receive gap positions relative to the un-gapped pulse shape. We call this strategy "gap cycling." We carry out theoretical analysis, simulation and experiments to characterize the signal chain, resulting artifacts, and their elimination for SWIFT. Theoretical analysis reveals the mechanism for gap-cycling's effectiveness in canceling interband crosstalk in the received data. We show phantom and in vivo results demonstrating bulls-eye artifact free images. Gap cycling is an effective method to remove bulls-eye artifact resulting from interband crosstalk in SWIFT data. © 2014 Wiley Periodicals, Inc.

Stability and Bifurcation Analysis of a Three-Species Food Chain Model with Fear

NASA Astrophysics Data System (ADS)

Panday, Pijush; Pal, Nikhil; Samanta, Sudip; Chattopadhyay, Joydev

In the present paper, we investigate the impact of fear in a tri-trophic food chain model. We propose a three-species food chain model, where the growth rate of middle predator is reduced due to the cost of fear of top predator, and the growth rate of prey is suppressed due to the cost of fear of middle predator. Mathematical properties such as equilibrium analysis, stability analysis, bifurcation analysis and persistence have been investigated. We also describe the global stability analysis of the equilibrium points. Our numerical simulations reveal that cost of fear in basal prey may exhibit bistability by producing unstable limit cycles, however, fear in middle predator can replace unstable limit cycles by a stable limit cycle or a stable interior equilibrium. We observe that fear can stabilize the system from chaos to stable focus through the period-halving phenomenon. We conclude that chaotic dynamics can be controlled by the fear factors. We apply basic tools of nonlinear dynamics such as Poincaré section and maximum Lyapunov exponent to identify the chaotic behavior of the system.

Thermomechanical behavior and microstructural evolution of a Ni(Pd)-rich Ni 24.3Ti 49.7Pd 26 high temperature shape memory alloy

DOE PAGES

Benafan, O.; Garg, A.; Noebe, R. D.; ...

2015-04-20

We investigated the effect of thermomechanical cycling on a slightly Ni(Pd)-rich Ni 24.3Ti 49.7Pd 26 (near stochiometric Ni–Ti basis with Pd replacing Ni) high temperature shape memory alloy. Furthermore, aged tensile specimens (400 °C/24 h/furnace cooled) were subjected to constant-stress thermal cycling in conjunction with microstructural assessment via in situ neutron diffraction and transmission electron microscopy (TEM), before and after testing. It was shown that in spite of the slightly Ni(Pd)-rich composition and heat treatment used to precipitation harden the alloy, the material exhibited dimensional instabilities with residual strain accumulation reaching 1.5% over 10 thermomechanical cycles. This was attributed tomore » insufficient strengthening of the material (insufficient volume fraction of precipitate phase) to prevent plasticity from occurring concomitant with the martensitic transformation. In situ neutron diffraction revealed the presence of retained martensite while cycling under 300 MPa stress, which was also confirmed by transmission electron microscopy of post-cycled samples. Neutron diffraction analysis of the post-thermally-cycled samples under no-load revealed residual lattice strains in the martensite and austenite phases, remnant texture in the martensite phase, and peak broadening of the austenite phase. The texture we developed in the martensite phase was composed mainly of those martensitic tensile variants observed during thermomechanical cycling. Presence of a high density of dislocations, deformation twins, and retained martensite was revealed in the austenite state via in-situ TEM in the post-cycled material, providing an explanation for the observed peak broadening in the neutron diffraction spectra. Despite the dimensional instabilities, this alloy exhibited a biased transformation strain on the order of 3% and a two-way shape memory effect (TWSME) strain of ~2%, at relatively high actuation temperatures.« less

Depletion of Plasmodium berghei plasmoredoxin reveals a non-essential role for life cycle progression of the malaria parasite.

PubMed

Buchholz, Kathrin; Rahlfs, Stefan; Schirmer, R Heiner; Becker, Katja; Matuschewski, Kai

2008-06-25

Proliferation of the pathogenic Plasmodium asexual blood stages in host erythrocytes requires an exquisite capacity to protect the malaria parasite against oxidative stress. This function is achieved by a complex antioxidant defence system composed of redox-active proteins and low MW antioxidants. Here, we disrupted the P. berghei plasmoredoxin gene that encodes a parasite-specific 22 kDa member of the thioredoxin superfamily. The successful generation of plasmoredoxin knockout mutants in the rodent model malaria parasite and phenotypic analysis during life cycle progression revealed a non-vital role in vivo. Our findings suggest that plasmoredoxin fulfils a specialized and dispensable role for Plasmodium and highlights the need for target validation to inform drug development strategies.

Stable isotope analyses on archived fish scales reveal the long-term effect of nitrogen loads on carbon cycling in rivers.

PubMed

Roussel, Jean-Marc; Perrier, Charles; Erkinaro, Jaakko; Niemelä, Eero; Cunjak, Richard A; Huteau, Dominique; Riera, Pascal

2014-02-01

Stable isotope analysis of organic matter in sediment records has long been used to track historical changes in productivity and carbon cycling in marine and lacustrine ecosystems. While flow dynamics preclude stratigraphic measurements of riverine sediments, such retrospective analysis is important for understanding biogeochemical cycling in running waters. Unique collections of riverine fish scales were used to analyse δ(15) N and δ(13) C variations in the food web of two European rivers that experience different degrees of anthropogenic pressure. Over the past four decades, dissolved inorganic N loading remained low and constant in the Teno River (70°N, Finland); in contrast, N loading increased fourfold in the Scorff River (47°N, France) over the same period. Archived scales of Atlantic salmon parr, a riverine life-stage that feeds on aquatic invertebrates, revealed high δ(15) N values in the Scorff River reflecting anthropogenic N inputs to that riverine environment. A strong correlation between dissolved inorganic N loads and δ(13) C values in fish scales was observed in the Scorff River, whereas no trend was found in the Teno River. This result suggests that anthropogenic N-nutrients enhanced atmospheric C uptake by primary producers and its transfer to fish. Our results illustrate for the first time that, as for lakes and marine ecosystems, historical changes in anthropogenic N loading can affect C cycling in riverine food webs, and confirm the long-term interactions between N and C biogeochemical cycles in running waters. © 2013 John Wiley & Sons Ltd.

The Analysis of Cell Cycle-related Proteins in Ovarian Clear Cell Carcinoma Versus High-grade Serous Carcinoma.

PubMed

Hazama, Yukiko; Moriya, Takuya; Sugihara, Mika; Sano, Rikiya; Shiota, Mitsuru; Nakamura, Takafumi; Shimoya, Koichiro

2017-10-10

In Japan, the frequency of ovarian clear cell carcinoma (CCC) is twice as high as that in the United States and Europe. Often, patient prognosis of CCC is poor because of chemoresistance. Here, we focus on the cell cycle, which is one of the mechanisms of chemoresistance. To detect the informative markers and improve the strategy of chemotherapy for CCC, we performed immunochemical staining of cell cycle-related proteins in ovarian malignant tumors. We detected that each of the 29 samples of CCC and high-grade serous carcinoma (HGSC) were necessary to reveal the significant differences in immunostaining and prognosis. We performed the immunostaining analysis using the antibodies of cell cycle-related proteins such as Ki-67, Cdt1, MCM7, and geminin. The positive rate of Cdt1 in the CCC group was significantly higher than that in the HGSC group (P<0.0001). However, the positive rate of geminin in the HGSC group was significantly higher than that in the CCC group (P<0.0001). The overall survival of CCC patients with high labeling index of Cdt1 was significantly worse than that of CCC patients with low labeling index of Cdt1 (P=0.004). The study results suggested that the cancer cells of CCC and HGSC exist in the G1 phase and S, G2, and M phases, respectively. The differences in cell cycle of CCC might be one of the reasons for chemotherapy resistance. Further investigations are necessary to reveal the usefulness of Cdt1 as a biomarker in CCC.

A new Gsdma3 mutation affecting anagen phase of first hair cycle

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

Tanaka, Shigekazu; Department of Genetics, School of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka 411-8540; Tamura, Masaru

2007-08-10

Recombination-induced mutation 3 (Rim3) is a spontaneous mouse mutation that exhibits dominant phenotype of hyperkeratosis and hair loss. Fine linkage analysis of Rim3 and sequencing revealed a novel single point mutation, G1124A leading to Ala348Thr, in Gsdma3 in chromosome 11. Transgenesis with BAC DNA harboring the Rim3-type Gsdma3 recaptured the Rim3 phenotype, providing direct evidence that Gsdma3 is the causative gene of Rim3. We examined the spatial expression of Gsdma3 and characterized the Rim3 phenotype in detail. Gsdma3 is expressed in differentiated epidermal cells in the skin, but not in the proliferating epidermal cells. Histological analysis of Rim3 mutant showedmore » hyperplasia of the epidermal cells in the upper hair follicles and abnormal anagen phase at the first hair cycle. Furthermore, immunohistochemical analysis revealed hyperproliferation and misdifferentiation of the upper follicular epidermis in Rim3 mutant. These results suggest that Gsdma3 is involved in the proliferation and differentiation of epidermal stem cells.« less

Dynamically monitoring the gene expression of dual fluorophore in the cell cycle with quantitative spectrum analysis

NASA Astrophysics Data System (ADS)

Lee, Ja-Yun; Wu, Tzong-Yuan; Hsu, I.-Jen

2008-04-01

The cloning and transcription techniques on gene cloned fluorescent proteins have been widely used in many applications. They have been used as reporters of some conditions in a series of reactions. However, it is usually difficult to monitor the specific target with the exactly number of proteins during the process in turbid media, especially at micrometer scales. We successfully revealed an alternative way to monitor the cell cycle behavior and quantitatively analyzed the target cells with green and red fluorescent proteins (GFP and RFP) during different phases of the cell cycle by quantitatively analyzing its behavior and also monitoring its spatial distribution.

Uncovering Hidden Layers of Cell Cycle Regulation through Integrative Multi-omic Analysis

PubMed Central

Aviner, Ranen; Shenoy, Anjana; Elroy-Stein, Orna; Geiger, Tamar

2015-01-01

Studying the complex relationship between transcription, translation and protein degradation is essential to our understanding of biological processes in health and disease. The limited correlations observed between mRNA and protein abundance suggest pervasive regulation of post-transcriptional steps and support the importance of profiling mRNA levels in parallel to protein synthesis and degradation rates. In this work, we applied an integrative multi-omic approach to study gene expression along the mammalian cell cycle through side-by-side analysis of mRNA, translation and protein levels. Our analysis sheds new light on the significant contribution of both protein synthesis and degradation to the variance in protein expression. Furthermore, we find that translation regulation plays an important role at S-phase, while progression through mitosis is predominantly controlled by changes in either mRNA levels or protein stability. Specific molecular functions are found to be co-regulated and share similar patterns of mRNA, translation and protein expression along the cell cycle. Notably, these include genes and entire pathways not previously implicated in cell cycle progression, demonstrating the potential of this approach to identify novel regulatory mechanisms beyond those revealed by traditional expression profiling. Through this three-level analysis, we characterize different mechanisms of gene expression, discover new cycling gene products and highlight the importance and utility of combining datasets generated using different techniques that monitor distinct steps of gene expression. PMID:26439921

Using historical photography to monitor and assess threats over time

Treesearch

Don Evans

2010-01-01

Analysis of aerial photography is perhaps the best way to assess changes in landcover conditions. In the United States, most national forests have repeat photography on approximately a 10-year cycle. Analysis of this rich photo record can reveal changes in insect damage, fuels buildup, unmanaged off-highway vehicle use, loss of open space, and other land-cover...

Bifurcation analysis of an automatic dynamic balancing mechanism for eccentric rotors

NASA Astrophysics Data System (ADS)

Green, K.; Champneys, A. R.; Lieven, N. J.

2006-04-01

We present a nonlinear bifurcation analysis of the dynamics of an automatic dynamic balancing mechanism for rotating machines. The principle of operation is to deploy two or more masses that are free to travel around a race at a fixed distance from the hub and, subsequently, balance any eccentricity in the rotor. Mathematically, we start from a Lagrangian description of the system. It is then shown how under isotropic conditions a change of coordinates into a rotating frame turns the problem into a regular autonomous dynamical system, amenable to a full nonlinear bifurcation analysis. Using numerical continuation techniques, curves are traced of steady states, limit cycles and their bifurcations as parameters are varied. These results are augmented by simulations of the system trajectories in phase space. Taking the case of a balancer with two free masses, broad trends are revealed on the existence of a stable, dynamically balanced steady-state solution for specific rotation speeds and eccentricities. However, the analysis also reveals other potentially attracting states—non-trivial steady states, limit cycles, and chaotic motion—which are not in balance. The transient effects which lead to these competing states, which in some cases coexist, are investigated.

Cell Cycle Control in the Early Embryonic Development of Aquatic Animal Species

PubMed Central

Siefert, Joseph C.; Clowdus, Emily A.; Sansam, Christopher L.

2016-01-01

The cell cycle is integrated with many aspects of embryonic development. Not only is proper control over the pace of cell proliferation important, but also the timing of cell cycle progression is coordinated with transcription, cell migration, and cell differentiation. Due to the ease with which the embryos of aquatic organisms can be observed and manipulated, they have been a popular choice for embryologists throughout history. In the cell cycle field, aquatic organisms have been extremely important because they have played a major role in the discovery and analysis of key regulators of the cell cycle. In particular, the frog Xenopus laevis has been instrumental for understanding how the basic embryonic cell cycle is regulated. More recently, the zebrafish has been used to understand how the cell cycle is remodeled during vertebrate development and how it is regulated during morphogenesis. This review describes how some of the unique strengths of aquatic species have been leveraged for cell cycle research and suggests how species such as Xenopus and zebrafish will continue to reveal the roles of the cell cycle in human biology and disease. PMID:26475527

Insulin-like growth factor II messenger RNA-binding protein-3 is an independent prognostic factor in uterine leiomyosarcoma.

PubMed

Yasutake, Nobuko; Ohishi, Yoshihiro; Taguchi, Kenichi; Hiraki, Yuka; Oya, Masafumi; Oshiro, Yumi; Mine, Mari; Iwasaki, Takeshi; Yamamoto, Hidetaka; Kohashi, Kenichi; Sonoda, Kenzo; Kato, Kiyoko; Oda, Yoshinao

2018-04-01

The aim of this study was to identify the prognostic factors of uterine leiomyosarcoma (ULMS). We reviewed 60 cases of surgically resected ULMSs and investigated conventional clinicopathological factors, together with the expression of insulin-like growth factor II messenger RNA-binding protein-3 (IMP3), hormone receptors and cell cycle regulatory markers by immunohistochemistry. Mediator complex subunit 12 (MED12) mutation analysis was also performed. Univariate analyses revealed that advanced stage (P < 0.0001), older age (P = 0.0244) and IMP3 expression (P = 0.0011) were significant predictors of a poor outcome. Multivariate analysis revealed advanced stage (P < 0.0001) and IMP3 (P = 0.0373) as independent predictors of a poor prognosis. Expressions of cell cycle markers and hormone receptors, and MED12 mutations (12% in ULMSs) were not identified as prognostic markers in this study. IMP3 expression in ULMS could be a marker of a poor prognosis. © 2017 John Wiley & Sons Ltd.

Cell cycle pathway dysregulation in human keratinocytes during chronic exposure to low arsenite.

PubMed

Al-Eryani, Laila; Waigel, Sabine; Jala, Venkatakrishna; Jenkins, Samantha F; States, J Christopher

2017-09-15

Arsenic is naturally prevalent in the earth's crust and widely distributed in air and water. Chronic low arsenic exposure is associated with several cancers in vivo, including skin cancer, and with transformation in vitro of cell lines including immortalized human keratinocytes (HaCaT). Arsenic also is associated with cell cycle dysregulation at different exposure levels in multiple cell lines. In this work, we analyzed gene expression in HaCaT cells to gain an understanding of gene expression changes contributing to transformation at an early time point. HaCaT cells were exposed to 0 or 100nM NaAsO 2 for 7weeks. Total RNA was purified and analyzed by microarray hybridization. Differential expression with fold change≥|1.5| and p-value≤0.05 was determined using Partek Genomic Suite™ and pathway and network analyses using MetaCore™ software (FDR≤0.05). Cell cycle analysis was performed using flow cytometry. 644 mRNAs were differentially expressed. Cell cycle/cell cycle regulation pathways predominated in the list of dysregulated pathways. Genes involved in replication origin licensing were enriched in the network. Cell cycle assay analysis showed an increase in G2/M compartment in arsenite-exposed cells. Arsenite exposure induced differential gene expression indicating dysregulation of cell cycle control, which was confirmed by cell cycle analysis. The results suggest that cell cycle dysregulation is an early event in transformation manifested in cells unable to transit G2/M efficiently. Further study at later time points will reveal additional changes in gene expression related to transformation processes. Copyright © 2017 Elsevier Inc. All rights reserved.

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

Vissers, Daniel R.; Isheim, Dieter; Zhan, Chun

Lithium-ion batteries utilizing 5 V spinel material, LixMn1.5Ni0.5O4 have received considerable interest in recent years for their ability to deliver high energy and power densities. In this paper, we report an atomic scale analysis of the surface layer of a core–shell 5 V spinel structure where a small amount of the manganese lattice sites have been substituted with cobalt in the shell to reach a stoichiometry of LixMn1.18Ni0.55Co0.27O4. Our analyses include electrochemical analysis, atom probe tomography (APT) analysis, kinetic analysis of the interfacial reactions, and high resolution scanning transmission electron microscopy (HR-TEM) analysis. The APT analysis is performed on themore » material before and after long-term cycling at room temperature to provide insights into the atomic scale phenomena within the surface layer of the electrode material. Our APT data reveals a 25–30 nano-meter (nm) region which forms after cycling. From our analyses, we believe that the outer few nanometers of this region stabilizes the 5 V spinel within the chemical environment of the lithium-ion cell such that its structure is not compromised and thereby enables this material to cycle without significant capacity fading.« less

Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer

PubMed Central

Jewell, Talia N M; Karaoz, Ulas; Brodie, Eoin L; Williams, Kenneth H; Beller, Harry R

2016-01-01

Groundwater ecosystems are conventionally thought to be fueled by surface-derived allochthonous organic matter and dominated by heterotrophic microbes living under often-oligotrophic conditions. However, in a 2-month study of nitrate amendment to a perennially suboxic aquifer in Rifle (CO), strain-resolved metatranscriptomic analysis revealed pervasive and diverse chemolithoautotrophic bacterial activity relevant to C, S, N and Fe cycling. Before nitrate injection, anaerobic ammonia-oxidizing (anammox) bacteria accounted for 16% of overall microbial community gene expression, whereas during the nitrate injection, two other groups of chemolithoautotrophic bacteria collectively accounted for 80% of the metatranscriptome: (1) members of the Fe(II)-oxidizing Gallionellaceae family and (2) strains of the S-oxidizing species, Sulfurimonas denitrificans. Notably, the proportion of the metatranscriptome accounted for by these three groups was considerably greater than the proportion of the metagenome coverage that they represented. Transcriptional analysis revealed some unexpected metabolic couplings, in particular, putative nitrate-dependent Fe(II) and S oxidation among nominally microaerophilic Gallionellaceae strains, including expression of periplasmic (NapAB) and membrane-bound (NarGHI) nitrate reductases. The three most active groups of chemolithoautotrophic bacteria in this study had overlapping metabolisms that allowed them to occupy different yet related metabolic niches throughout the study. Overall, these results highlight the important role that chemolithoautotrophy can have in aquifer biogeochemical cycling, a finding that has broad implications for understanding terrestrial carbon cycling and is supported by recent studies of geochemically diverse aquifers. PMID:26943628

Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer

DOE PAGES

Jewell, Talia N. M.; Karaoz, Ulas; Brodie, Eoin L.; ...

2016-03-04

Groundwater ecosystems are conventionally thought to be fueled by surface-derived allochthonous organic matter and dominated by heterotrophic microbes living under often-oligotrophic conditions. However, in a 2-month study of nitrate amendment to a perennially suboxic aquifer in Rifle (CO), strain-resolved metatranscriptomic analysis revealed pervasive and diverse chemolithoautotrophic bacterial activity relevant to C, S, N and Fe cycling. Before nitrate injection, anaerobic ammonia-oxidizing (anammox) bacteria accounted for 16% of overall microbial community gene expression, whereas during the nitrate injection, two other groups of chemolithoautotrophic bacteria collectively accounted for 80% of the metatranscriptome: (1) members of the Fe(II)-oxidizing Gallionellaceae family and (2) strainsmore » of the S-oxidizing species, Sulfurimonas denitrificans. Notably, the proportion of the metatranscriptome accounted for by these three groups was considerably greater than the proportion of the metagenome coverage that they represented. Transcriptional analysis revealed some unexpected metabolic couplings, in particular, putative nitrate-dependent Fe(II) and S oxidation among nominally microaerophilic Gallionellaceae strains, including expression of periplasmic (NapAB) and membrane-bound (NarGHI) nitrate reductases. The three most active groups of chemolithoautotrophic bacteria in this study had overlapping metabolisms that allowed them to occupy different yet related metabolic niches throughout the study. Overall, these results highlight the important role that chemolithoautotrophy can have in aquifer biogeochemical cycling, a finding that has broad implications for understanding terrestrial carbon cycling and is supported by recent studies of geochemically diverse aquifers.« less

Performance Cycle Analysis of a Two-Spool, Separate-Exhaust Turbofan With Interstage Turbine Burner

NASA Technical Reports Server (NTRS)

Liew, K. H.; Urip, E.; Yang, S. L.; Mattingly, J. D.; Marek, C. J.

2005-01-01

This paper presents the performance cycle analysis of a dual-spool, separate-exhaust turbofan engine, with an Interstage Turbine Burner serving as a secondary combustor. The ITB, which is located at the transition duct between the high- and the low-pressure turbines, is a relatively new concept for increasing specific thrust and lowering pollutant emissions in modern jet engine propulsion. A detailed performance analysis of this engine has been conducted for steady-state engine performance prediction. A code is written and is capable of predicting engine performances (i.e., thrust and thrust specific fuel consumption) at varying flight conditions and throttle settings. Two design-point engines were studied to reveal trends in performance at both full and partial throttle operations. A mission analysis is also presented to assure the advantage of saving fuel by adding ITB.

The logic of kinetic regulation in the thioredoxin system

PubMed Central

2011-01-01

Background The thioredoxin system consisting of NADP(H), thioredoxin reductase and thioredoxin provides reducing equivalents to a large and diverse array of cellular processes. Despite a great deal of information on the kinetics of individual thioredoxin-dependent reactions, the kinetic regulation of this system as an integrated whole is not known. We address this by using kinetic modeling to identify and describe kinetic behavioral motifs found within the system. Results Analysis of a realistic computational model of the Escherichia coli thioredoxin system revealed several modes of kinetic regulation in the system. In keeping with published findings, the model showed that thioredoxin-dependent reactions were adaptable (i.e. changes to the thioredoxin system affected the kinetic profiles of these reactions). Further and in contrast to other systems-level descriptions, analysis of the model showed that apparently unrelated thioredoxin oxidation reactions can affect each other via their combined effects on the thioredoxin redox cycle. However, the scale of these effects depended on the kinetics of the individual thioredoxin oxidation reactions with some reactions more sensitive to changes in the thioredoxin cycle and others, such as the Tpx-dependent reduction of hydrogen peroxide, less sensitive to these changes. The coupling of the thioredoxin and Tpx redox cycles also allowed for ultrasensitive changes in the thioredoxin concentration in response to changes in the thioredoxin reductase concentration. We were able to describe the kinetic mechanisms underlying these behaviors precisely with analytical solutions and core models. Conclusions Using kinetic modeling we have revealed the logic that underlies the functional organization and kinetic behavior of the thioredoxin system. The thioredoxin redox cycle and associated reactions allows for a system that is adaptable, interconnected and able to display differential sensitivities to changes in this redox cycle. This work provides a theoretical, systems-biological basis for an experimental analysis of the thioredoxin system and its associated reactions. PMID:21266044

Recurrent epidemic cycles driven by intervention in a population of two susceptibility types

NASA Astrophysics Data System (ADS)

Juanico, Drandreb Earl O.

2014-03-01

Epidemics have been known to persist in the form of recurrence cycles. Despite intervention efforts through vaccination and targeted social distancing, infectious diseases like influenza continue to appear intermittently over time. I have undertaken an analysis of a stochastic epidemic model to explore the hypothesis that intervention efforts actually drive epidemic cycles. Time series from simulations of the model reveal oscillations exhibiting a similar temporal signature as influenza epidemics. The power-spectral density indicates a resonant frequency, which approximately corresponds to the apparent annual seasonality of influenza in temperate zones. Asymptotic solution to the backward Kolmogorov equation of the dynamics corresponds to an exponentially-decaying mean-exit time as a function of the intervention rate. Intervention must be implemented at a sufficiently high rate to extinguish the infection. The results demonstrate that intervention efforts can induce epidemic cycles, and that the temporal signature of cycles can provide early warning of imminent outbreaks.

A Blind Circadian Clock in Cavefish Reveals that Opsins Mediate Peripheral Clock Photoreception

PubMed Central

Cavallari, Nicola; Frigato, Elena; Vallone, Daniela; Fröhlich, Nadine; Lopez-Olmeda, Jose Fernando; Foà, Augusto; Berti, Roberto; Sánchez-Vázquez, Francisco Javier; Bertolucci, Cristiano; Foulkes, Nicholas S.

2011-01-01

The circadian clock is synchronized with the day-night cycle primarily by light. Fish represent fascinating models for deciphering the light input pathway to the vertebrate clock since fish cell clocks are regulated by direct light exposure. Here we have performed a comparative, functional analysis of the circadian clock involving the zebrafish that is normally exposed to the day-night cycle and a cavefish species that has evolved in perpetual darkness. Our results reveal that the cavefish retains a food-entrainable clock that oscillates with an infradian period. Importantly, however, this clock is not regulated by light. This comparative study pinpoints the two extra-retinal photoreceptors Melanopsin (Opn4m2) and TMT-opsin as essential upstream elements of the peripheral clock light input pathway. PMID:21909239

Propionibacterium acnes inhibits FOXM1 and induces cell cycle alterations in human primary prostate cells.

PubMed

Sayanjali, Behnam; Christensen, Gitte J M; Al-Zeer, Munir A; Mollenkopf, Hans-Joachim; Meyer, Thomas F; Brüggemann, Holger

2016-11-01

Propionibacterium acnes has been detected in diseased human prostate tissue, and cell culture experiments suggest that the bacterium can establish a low-grade inflammation. Here, we investigated its impact on human primary prostate epithelial cells. Microarray analysis confirmed the inflammation-inducing capability of P. acnes but also showed deregulation of genes involved in the cell cycle. qPCR experiments showed that viable P. acnes downregulates a master regulator of cell cycle progression, FOXM1. Flow cytometry experiments revealed that P. acnes increases the number of cells in S-phase. We tested the hypothesis that a P. acnes-produced berninamycin-like thiopeptide is responsible for this effect, since it is related to the FOXM1 inhibitor siomycin. The thiopeptide biosynthesis gene cluster was strongly expressed; it is present in subtype IB of P. acnes, but absent from type IA, which is most abundant on human skin. A knock-out mutant lacking the gene encoding the berninamycin-like peptide precursor was unable to downregulate FOXM1 and to halt the cell cycle. Our study reveals a novel host cell-interacting activity of P. acnes. Copyright © 2016 The Authors. Published by Elsevier GmbH.. All rights reserved.

A Novel Analysis Of The Connection Between Indian Monsoon Rainfall And Solar Activity

NASA Astrophysics Data System (ADS)

Bhattacharyya, S.; Narasimha, R.

2005-12-01

The existence of possible correlations between the solar cycle period as extracted from the yearly means of sunspot numbers and any periodicities that may be present in the Indian monsoon rainfall has been addressed using wavelet analysis. The wavelet transform coefficient maps of sunspot-number time series and those of the homogeneous Indian monsoon rainfall annual time series data reveal striking similarities, especially around the 11-year period. A novel method to analyse and quantify this similarity devising statistical schemes is suggested in this paper. The wavelet transform coefficient maxima at the 11-year period for the sunspot numbers and the monsoon rainfall have each been modelled as a point process in time and a statistical scheme for identifying a trend or dependence between the two processes has been devised. A regression analysis of parameters in these processes reveals a nearly linear trend with small but systematic deviations from the regressed line. Suitable function models for these deviations have been obtained through an unconstrained error minimisation scheme. These models provide an excellent fit to the time series of the given wavelet transform coefficient maxima obtained from actual data. Statistical significance tests on these deviations suggest with 99% confidence that the deviations are sample fluctuations obtained from normal distributions. In fact our earlier studies (see, Bhattacharyya and Narasimha, 2005, Geophys. Res. Lett., Vol. 32, No. 5) revealed that average rainfall is higher during periods of greater solar activity for all cases, at confidence levels varying from 75% to 99%, being 95% or greater in 3 out of 7 of them. Analysis using standard wavelet techniques reveals higher power in the 8--16 y band during the higher solar activity period, in 6 of the 7 rainfall time series, at confidence levels exceeding 99.99%. Furthermore, a comparison between the wavelet cross spectra of solar activity with rainfall and noise (including those simulating the rainfall spectrum and probability distribution) revealed that over the two test-periods respectively of high and low solar activity, the average cross power of the solar activity index with rainfall exceeds that with the noise at z-test confidence levels exceeding 99.99% over period-bands covering the 11.6 y sunspot cycle (see, Bhattacharyya and Narasimha, SORCE 2005 14-16th September, at Durango, Colorado USA). These results provide strong evidence for connections between Indian rainfall and solar activity. The present study reveals in addition the presence of subharmonics of the solar cycle period in the monsoon rainfall time series together with information on their phase relationships.

Regional High-Frequency Stratigraphic Cyclicity Analysis of the Upper Cretaceous Juana Lopez Member of the Mancos Shale, New Mexico

NASA Astrophysics Data System (ADS)

Wiercigroch, M.; Bhattacharya, J.

2017-12-01

The Earth is considered to have been in a "greenhouse state" during the Cretaceous Period. High-frequency sedimentary cycles are observed throughout the Cretaceous section of the Western Interior Seaway. Even though this warm Cretaceous climate suggests an ice-free planet Earth, there has been much debate as to whether the observed high-frequency sedimentary cycles are climate-driven Milankovitch-scale cycles that would suggest glaciers during the Cretaceous Period. This study tests the hypothesis of a glacio-eustatic origin of high-frequency cyclicity in the Turonian Juana Lopez Member of the Mancos Shale in the San Juan Basin, New Mexico. Data for this study was obtained from two stratigraphic measured sections which are 3.2 km apart, and located southwest of Shiprock. The two sections are found approximately 60 km away from the Turonian shoreline in an offshore marine environment. A high-resolution thin bed facies analysis on both sections reveals the Juana Lopez to be deposited in a fluvial-dominated, mixed wave- and fluvial-influenced environment. The Juana Lopez is shown to be an overall coarsening-upward sequence, displaying a shallowing regressive environment. Correlations between the two sections reveal 13 correlated parasequences identified through the violation of Walther's Law. An average cyclicity frequency of ca 90 kyr was determined for the sequences by bracketing the Inocermus dimidus and Scaphites whitfieldi biostratigraphic zones within the Juana Lopez sections. This cyclicity represents short eccentricity Milankovitch cycles. Many studies have confirmed that the observed Milankovitch-scaled cyclicity in the Cretaceous must be controlled by glacio-eustasy. With similar Milankovitch cyclicity found in the Juana Lopez, the short eccentricity Milankovitch cycles are interpreted as being glacio-eustatic in origin, which supports the presence of ice in the Cretaceous Period.

Evidence of carbon fixation pathway in a bacterium from candidate phylum SBR1093 revealed with genomic analysis.

PubMed

Wang, Zhiping; Guo, Feng; Liu, Lili; Zhang, Tong

2014-01-01

Autotrophic CO2 fixation is the most important biotransformation process in the biosphere. Research focusing on the diversity and distribution of relevant autotrophs is significant to our comprehension of the biosphere. In this study, a draft genome of a bacterium from candidate phylum SBR1093 was reconstructed with the metagenome of an industrial activated sludge. Based on comparative genomics, this autotrophy may occur via a newly discovered carbon fixation path, the hydroxypropionate-hydroxybutyrate (HPHB) cycle, which was demonstrated in a previous work to be uniquely possessed by some genera from Archaea. This bacterium possesses all of the thirteen enzymes required for the HPHB cycle; these enzymes share 30∼50% identity with those in the autotrophic species of Archaea that undergo the HPHB cycle and 30∼80% identity with the corresponding enzymes of the mixotrophic species within Bradyrhizobiaceae. Thus, this bacterium might have an autotrophic growth mode in certain conditions. A phylogenetic analysis based on the 16S rRNA gene reveals that the phylotypes within candidate phylum SBR1093 are primarily clustered into 5 clades with a shallow branching pattern. This bacterium is clustered with phylotypes from organically contaminated environments, implying a demand for organics in heterotrophic metabolism. Considering the types of regulators, such as FnR, Fur, and ArsR, this bacterium might be a facultative aerobic mixotroph with potential multi-antibiotic and heavy metal resistances. This is the first report on Bacteria that may perform potential carbon fixation via the HPHB cycle, thus may expand our knowledge of the distribution and importance of the HPHB cycle in the biosphere.

Integrated Analysis of the Transcriptome and Metabolome of Corynebacterium glutamicum during Penicillin-Induced Glutamic Acid Production.

PubMed

Hirasawa, Takashi; Saito, Masaki; Yoshikawa, Katsunori; Furusawa, Chikara; Shmizu, Hiroshi

2018-05-01

Corynebacterium glutamicum is known for its ability to produce glutamic acid and has been utilized for the fermentative production of various amino acids. Glutamic acid production in C. glutamicum is induced by penicillin. In this study, the transcriptome and metabolome of C. glutamicum is analyzed to understand the mechanism of penicillin-induced glutamic acid production. Transcriptomic analysis with DNA microarray revealed that expression of some glycolysis- and TCA cycle-related genes, which include those encoding the enzymes involved in conversion of glucose to 2-oxoglutaric acid, is upregulated after penicillin addition. Meanwhile, expression of some TCA cycle-related genes, encoding the enzymes for conversion of 2-oxoglutaric acid to oxaloacetic acid, and the anaplerotic reactions decreased. In addition, expression of NCgl1221 and odhI, encoding proteins involved in glutamic acid excretion and inhibition of the 2-oxoglutarate dehydrogenase, respectively, is upregulated. Functional category enrichment analysis of genes upregulated and downregulated after penicillin addition revealed that genes for signal transduction systems are enriched among upregulated genes, whereas those for energy production and carbohydrate and amino acid metabolisms are enriched among the downregulated genes. As for the metabolomic analysis using capillary electrophoresis time-of-flight mass spectrometry, the intracellular content of most metabolites of the glycolysis and the TCA cycle decreased dramatically after penicillin addition. Overall, these results indicate that the cellular metabolism and glutamic acid excretion are mainly optimized at the transcription level during penicillin-induced glutamic acid production by C. glutamicum. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A factor analysis approach to examining relationships among ovarian steroid concentrations, gonadotrophin concentrations and menstrual cycle length characteristics in healthy, cycling women

PubMed Central

Barrett, E.S.; Thune, I.; Lipson, S.F.; Furberg, A.-S.; Ellison, P.T.

2013-01-01

STUDY QUESTION How are ovarian steroid concentrations, gonadotrophins and menstrual cycle characteristics inter-related within normal menstrual cycles? SUMMARY ANSWER Within cycles, measures of estradiol production are highly related to one another, as are measures of progesterone production; however, the two hormones also show some independence from one another, and measures of cycle length and gonadotrophin concentrations show even greater independence, indicating minimal integration within cycles. WHAT IS KNOWN ALREADY The menstrual cycle is typically conceptualized as a cohesive unit, with hormone levels, follicular development and ovulation all closely inter-related within a single cycle. Empirical support for this idea is limited, however, and to our knowledge, no analysis has examined the relationships among all of these components simultaneously. STUDY DESIGN, SIZE, DURATION A total of 206 healthy, cycling Norwegian women participated in a prospective cohort study (EBBA-I) over the duration of a single menstrual cycle. Of these, 192 contributed hormonal and cycle data to the current analysis. PARTICIPANTS/MATERIALS, SETTING, METHODS Subjects provided daily saliva samples throughout the menstrual cycle from which estradiol and progesterone concentrations were measured. FSH and LH concentrations were measured in serum samples from three points in the same menstrual cycle and cycle length characteristics were calculated based on hormonal data and menstrual records. A factor analysis was conducted to examine the underlying relationships among 22 variables derived from the hormonal data and menstrual cycle characteristics. MAIN RESULTS AND THE ROLE OF CHANCE Six rotated factors emerged, explaining 80% of the variance in the data. Of these, factors representing estradiol and progesterone concentrations accounted for 37 and 13% of the variance, respectively. There was some association between measures of estradiol and progesterone production within cycles; however, cycle length characteristics and gonadotrophin concentrations showed little association with any measure of ovarian hormone concentrations. LIMITATIONS, REASONS FOR CAUTION Our summary measures of ovarian hormones may be imprecise in women with extremely long or short cycles, which could affect the patterns emerging in the factor analysis. Given that we only had data from one cycle on each woman, we cannot address how cycle characteristics may covary within individual women across multiple cycles. WIDER IMPLICATIONS OF THE FINDINGS Our findings are generalizable to other healthy populations with typical cycles, however, may not be applicable to cycles that are anovulatory, extreme in length or otherwise atypical. The results support previous findings that measures of estradiol production are highly correlated across the cycle, as are measures of progesterone production. Estradiol and progesterone concentrations are associated with one another, furthermore. However factor analysis also revealed more complex underlying patterns in the menstrual cycle, highlighting the fact that gonadotrophin concentrations and cycle length characteristics are virtually independent of ovarian hormones. These results suggest that despite integration of follicular and luteal ovarian steroid production across the cycle, cycle quality is a multi-faceted construct, rather than a single dimension. STUDY FUNDING/COMPETING INTEREST(S) The EBBA-I study was supported by a grant from the Norwegian Cancer Society (49 258, 05087); Foundation for the Norwegian Health and Rehabilitation Organizations (59010-2000/2001/2002); Aakre Foundation (5695-2000, 5754-2002) and Health Region East. The current analyses were completed under funding from the National Institutes of Health (K12 ES019852). No competing interests declared. PMID:23250924

Differences in cumulus cells gene expression between modified natural and stimulated in vitro fertilization cycles.

PubMed

Papler, Tanja Burnik; Bokal, Eda Vrtačnik; Tacer, Klementina Fon; Juvan, Peter; Virant Klun, Irma; Devjak, Rok

2014-01-01

The aim of our study was to determine whether there are any differences in the cumulus cell gene expression profile of mature oocytes derived from modified natural IVF and controlled ovarian hyperstimulation cycles and if these changes could help us understand why modified natural IVF has lower success rates. Cumulus cells surrounding mature oocytes that developed to morulae or blastocysts on day 5 after oocyte retrieval were submitted to microarray analysis. The obtained data were then validated using quantitative real-time PCR. There were 66 differentially expressed genes between cumulus cells of modified natural IVF and controlled ovarian hyperstimulation cycles. Gene ontology analysis revealed the oxidation-reduction process, glutathione metabolic process, xenobiotic metabolic process and gene expression were significantly enriched biological processes in MNIVF cycles. Among differentially expressed genes we observed a large group of small nucleolar RNA's whose role in folliculogenesis has not yet been established. The increased expression of genes involved in the oxidation-reduction process probably points to hypoxic conditions in modified natural IVF cycles. This finding opens up new perspectives for the establishment of the potential role that oxidation-reduction processes have in determining success rates of modified natural IVF.

RNA-seq analysis of Drosophila clock and non-clock neurons reveals neuron-specific cycling and novel candidate neuropeptides.

PubMed

Abruzzi, Katharine C; Zadina, Abigail; Luo, Weifei; Wiyanto, Evelyn; Rahman, Reazur; Guo, Fang; Shafer, Orie; Rosbash, Michael

2017-02-01

Locomotor activity rhythms are controlled by a network of ~150 circadian neurons within the adult Drosophila brain. They are subdivided based on their anatomical locations and properties. We profiled transcripts "around the clock" from three key groups of circadian neurons with different functions. We also profiled a non-circadian outgroup, dopaminergic (TH) neurons. They have cycling transcripts but fewer than clock neurons as well as low expression and poor cycling of clock gene transcripts. This suggests that TH neurons do not have a canonical circadian clock and that their gene expression cycling is driven by brain systemic cues. The three circadian groups are surprisingly diverse in their cycling transcripts and overall gene expression patterns, which include known and putative novel neuropeptides. Even the overall phase distributions of cycling transcripts are distinct, indicating that different regulatory principles govern transcript oscillations. This surprising cell-type diversity parallels the functional heterogeneity of the different neurons.

Inter- and intraexaminer reliability of bitewing radiography and near-infrared light transillumination for proximal caries detection and assessment.

PubMed

Litzenburger, Friederike; Heck, Katrin; Pitchika, Vinay; Neuhaus, Klaus W; Jost, Fabian N; Hickel, Reinhard; Jablonski-Momeni, Anahita; Welk, Alexander; Lederer, Alexander; Kühnisch, Jan

2018-02-01

The purpose of this in vitro study was to evaluate the inter- and intraexaminer reliability of digital bitewing (DBW) radiography and near-infrared light transillumination (NIRT) for proximal caries detection and assessment in posterior teeth. From a pool of 85 patients, 100 corresponding pairs of DBW and NIRT images (~1/3 healthy, ~1/3 with enamel caries and ~1/3 with dentin caries) were chosen. 12 dentists with different professional status and clinical experience repeated the evaluation in two blinded cycles. Two experienced dentists provided a reference diagnosis after analysing all images independently. Statistical analysis included the calculation of simple (κ) and weighted Kappa (wκ) values as a measure of reliability. Logistic regression with a backward elimination model was used to investigate the influence of the diagnostic method, evaluation cycle, type of tooth, and clinical experience on reliability. Altogether, inter- and intraexaminer reliability exhibited good to excellent κ and wκ values for DBW radiography (Inter: κ = 0.60/ 0.63; wκ = 0.74/0.76; Intra: κ = 0.64; wκ = 0.77) and NIRT (Inter: κ = 0.74/0.64; wκ = 0.86/0.82; Intra: κ = 0.68; wκ = 0.84). The backward elimination model revealed NIRT to be significantly more reliable than DBW radiography. This study revealed a good to excellent inter- and intraexaminer reliability for proximal caries detection using DBW and NIRT images. The logistic regression analysis revealed significantly better reliability for NIRT. Additionally, the first evaluation cycle was more reliable according to the reference diagnoses.

Transcriptome Analysis of Polyhydroxybutyrate Cycle Mutants Reveals Discrete Loci Connecting Nitrogen Utilization and Carbon Storage in Sinorhizobium meliloti.

PubMed

D'Alessio, Maya; Nordeste, Ricardo; Doxey, Andrew C; Charles, Trevor C

2017-01-01

Polyhydroxybutyrate (PHB) and glycogen polymers are produced by bacteria as carbon storage compounds under unbalanced growth conditions. To gain insights into the transcriptional mechanisms controlling carbon storage in Sinorhizobium meliloti , we investigated the global transcriptomic response to the genetic disruption of key genes in PHB synthesis and degradation and in glycogen synthesis. Under both nitrogen-limited and balanced growth conditions, transcriptomic analysis was performed with genetic mutants deficient in PHB synthesis ( phbA , phbB , phbAB , and phbC ), PHB degradation ( bdhA , phaZ , and acsA2 ), and glycogen synthesis ( glgA1 ). Three distinct genomic regions of the pSymA megaplasmid exhibited altered expression in the wild type and the PHB cycle mutants that was not seen in the glycogen synthesis mutant. An Fnr family transcriptional motif was identified in the upstream regions of a cluster of genes showing similar transcriptional patterns across the mutants. This motif was found at the highest density in the genomic regions with the strongest transcriptional effect, and the presence of this motif upstream of genes in these regions was significantly correlated with decreased transcript abundance. Analysis of the genes in the pSymA regions revealed that they contain a genomic overrepresentation of Fnr family transcription factor-encoding genes. We hypothesize that these loci, containing mostly nitrogen utilization, denitrification, and nitrogen fixation genes, are regulated in response to the intracellular carbon/nitrogen balance. These results indicate a transcriptional regulatory association between intracellular carbon levels (mediated through the functionality of the PHB cycle) and the expression of nitrogen metabolism genes. IMPORTANCE The ability of bacteria to store carbon and energy as intracellular polymers uncouples cell growth and replication from nutrient uptake and provides flexibility in the use of resources as they are available to the cell. The impact of carbon storage on cellular metabolism would be reflected in global transcription patterns. By investigating the transcriptomic effects of genetically disrupting genes involved in the PHB carbon storage cycle, we revealed a relationship between intracellular carbon storage and nitrogen metabolism. This work demonstrates the utility of combining transcriptome sequencing with metabolic pathway mutations for identifying underlying gene regulatory mechanisms.

Evidence for the Existence of One Antenna-Associated, Lipid-Dissolved and Two Protein-Bound Pools of Diadinoxanthin Cycle Pigments in Diatoms[C][W

PubMed Central

Lepetit, Bernard; Volke, Daniela; Gilbert, Matthias; Wilhelm, Christian; Goss, Reimund

2010-01-01

We studied the localization of diadinoxanthin cycle pigments in the diatoms Cyclotella meneghiniana and Phaeodactylum tricornutum. Isolation of pigment protein complexes revealed that the majority of high-light-synthesized diadinoxanthin and diatoxanthin is associated with the fucoxanthin chlorophyll protein (FCP) complexes. The characterization of intact cells, thylakoid membranes, and pigment protein complexes by absorption and low-temperature fluorescence spectroscopy showed that the FCPs contain certain amounts of protein-bound diadinoxanthin cycle pigments, which are not significantly different in high-light and low-light cultures. The largest part of high-light-formed diadinoxanthin cycle pigments, however, is not bound to antenna apoproteins but located in a lipid shield around the FCPs, which is copurified with the complexes. This lipid shield is primarily composed of the thylakoid membrane lipid monogalactosyldiacylglycerol. We also show that the photosystem I (PSI) fraction contains a tightly connected FCP complex that is enriched in protein-bound diadinoxanthin cycle pigments. The peripheral FCP and the FCP associated with PSI are composed of different apoproteins. Tandem mass spectrometry analysis revealed that the peripheral FCP is composed mainly of the light-harvesting complex protein Lhcf and also significant amounts of Lhcr. The PSI fraction, on the other hand, shows an enrichment of Lhcr proteins, which are thus responsible for the diadinoxanthin cycle pigment binding. The existence of lipid-dissolved and protein-bound diadinoxanthin cycle pigments in the peripheral antenna and in PSI is discussed with respect to different specific functions of the xanthophylls. PMID:20935178

Nuclear Reprogramming: Kinetics of Cell Cycle and Metabolic Progression as Determinants of Success

PubMed Central

Balbach, Sebastian Thomas; Esteves, Telma Cristina; Houghton, Franchesca Dawn; Siatkowski, Marcin; Pfeiffer, Martin Johannes; Tsurumi, Chizuko; Kanzler, Benoit; Fuellen, Georg; Boiani, Michele

2012-01-01

Establishment of totipotency after somatic cell nuclear transfer (NT) requires not only reprogramming of gene expression, but also conversion of the cell cycle from quiescence to the precisely timed sequence of embryonic cleavage. Inadequate adaptation of the somatic nucleus to the embryonic cell cycle regime may lay the foundation for NT embryo failure and their reported lower cell counts. We combined bright field and fluorescence imaging of histone H2b-GFP expressing mouse embryos, to record cell divisions up to the blastocyst stage. This allowed us to quantitatively analyze cleavage kinetics of cloned embryos and revealed an extended and inconstant duration of the second and third cell cycles compared to fertilized controls generated by intracytoplasmic sperm injection (ICSI). Compared to fertilized embryos, slow and fast cleaving NT embryos presented similar rates of errors in M phase, but were considerably less tolerant to mitotic errors and underwent cleavage arrest. Although NT embryos vary substantially in their speed of cell cycle progression, transcriptome analysis did not detect systematic differences between fast and slow NT embryos. Profiling of amino acid turnover during pre-implantation development revealed that NT embryos consume lower amounts of amino acids, in particular arginine, than fertilized embryos until morula stage. An increased arginine supplementation enhanced development to blastocyst and increased embryo cell numbers. We conclude that a cell cycle delay, which is independent of pluripotency marker reactivation, and metabolic restraints reduce cell counts of NT embryos and impede their development. PMID:22530006

Arsenic metabolism in high altitude modern stromatolites revealed by metagenomic analysis.

PubMed

Kurth, Daniel; Amadio, Ariel; Ordoñez, Omar F; Albarracín, Virginia H; Gärtner, Wolfgang; Farías, María E

2017-04-21

Modern stromatolites thrive only in selected locations in the world. Socompa Lake, located in the Andean plateau at 3570 masl, is one of the numerous extreme Andean microbial ecosystems described over recent years. Extreme environmental conditions include hypersalinity, high UV incidence, and high arsenic content, among others. After Socompa's stromatolite microbial communities were analysed by metagenomic DNA sequencing, taxonomic classification showed dominance of Proteobacteria, Bacteroidetes and Firmicutes, and a remarkably high number of unclassified sequences. A functional analysis indicated that carbon fixation might occur not only by the Calvin-Benson cycle, but also through alternative pathways such as the reverse TCA cycle, and the reductive acetyl-CoA pathway. Deltaproteobacteria were involved both in sulfate reduction and nitrogen fixation. Significant differences were found when comparing the Socompa stromatolite metagenome to the Shark Bay (Australia) smooth mat metagenome: namely, those involving stress related processes, particularly, arsenic resistance. An in-depth analysis revealed a surprisingly diverse metabolism comprising all known types of As resistance and energy generating pathways. While the ars operon was the main mechanism, an important abundance of arsM genes was observed in selected phyla. The data resulting from this work will prove a cornerstone for further studies on this rare microbial community.

Heartbeat of the Sun from Principal Component Analysis and prediction of solar activity on a millenium timescale

PubMed Central

Zharkova, V. V.; Shepherd, S. J.; Popova, E.; Zharkov, S. I.

2015-01-01

We derive two principal components (PCs) of temporal magnetic field variations over the solar cycles 21–24 from full disk magnetograms covering about 39% of data variance, with σ = 0.67. These PCs are attributed to two main magnetic waves travelling from the opposite hemispheres with close frequencies and increasing phase shift. Using symbolic regeression analysis we also derive mathematical formulae for these waves and calculate their summary curve which we show is linked to solar activity index. Extrapolation of the PCs backward for 800 years reveals the two 350-year grand cycles superimposed on 22 year-cycles with the features showing a remarkable resemblance to sunspot activity reported in the past including the Maunder and Dalton minimum. The summary curve calculated for the next millennium predicts further three grand cycles with the closest grand minimum occurring in the forthcoming cycles 26–27 with the two magnetic field waves separating into the opposite hemispheres leading to strongly reduced solar activity. These grand cycle variations are probed by α − Ω dynamo model with meridional circulation. Dynamo waves are found generated with close frequencies whose interaction leads to beating effects responsible for the grand cycles (350–400 years) superimposed on a standard 22 year cycle. This approach opens a new era in investigation and confident prediction of solar activity on a millenium timescale. PMID:26511513

The Cosmic Skidmark: witnessing galaxy transformation at z = 0.19

NASA Astrophysics Data System (ADS)

Murphy, David N. A.

2015-02-01

We present an early-look analysis of the ``Cosmic Skidmark''. Discovered following visual inspection of the Geach, Murphy & Bower (2011) SDSS Stripe 82 cluster catalogue generated by ORCA (an automated cluster algorithm searching for red-sequences; Murphy, Geach & Bower 2012), this z = 0.19 1.4L* galaxy appears to have been caught in the rare act of transformation while accreting onto an estimated 1013-1014 h -1 M⊙-mass galaxy group. SDSS spectroscopy reveals clear signatures of star formation whilst deep optical imaging reveals a pronounced 50 kpc cometary tail. Pending completion of our ALMA Cycle 2 and IFU observations, we show here preliminary analysis of this target.

Variations in the temperature and circulation of the atmosphere during the 11-year cycle of solar activity derived from the ERA-Interim reanalysis data

NASA Astrophysics Data System (ADS)

Gruzdev, A. N.

2017-07-01

Using the data of the ERA-Interim reanalysis, we have obtained estimates of changes in temperature, the geopotential and its large-scale zonal harmonics, wind velocity, and potential vorticity in the troposphere and stratosphere of the Northern and Southern hemispheres during the 11-year solar cycle. The estimates have been obtained using the method of multiple linear regression. Specific features of response of the indicated atmospheric parameters to the solar cycle have been revealed in particular regions of the atmosphere for a whole year and depending on the season. The results of the analysis indicate the existence of a reliable statistical relationship of large-scale dynamic and thermodynamic processes in the troposphere and stratosphere with the 11-year solar cycle.

Life cycle design metrics for energy generation technologies: Method, data, and case study

NASA Astrophysics Data System (ADS)

Cooper, Joyce; Lee, Seung-Jin; Elter, John; Boussu, Jeff; Boman, Sarah

A method to assist in the rapid preparation of Life Cycle Assessments of emerging energy generation technologies is presented and applied to distributed proton exchange membrane fuel cell systems. The method develops life cycle environmental design metrics and allows variations in hardware materials, transportation scenarios, assembly energy use, operating performance and consumables, and fuels and fuel production scenarios to be modeled and comparisons to competing systems to be made. Data and results are based on publicly available U.S. Life Cycle Assessment data sources and are formulated to allow the environmental impact weighting scheme to be specified. A case study evaluates improvements in efficiency and in materials recycling and compares distributed proton exchange membrane fuel cell systems to other distributed generation options. The results reveal the importance of sensitivity analysis and system efficiency in interpreting case studies.

Loading Mode and Environment Effects on Surface Profile Characteristics of Martensite Plates in Cu-Based SMAs

NASA Astrophysics Data System (ADS)

Suru, Marius-Gabriel; Paraschiv, Adrian-Liviu; Lohan, Nicoleta Monica; Pricop, Bogdan; Ozkal, Burak; Bujoreanu, Leandru-Gheorghe

2014-07-01

The present work reports the influence of the loading mode provided during training under constant stress, in bending, applied to lamellar specimens of Cu-Zn-Al shape memory alloys (SMAs). During training, the specimens were bent by a load fastened at their free end, while being martensitic at room temperature and they lifted the load by one-way effect (1WE), during heating up to austenitic field. On cooling to martensite field, the lower concave surface of bent specimens was compressed, and during heating it was elongated, being subjected to a series of tension-compression cycles, during heating-cooling, respectively. Conversely, the upper convex surface of bent specimens was elongated during cooling and compressed during heating, being subjected to compression-tension cycles. Furthermore, 2WE-trained actuators were tested by means of a hydraulic installation where, this time heating-cooling cycles were performed in oil conditions. Considering that the lower concave surface of the specimens was kept in compressed state, while the upper convex surface was kept in elongated state, the study reveals the influence of the two loading modes and environments on the width of martensite plates of the specimens trained under various numbers of cycles. In this purpose, Cu-Zn-Al specimens, trained under 100-300-500 cycles, were prepared and analyzed by atomic force microscopy (AFM) as well as optical and scanning electron microscopy (OM and SEM, respectively). The analysis also included AFM micrographs corroborated with statistical evaluations in order to reveal the effects of loading mode (tension or compression) in different environmental conditions of the specimens, on the surface profile characteristics of martensite plates, revealed by electropolishing.

A systematic analysis of the early transcribed membrane protein family throughout the life cycle of Plasmodium yoelii.

PubMed

MacKellar, Drew C; Vaughan, Ashley M; Aly, Ahmed S I; DeLeon, Sasha; Kappe, Stefan H I

2011-11-01

The early transcribed membrane proteins (ETRAMPs) are a family of small, highly charged transmembrane proteins unique to malaria parasites. Some members of the ETRAMP family have been localized to the parasitophorous vacuole membrane that separates the intracellular parasite from the host cell and thus presumably have a role in host-parasite interactions. Although it was previously shown that two ETRAMPs are critical for rodent malaria parasite liver-stage development, the importance of most ETRAMPs during the parasite life cycle remains unknown. Here, we comprehensively identify nine new etramps in the genome of the rodent malaria parasite Plasmodium yoelii, and elucidate their conservation in other malaria parasites. etramp expression profiles are diverse throughout the parasite life cycle as measured by RT-PCR. Epitope tagging of two ETRAMPs demonstrates protein expression in blood and liver stages, and reveals differences in both their timing of expression and their subcellular localization. Gene targeting studies of each of the nine uncharacterized etramps show that two are refractory to deletion and thus likely essential for blood-stage replication. Seven etramps are not essential for any life cycle stage. Systematic characterization of the members of the ETRAMP family reveals the diversity in importance of each family member at the interface between host and parasite throughout the developmental cycle of the malaria parasite. © 2011 Blackwell Publishing Ltd.

Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana.

PubMed

Van Leene, Jelle; Hollunder, Jens; Eeckhout, Dominique; Persiau, Geert; Van De Slijke, Eveline; Stals, Hilde; Van Isterdael, Gert; Verkest, Aurine; Neirynck, Sandy; Buffel, Yelle; De Bodt, Stefanie; Maere, Steven; Laukens, Kris; Pharazyn, Anne; Ferreira, Paulo C G; Eloy, Nubia; Renne, Charlotte; Meyer, Christian; Faure, Jean-Denis; Steinbrenner, Jens; Beynon, Jim; Larkin, John C; Van de Peer, Yves; Hilson, Pierre; Kuiper, Martin; De Veylder, Lieven; Van Onckelen, Harry; Inzé, Dirk; Witters, Erwin; De Jaeger, Geert

2010-08-10

Cell proliferation is the main driving force for plant growth. Although genome sequence analysis revealed a high number of cell cycle genes in plants, little is known about the molecular complexes steering cell division. In a targeted proteomics approach, we mapped the core complex machinery at the heart of the Arabidopsis thaliana cell cycle control. Besides a central regulatory network of core complexes, we distinguished a peripheral network that links the core machinery to up- and downstream pathways. Over 100 new candidate cell cycle proteins were predicted and an in-depth biological interpretation demonstrated the hypothesis-generating power of the interaction data. The data set provided a comprehensive view on heterodimeric cyclin-dependent kinase (CDK)-cyclin complexes in plants. For the first time, inhibitory proteins of plant-specific B-type CDKs were discovered and the anaphase-promoting complex was characterized and extended. Important conclusions were that mitotic A- and B-type cyclins form complexes with the plant-specific B-type CDKs and not with CDKA;1, and that D-type cyclins and S-phase-specific A-type cyclins seem to be associated exclusively with CDKA;1. Furthermore, we could show that plants have evolved a combinatorial toolkit consisting of at least 92 different CDK-cyclin complex variants, which strongly underscores the functional diversification among the large family of cyclins and reflects the pivotal role of cell cycle regulation in the developmental plasticity of plants.

Further evidences for sleep instability and impaired spindle-delta dynamics in schizophrenia: a whole-night polysomnography study with neuroloop-gain and sleep-cycle analysis.

PubMed

Sasidharan, Arun; Kumar, Sunil; Nair, Ajay Kumar; Lukose, Ammu; Marigowda, Vrinda; John, John P; Kutty, Bindu M

2017-10-01

Sleep offers a unique window into the brain dysfunctions in schizophrenia. Many past sleep studies have reported abnormalities in both macro-sleep architecture (like increased awakenings) as well as micro-sleep-architecture (like spindle deficits) in patients with schizophrenia (PSZ). The present study attempts to replicate previous reports of macro- and micro-sleep-architectural abnormalities in schizophrenia. In addition, the study also examined sleep-stage changes and spindle-delta dynamics across sleep-cycles to provide further evidence in support of the dysfunctional thalamocortical mechanisms causing sleep instability and poor sleep maintenance associated with schizophrenia pathophysiology. Whole-night polysomnography was carried out among 45 PSZ and 39 age- and gender-matched healthy control subjects. Sleep-stage dynamics were assessed across sleep-cycles using a customized software algorithm. Spindle-delta dynamics across sleep-cycles were determined using neuroloop-gain analysis. PSZ showed macro-sleep architecture abnormalities such as prolonged sleeplessness, increased intermittent-awakenings, long sleep-onset latency, reduced non-rapid eye movement (NREM) stage 2 sleep, increased stage transitions, and poor sleep efficiency. They also showed reduced spindle density (sigma neuroloop-gain) but comparable slow wave density (delta neuroloop-gain) throughout the sleep. Sleep-cycle-wise analysis revealed transient features of sleep instability due to significantly increased intermittent awakenings especially in the first and third sleep-cycles, and unstable and recurrent stage transitions in both NREM (first sleep-cycle) and rapid eye movement (REM) sleep-periods (second sleep-cycle). Spindle deficits were persistent across the first three cycles and were positively correlated with sleep disruption during the subsequent REM sleep. In addition to replicating previously reported sleep deficits in PSZ, the current study showed subtle deficits in NREM-REM alterations across whole-night polysomnography. These results point towards a possible maladaptive interplay between unstable thalamocortical networks, resulting in sleep-cycle-specific instability patterns associated with schizophrenia pathophysiology. Copyright © 2017 Elsevier B.V. All rights reserved.

Nuclear receptor TLX regulates cell cycle progression in neural stem cells of the developing brain.

PubMed

Li, Wenwu; Sun, Guoqiang; Yang, Su; Qu, Qiuhao; Nakashima, Kinichi; Shi, Yanhong

2008-01-01

TLX is an orphan nuclear receptor that is expressed exclusively in vertebrate forebrains. Although TLX is known to be expressed in embryonic brains, the mechanism by which it influences neural development remains largely unknown. We show here that TLX is expressed specifically in periventricular neural stem cells in embryonic brains. Significant thinning of neocortex was observed in embryonic d 14.5 TLX-null brains with reduced nestin labeling and decreased cell proliferation in the germinal zone. Cell cycle analysis revealed both prolonged cell cycles and increased cell cycle exit in TLX-null embryonic brains. Increased expression of a cyclin-dependent kinase inhibitor p21 and decreased expression of cyclin D1 provide a molecular basis for the deficiency of cell cycle progression in embryonic brains of TLX-null mice. Furthermore, transient knockdown of TLX by in utero electroporation led to precocious cell cycle exit and differentiation of neural stem cells followed by outward migration. Together these results indicate that TLX plays an important role in neural development by regulating cell cycle progression and exit of neural stem cells in the developing brain.

Nuclear Receptor TLX Regulates Cell Cycle Progression in Neural Stem Cells of the Developing Brain

PubMed Central

Li, Wenwu; Sun, Guoqiang; Yang, Su; Qu, Qiuhao; Nakashima, Kinichi; Shi, Yanhong

2008-01-01

TLX is an orphan nuclear receptor that is expressed exclusively in vertebrate forebrains. Although TLX is known to be expressed in embryonic brains, the mechanism by which it influences neural development remains largely unknown. We show here that TLX is expressed specifically in periventricular neural stem cells in embryonic brains. Significant thinning of neocortex was observed in embryonic d 14.5 TLX-null brains with reduced nestin labeling and decreased cell proliferation in the germinal zone. Cell cycle analysis revealed both prolonged cell cycles and increased cell cycle exit in TLX-null embryonic brains. Increased expression of a cyclin-dependent kinase inhibitor p21 and decreased expression of cyclin D1 provide a molecular basis for the deficiency of cell cycle progression in embryonic brains of TLX-null mice. Furthermore, transient knockdown of TLX by in utero electroporation led to precocious cell cycle exit and differentiation of neural stem cells followed by outward migration. Together these results indicate that TLX plays an important role in neural development by regulating cell cycle progression and exit of neural stem cells in the developing brain. PMID:17901127

Melanogenesis stimulation in B16-F10 melanoma cells induces cell cycle alterations, increased ROS levels and a differential expression of proteins as revealed by proteomic analysis

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

Cunha, Elizabeth S.; Kawahara, Rebeca; Kadowaki, Marina K.

Considering that stimulation of melanogenesis may lead to alterations of cellular responses, besides melanin production, our main goal was to study the cellular effects of melanogenesis stimulation of B16-F10 melanoma cells. Our results show increased levels of the reactive oxygen species after 15 h of melanogenesis stimulation. Following 48 h of melanogenesis stimulation, proliferation was inhibited (by induction of cell cycle arrest in the G1 phase) and the expression levels of p21 mRNA were increased. In addition, melanogenesis stimulation did not induce cellular senescence. Proteomic analysis demonstrated the involvement of proteins from other pathways besides those related to the cellmore » cycle, including protein disulfide isomerase A3, heat-shock protein 70, and fructose biphosphate aldolase A (all up-regulated), and lactate dehydrogenase (down-regulated). In RT-qPCR experiments, the levels of pyruvate kinase M2 mRNA dropped, whereas the levels of ATP synthase (beta-F1) mRNA increased. These data indicate that melanogenesis stimulation of B16-F10 cells leads to alterations in metabolism and cell cycle progression that may contribute to an induction of cell quiescence, which may provide a mechanism of resistance against cellular injury promoted by melanin synthesis. -- Highlights: Black-Right-Pointing-Pointer Melanogenesis stimulation by L-tyrosine+NH{sub 4}Cl in B16-F10 melanoma cells increases ROS levels. Black-Right-Pointing-Pointer Melanogenesis inhibits cell proliferation, and induced cell cycle arrest in the G1 phase. Black-Right-Pointing-Pointer Proteomic analysis showed alterations in proteins of the cell cycle and glucose metabolism. Black-Right-Pointing-Pointer RT-qPCR analysis confirmed alterations of metabolic targets after melanogenesis stimulation.« less

A spatiotemporal structure: common to subatomic systems, biological processes, and economic cycles

NASA Astrophysics Data System (ADS)

Naitoh, Ken

2012-03-01

A theoretical model derived based on a quasi-stability concept applied to momentum conservation (Naitoh, JJIAM, 2001, Artificial Life Robotics, 2008, 2010) has revealed the spatial structure of various systems. This model explains the reason why particles such as biological cells, nitrogenous bases, and liquid droplets have bimodal size ratios of about 2:3 and 1:1. This paper shows that the same theory holds true for several levels of parcels from baryons to stars in the cosmos: specifically, at the levels of nuclear force, van der Waals force, surface tension, and the force of gravity. A higher order of analysis clarifies other asymmetric ratios related to the halo structure seen in atoms and amino acids. We will also show that our minimum hypercycle theory for explaining the morphogenetic cycle (Naitoh, Artificial Life Robotics, 2008) reveals other temporal cycles such as those of economic systems and the circadian clock as well as the fundamental neural network pattern (topological pattern). Finally, a universal equation describing the spatiotemporal structure of several systems will be derived, which also leads to a general concept of quasi-stability.

Analysis of uncultured extremophilic snow algae by non-invasive single cell Raman spectroscopy

NASA Astrophysics Data System (ADS)

Beer, Thomas; Tanaka, Zuki; Netzter, Nathan; Rothschild, Lynn J.; Chen, Bin

2011-10-01

The study of life in extreme environments is a critical component of Astrobiology. But many of the so-called "extremophiles" are not readily cultivatable and therefore difficult to study under laboratory conditions. An example of such an extremophile is the snow alga Chlamydomonas cd. nivalis which expresses still unstudied secondary metabolites within its life cycle. In this paper, we present the first time the non-invasive single cell Raman spectroscopy of the life cycle dependent metabolite composition of C. nivalis. These secondary metabolites are likely related to the adaptation of C. nivalis to various stress factors. Normalized carotenoid Raman spectra intensities reveal characteristic ratio differences that allow identification of life cycle stages and putative secondary metabolites.

A broken krebs cycle in macrophages.

PubMed

O'Neill, Luke A J

2015-03-17

Macrophages undergo metabolic rewiring during polarization but details of this process are unclear. In this issue of Immunity, Jha et al. (2015) report a systems approach for unbiased analysis of cellular metabolism that reveals key metabolites and metabolic pathways required for distinct macrophage polarization states. Copyright © 2015 Elsevier Inc. All rights reserved.

Analysis of Peer Review Comments: QM Recommendations and Feedback Intervention Theory

ERIC Educational Resources Information Center

Schwegler, Andria F.; Altman, Barbara W.

2015-01-01

Because feedback is a critical component of the continuous improvement cycle of the Quality Matters (QM) peer review process, the present research analyzed the feedback that peer reviewers provided to course developers after a voluntary, nonofficial QM peer review of online courses. Previous research reveals that the effects of feedback on…

Two proximal activating protein-1-binding sites are sufficient to stimulate transcription of the ovine follicle-stimulating hormone-beta gene

EPA Science Inventory

FSH is an important regulator of mammalian gametogenesis and the female reproductive cycle. Although little is known about the transcriptional regulation of the beta-subunit (the rate-limiting subunit of FSH synthesis), sequence analysis of the ovine FSHbeta promoter has revealed...

75 FR 74668 - Airworthiness Directives; The Boeing Company Model 777-200, -200LR, -300, and -300ER Series...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-01

... investigative actions include a surface high- frequency eddy current inspection for cracking of the inner.... The related investigative actions include a surface high-frequency eddy current inspection for... total flight hours and 5,335 total flight cycles. Analysis by the manufacturer revealed that the broken...

Cell cycle synchronization and analysis of apoptosis-related gene in skin fibroblasts from domestic cat (Felis silvestris catus) and kodkod (Leopardus guigna).

PubMed

Veraguas, D; Gallegos, P F; Castro, F O; Rodriguez-Alvarez, L

2017-10-01

The kodkod population is in constant decrease and the somatic cell nuclear transfer (SCNT) might help to preserve the genetic pool of this species. The cell cycle synchronization of donor cells plays a crucial role in SCNT. The objective of this research was to evaluate two different methods for quiescence induction, serum starvation (SS) and contact inhibition (CI), both for 1, 3 and 5 days, on skin fibroblast from domestic cat and kodkod. Flow cytometry analysis revealed that in domestic cat, SS and CI, both at 3 and 5 days, increased the percentage of fibroblasts in G0/G1 compared to growing cells (GC) (p < .05). In kodkod, only SS for 3 and 5 days and CI for 1 and 3 days increased the percentage of fibroblasts in G0/G1 compared to GC (p < .05). Viability analysis by differential staining revealed that SS for 5 days decreased the proportion of live fibroblasts in domestic cat and kodkod (p < .05). Regarding gene expression analysis, in domestic cat fibroblasts, no differences were found in the BAX/BCL2 ratio in SS and CI (both at 1, 3 and 5 days) compared to GC. In kodkod fibroblasts, BAX/BCL2 ratio was increased in CI at 3 and 5 days compared to SS at 3 and 5 days (p < .05). In conclusion, in kodkod fibroblasts SS for 5 days and CI after 3 days might have a negative impact on cellular viability. According to these results, we suggest SS for 3 days for cell cycle synchronization in kodkod fibroblasts. © 2017 Blackwell Verlag GmbH.

The diet of a nocturnal pelagic predator, the Bulwer's petrel, across the lunar cycle.

PubMed

Waap, S; Symondson, W O C; Granadeiro, J P; Alonso, H; Serra-Gonçalves, C; Dias, M P; Catry, P

2017-05-03

The lunar cycle is believed to strongly influence the vertical distribution of many oceanic taxa, with implications for the foraging behaviour of nocturnal marine predators. Most studies to date testing lunar effects on foraging have focused on predator activity at-sea, with some birds and marine mammals demonstrating contrasting behavioural patterns, depending on the lunar-phase. However, to date no study has focused on how the lunar cycle might actually affect predator-prey interactions in the upper layers of the ocean. Here, we tested whether the diet of the predominantly nocturnal pelagic predator, the Bulwer's petrel (Bulweria bulwerii) would change throughout the lunar cycle, using molecular analysis to augment detection and taxonomic resolution of prey collected from stomach-contents. We found no evidence of dietary shifts in species composition or diversity, with Bulwer's petrel always consuming a wide range of mesopelagic species. Other co-variables potentially affecting light availability at-sea, such as percentage of cloud cover, did not confound our results. Moreover, many of the species found are thought not to reach the sea-surface. Our findings reveal that nocturnal predators are probably more specialized than previously assumed, irrespective of ambient-light, but also reveal deficiencies in our current understanding of species vertical distribution and predation-dynamics at-sea.

Microbial contributions to coupled arsenic and sulfur cycling in the acid-sulfide hot spring Champagne Pool, New Zealand.

PubMed

Hug, Katrin; Maher, William A; Stott, Matthew B; Krikowa, Frank; Foster, Simon; Moreau, John W

2014-01-01

Acid-sulfide hot springs are analogs of early Earth geothermal systems where microbial metal(loid) resistance likely first evolved. Arsenic is a metalloid enriched in the acid-sulfide hot spring Champagne Pool (Waiotapu, New Zealand). Arsenic speciation in Champagne Pool follows reaction paths not yet fully understood with respect to biotic contributions and coupling to biogeochemical sulfur cycling. Here we present quantitative arsenic speciation from Champagne Pool, finding arsenite dominant in the pool, rim and outflow channel (55-75% total arsenic), and dithio- and trithioarsenates ubiquitously present as 18-25% total arsenic. In the outflow channel, dimethylmonothioarsenate comprised ≤9% total arsenic, while on the outflow terrace thioarsenates were present at 55% total arsenic. We also quantified sulfide, thiosulfate, sulfate and elemental sulfur, finding sulfide and sulfate as major species in the pool and outflow terrace, respectively. Elemental sulfur concentration reached a maximum at the terrace. Phylogenetic analysis of 16S rRNA genes from metagenomic sequencing revealed the dominance of Sulfurihydrogenibium at all sites and an increased archaeal population at the rim and outflow channel. Several phylotypes were found closely related to known sulfur- and sulfide-oxidizers, as well as sulfur- and sulfate-reducers. Bioinformatic analysis revealed genes underpinning sulfur redox transformations, consistent with sulfur speciation data, and illustrating a microbial role in sulfur-dependent transformation of arsenite to thioarsenate. Metagenomic analysis also revealed genes encoding for arsenate reductase at all sites, reflecting the ubiquity of thioarsenate and a need for microbial arsenate resistance despite anoxic conditions. Absence of the arsenite oxidase gene, aio, at all sites suggests prioritization of arsenite detoxification over coupling to energy conservation. Finally, detection of methyl arsenic in the outflow channel, in conjunction with increased sequences from Aquificaceae, supports a role for methyltransferase in thermophilic arsenic resistance. Our study highlights microbial contributions to coupled arsenic and sulfur cycling at Champagne Pool, with implications for understanding the evolution of microbial arsenic resistance in sulfidic geothermal systems.

Hollow Co2P nanoflowers assembled from nanorods for ultralong cycle-life supercapacitors.

PubMed

Cheng, Ming; Fan, Hongsheng; Xu, Yingying; Wang, Rongming; Zhang, Xixiang

2017-09-28

Hollow Co 2 P nanoflowers (Co 2 P HNFs) were successfully prepared via a one-step, template-free method. Microstructure analysis reveals that Co 2 P HNFs are assembled from nanorods and possess abundant mesopores and an amorphous carbon shell. Density functional theory calculations and electrochemical measurements demonstrate the high electrical conductivity of Co 2 P. Benefiting from the unique nanostructures, when employed as an electrode material for supercapacitors, Co 2 P HNFs exhibit a high specific capacitance, an outstanding rate capability, and an ultralong cycling stability. Furthermore, the constructed Co 2 P HNF//AC ASC exhibits a high energy density of 30.5 W h kg -1 at a power density of 850 W kg -1 , along with a superior cycling performance (108.0% specific capacitance retained after 10 000 cycles at 5 A g -1 ). These impressive results make Co 2 P HNFs a promising candidate for supercapacitor applications.

Comparison profiles of cycle control, side effects and sexual satisfaction of three hormonal contraceptives.

PubMed

Sabatini, Rosa; Cagiano, Raffaele

2006-09-01

The objective of this study was to compare cycle control, tolerability and sexual well-being with the use of three hormonal contraceptives. In this prospective randomized study, the effects of two combined oral contraceptives [20 microg of ethinylestradiol (EE)/100 microg of levonorgestrel and 15 microg of EE/60 microg of gestodene] were compared with those of the vaginal ring (15 microg of EE/120 microg of etonogestrel). One-year data from 280 women were obtained. We investigated the pattern of menstrual cycle and the incidence of weight gain, nausea, headache, breast tenderness, irritability, depression and vaginal dryness. Moreover, desire and sexual satisfaction were evaluated. Finally, the cumulative rate of discontinuation in the three groups was estimated. The analysis of adverse events revealed two crucial points for acceptability, compliance and continuation: poor cycle control and disturbance of sexual intercourse due to vaginal dryness and loss of desire.

Krebs cycle metabolon: structural evidence of substrate channeling revealed by cross-linking and mass spectrometry.

PubMed

Wu, Fei; Minteer, Shelley

2015-02-02

It has been hypothesized that the high metabolic flux in the mitochondria is due to the self-assembly of enzyme supercomplexes (called metabolons) that channel substrates from one enzyme to another, but there has been no experimental confirmation of this structure or the channeling. A structural investigation of enzyme organization within the Krebs cycle metabolon was accomplished by in vivo cross-linking and mass spectrometry. Eight Krebs cycle enzyme components were isolated upon chemical fixation, and interfacial residues between mitochondrial malate dehydrogenase, citrate synthase, and aconitase were identified. Using constraint protein docking, a low-resolution structure for the three-enzyme complex was achieved, as well as the two-fold symmetric octamer. Surface analysis showed formation of electrostatic channeling upon protein-protein association, which is the first structural evidence of substrate channeling in the Krebs cycle metabolon. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A temporal/spectral analysis of small grain crops and confusion crops. [North Dakota

NASA Technical Reports Server (NTRS)

Johnson, W. R. (Principal Investigator)

1981-01-01

Spectral data from the LANDSAT-2 satellite were used to study the growth cycles of fields of wheat, barley, alfalfa, corn, sunflowers, soybeans, rye, flax, oats, millet, grass, and hay. Signatures of pastures, trees, and idle fallow were also studied. The growth cycles were portrayed in the form of temporal plots of the greeness-brightness transformation vector applied to average channel pixel values within the fields, all of which were in three counties in North Dakota. The plots of each crop reveal characteristics which can be used in crop classification procedures.

Large Geomagnetic Storms: Introduction to Special Section

NASA Technical Reports Server (NTRS)

Gopalswamy, N.

2010-01-01

Solar cycle 23 witnessed the accumulation of rich data sets that reveal various aspects of geomagnetic storms in unprecedented detail both at the Sun where the storm causing disturbances originate and in geospace where the effects of the storms are directly felt. During two recent coordinated data analysis workshops (CDAWs) the large geomagnetic storms (Dst < or = -100 nT) of solar cycle 23 were studied in order to understand their solar, interplanetary, and geospace connections. This special section grew out of these CDAWs with additional contributions relevant to these storms. Here I provide a brief summary of the results presented in the special section.

Environmental drivers of heterogeneity in the trophic-functional structure of protozoan communities during an annual cycle in a coastal ecosystem.

PubMed

Xu, Guangjian; Yang, Eun Jin; Xu, Henglong

2017-08-15

Trophic-functional groupings are an important biological trait to summarize community structure in functional space. The heterogeneity of the tropic-functional pattern of protozoan communities and its environmental drivers were studied in coastal waters of the Yellow Sea during a 1-year cycle. Samples were collected using the glass slide method at four stations within a water pollution gradient. A second-stage matrix-based analysis was used to summarize spatial variation in the annual pattern of the functional structure. A clustering analysis revealed significant variability in the trophic-functional pattern among the four stations during the 1-year cycle. The heterogeneity in the trophic-functional pattern of the communities was significantly related to changes in environmental variables, particularly ammonium-nitrogen and nitrates, alone or in combination with dissolved oxygen. These results suggest that the heterogeneity in annual patterns of protozoan trophic-functional structure may reflect water quality status in coastal ecosystems. Copyright © 2017. Published by Elsevier Ltd.

Characterization of physiochemical properties of polymeric and electrochemical materials for aerospace flight

NASA Technical Reports Server (NTRS)

Rock, M.; Kunigahalli, V.; Khan, S.; Mcnair, A.

1984-01-01

Nickel-cadmium rechargeable batteries are a vital and reliable energy storage source for aerospace applications. As the demand for longer life and more reliable space batteries increases, the understanding and solving of cell aging factors and mechanisms become essential. Over the years, many cell designs and manufacturing process changes have been developed and implemented. Cells fabricated with various design features were life cycled in a simulated low-Earth orbit regime. Following the test program, a comprehensive electrochemical analysis of cell components was undertaken to study cell degradation mechanisms. Discharge voltage degradation or voltage plateau has been observed during orbit cycling, but, its cause and explanation have been the subject of much discussion. A Hg/HgO reference electrode was used to monitor the reference versus each electrode potential during the discharge of a cycled cell. The results indicate that the negative electrode was responsible for the voltage plateau. Cell analysis revealed large crystals of cadmium hydroxide on the surface of the negative electrode and throughout the separator.

Center-iodized graphene as an advanced anode material to significantly boost the performance of lithium-ion batteries.

PubMed

Chen, Jie; Xu, Mao-Wen; Wu, Jinggao; Li, Chang Ming

2018-05-17

Iodine edge-doped graphene can improve the capacity and stability of lithium-ion batteries (LIBs). Our theoretical calculations indicate that center-iodization can further significantly enhance the anode catalytic process. To experimentally prove the theoretical prediction, iodine-doped graphene materials were prepared by one-pot hydrothermal and ball-milling approaches to realize different doping-sites. Results show that the center-iodinated graphene (CIG) anode exhibits a remarkably high reversible capacity (1121 mA h g-1 after 180 cycles at 0.5 A g-1), long-cycle life (0.01% decay per cycle over 300 cycles at 1 A g-1) and high-rate capacity (374 mA h g-1 after 800 cycles at 8 A g-1), which greatly improves the performance of the edge-iodinated graphene anode and these results are in good agreement with the theoretical analysis. More importantly, the CIG anode also delivers a high-rate capacity and excellent cycling stability (279 mA h g-1 after 500 cycles at 10 A g-1) in full-cells. Both the theoretical analysis and experimental investigation reveal the enhancement mechanism, in which the center-iodization increases the surface charge for fast electron transfer rate, improves the conductivity for charge transport and rationalizes the pore structure for enhanced mass transport and ion insertion/desertion, thus resulting in a high rate capacity and long cycle life. This work not only discloses the critical role of catalytic sites including both amounts and site positions but also offers great potential for high-power rechargeable LIB applications.

Cell cycle arrest and induction of apoptosis by cajanin stilbene acid from Cajanus cajan in breast cancer cells.

PubMed

Fu, Yujie; Kadioglu, Onat; Wiench, Benjamin; Wei, Zuofu; Gao, Chang; Luo, Meng; Gu, Chengbo; Zu, Yuangang; Efferth, Thomas

2015-04-15

The low abundant cajanin stilbene acid (CSA) from Pigeon Pea (Cajanus cajan) has been shown to kill estrogen receptor α positive cancer cells in vitro and in vivo. Downstream effects such as cell cycle and apoptosis-related mechanisms have not been analyzed yet. We analyzed the activity of CSA by means of flow cytometry (cell cycle distribution, mitochondrial membrane potential, MMP), confocal laser scanning microscopy (MMP), DNA fragmentation assay (apoptosis), Western blotting (Bax and Bcl-2 expression, caspase-3 activation) as well as mRNA microarray hybridization and Ingenuity pathway analysis. CSA induced G2/M arrest and apoptosis in a concentration-dependent manner from 8.88 to 14.79 µM. The MMP broke down, Bax was upregulated, Bcl-2 downregulated and caspase-3 activated. Microarray profiling revealed that CSA affected BRCA-related DNA damage response and cell cycle-regulated chromosomal replication pathways. CSA inhibited breast cancer cells by DNA damage and cell cycle-related signaling pathways leading to cell cycle arrest and apoptosis. Copyright © 2015 Elsevier GmbH. All rights reserved.

Systematic Analysis of Cell Cycle Effects of Common Drugs Leads to the Discovery of a Suppressive Interaction between Gemfibrozil and Fluoxetine

PubMed Central

Hoose, Scott A.; Duran, Camille; Malik, Indranil; Eslamfam, Shabnam; Shasserre, Samantha C.; Downing, S. Sabina; Hoover, Evelyn M.; Dowd, Katherine E.; Smith, Roger; Polymenis, Michael

2012-01-01

Screening chemical libraries to identify compounds that affect overall cell proliferation is common. However, in most cases, it is not known whether the compounds tested alter the timing of particular cell cycle transitions. Here, we evaluated an FDA-approved drug library to identify pharmaceuticals that alter cell cycle progression in yeast, using DNA content measurements by flow cytometry. This approach revealed strong cell cycle effects of several commonly used pharmaceuticals. We show that the antilipemic gemfibrozil delays initiation of DNA replication, while cells treated with the antidepressant fluoxetine severely delay progression through mitosis. Based on their effects on cell cycle progression, we also examined cell proliferation in the presence of both compounds. We discovered a strong suppressive interaction between gemfibrozil and fluoxetine. Combinations of interest among diverse pharmaceuticals are difficult to identify, due to the daunting number of possible combinations that must be evaluated. The novel interaction between gemfibrozil and fluoxetine suggests that identifying and combining drugs that show cell cycle effects might streamline identification of drug combinations with a pronounced impact on cell proliferation. PMID:22567160

Systematic analysis of cell cycle effects of common drugs leads to the discovery of a suppressive interaction between gemfibrozil and fluoxetine.

PubMed

Hoose, Scott A; Duran, Camille; Malik, Indranil; Eslamfam, Shabnam; Shasserre, Samantha C; Downing, S Sabina; Hoover, Evelyn M; Dowd, Katherine E; Smith, Roger; Polymenis, Michael

2012-01-01

Screening chemical libraries to identify compounds that affect overall cell proliferation is common. However, in most cases, it is not known whether the compounds tested alter the timing of particular cell cycle transitions. Here, we evaluated an FDA-approved drug library to identify pharmaceuticals that alter cell cycle progression in yeast, using DNA content measurements by flow cytometry. This approach revealed strong cell cycle effects of several commonly used pharmaceuticals. We show that the antilipemic gemfibrozil delays initiation of DNA replication, while cells treated with the antidepressant fluoxetine severely delay progression through mitosis. Based on their effects on cell cycle progression, we also examined cell proliferation in the presence of both compounds. We discovered a strong suppressive interaction between gemfibrozil and fluoxetine. Combinations of interest among diverse pharmaceuticals are difficult to identify, due to the daunting number of possible combinations that must be evaluated. The novel interaction between gemfibrozil and fluoxetine suggests that identifying and combining drugs that show cell cycle effects might streamline identification of drug combinations with a pronounced impact on cell proliferation.

Performance analysis of a bio-gasification based combined cycle power plant employing indirectly heated humid air turbine

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

Mukherjee, S., E-mail: sankha.deepp@gmail.com; Mondal, P., E-mail: mondal.pradip87@gmail.com; Ghosh, S., E-mail: sudipghosh.becollege@gmail.com

Rapid depletion of fossil fuel has forced mankind to look into alternative fuel resources. In this context, biomass based power generation employing gas turbine appears to be a popular choice. Bio-gasification based combined cycle provides a feasible solution as far as grid-independent power generation is concerned for rural electrification projects. Indirectly heated gas turbine cycles are promising alternatives as they avoid downstream gas cleaning systems. Advanced thermodynamic cycles have become an interesting area of study to improve plant efficiency. Water injected system is one of the most attractive options in this field of applications. This paper presents a theoretical modelmore » of a biomass gasification based combined cycle that employs an indirectly heated humid air turbine (HAT) in the topping cycle. Maximum overall electrical efficiency is found to be around 41%. Gas turbine specific air consumption by mass is minimum when pressure ratio is 6. The study reveals that, incorporation of the humidification process helps to improve the overall performance of the plant.« less

Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana

PubMed Central

Van Leene, Jelle; Hollunder, Jens; Eeckhout, Dominique; Persiau, Geert; Van De Slijke, Eveline; Stals, Hilde; Van Isterdael, Gert; Verkest, Aurine; Neirynck, Sandy; Buffel, Yelle; De Bodt, Stefanie; Maere, Steven; Laukens, Kris; Pharazyn, Anne; Ferreira, Paulo C G; Eloy, Nubia; Renne, Charlotte; Meyer, Christian; Faure, Jean-Denis; Steinbrenner, Jens; Beynon, Jim; Larkin, John C; Van de Peer, Yves; Hilson, Pierre; Kuiper, Martin; De Veylder, Lieven; Van Onckelen, Harry; Inzé, Dirk; Witters, Erwin; De Jaeger, Geert

2010-01-01

Cell proliferation is the main driving force for plant growth. Although genome sequence analysis revealed a high number of cell cycle genes in plants, little is known about the molecular complexes steering cell division. In a targeted proteomics approach, we mapped the core complex machinery at the heart of the Arabidopsis thaliana cell cycle control. Besides a central regulatory network of core complexes, we distinguished a peripheral network that links the core machinery to up- and downstream pathways. Over 100 new candidate cell cycle proteins were predicted and an in-depth biological interpretation demonstrated the hypothesis-generating power of the interaction data. The data set provided a comprehensive view on heterodimeric cyclin-dependent kinase (CDK)–cyclin complexes in plants. For the first time, inhibitory proteins of plant-specific B-type CDKs were discovered and the anaphase-promoting complex was characterized and extended. Important conclusions were that mitotic A- and B-type cyclins form complexes with the plant-specific B-type CDKs and not with CDKA;1, and that D-type cyclins and S-phase-specific A-type cyclins seem to be associated exclusively with CDKA;1. Furthermore, we could show that plants have evolved a combinatorial toolkit consisting of at least 92 different CDK–cyclin complex variants, which strongly underscores the functional diversification among the large family of cyclins and reflects the pivotal role of cell cycle regulation in the developmental plasticity of plants. PMID:20706207

Reinforcement of double dynamo waves as a source of solar activity and its prediction on millennium timescale

NASA Astrophysics Data System (ADS)

Popova, E.; Zharkova, V. V.; Shepherd, S. J.; Zharkov, S.

2016-12-01

Using the principal components of solar magnetic field variations derived from the synoptic maps for solar cycles 21-24 with Principal Components Analysis (PCA) (Zharkova et al, 2015) we confirm our previous prediction of the upcoming Maunder minimum to occur in cycles 25-27, or in 2020-2055. We also use a summary curve of the two eigen vectors of solar magnetic field oscillations (or two dynamo waves) to extrapolate solar activity backwards to the three millennia and to compare it with relevant historic and Holocene data. Extrapolation of the summary curve confirms the eight grand cycles of 350-400-years superimposed on 22 year-cycles caused by beating effect of the two dynamo waves generated in the two (deep and shallow) layers of the solar interior. The grand cycles in different periods comprise a different number of individual 22-year cycles; the longer the grand cycles the larger number of 22 year cycles and the smaller their amplitudes. We also report the super-grand cycle of about 2000 years often found in solas activity with spectral analysis. Furthermore, the summary curve reproduces a remarkable resemblance to the sunspot and terrestrial activity reported in the past: the recent Maunder Minimum (1645-1715), Dalton minimum (1790-1815), Wolf minimum (1200), Homeric minimum (800-900 BC), the Medieval Warmth Period (900-1200), the Roman Warmth Period (400-10BC) and so on. Temporal variations of these dynamo waves are modelled with the two layer mean dynamo model with meridional circulation revealing a remarkable resemblance of the butterfly diagram to the one derived for the last Maunder minimum in 17 century and predicting the one for the upcoming Maunder minimum in 2020-2055.

Solar Cycle Variations of SABER CO2 and MLS H2O in the Mesosphere and Lower Thermosphere Region

NASA Astrophysics Data System (ADS)

Salinas, C. C. J.; Chang, L. C.; Liang, M. C.; Qian, L.; Yue, J.; Russell, J. M., III; Mlynczak, M. G.

2017-12-01

This work aims to present the solar cycle variations of SABER CO2 and MLS H2O in the Mesosphere and Lower Thermosphere region. These observations are then compared to SD-WACCM outputs of CO2 and H2O in order to understand their physical mechanisms. After which, we attempt to model their solar cycle variations using the default TIME-GCM and the TIME-GCM with MERRA reanalysis as lower-boundary conditions. Comparing the outputs of the default TIME-GCM and TIME-GCM with MERRA will give us insight into the importance of solar forcing and lower atmospheric forcing on the solar cycle variations of CO2 and H2O. The solar cycle influence in the parameters are calculated by doing a multiple linear regression with the F10.7 index. The solar cycle of SABER CO2 is reliable above 1e-2 mb and below 1e-3 mb. Preliminary results from the observations show that SABER CO2 has a stronger negative anomaly due to the solar cycle over the winter hemisphere. MLS H2O is reliable until 1e-2. Preliminary results from the observations show that MLS H2O also has a stronger negative anomaly due to the solar cycle over the winter hemisphere. Both SD-WACCM and the default TIME-GCM reproduce these stronger anomalies over the winter hemisphere. An analysis of the tendency equations in SD-WACCM and default TIME-GCM then reveal that for CO2, the stronger winter anomaly may be attributed to stronger downward transport over the winter hemisphere. For H2O, an analysis of the tendency equations in SD-WACCM reveal that the stronger winter anomaly may be attributed to both stronger downward transport and stronger photochemical loss. On the other hand, in the default TIME-GCM, the stronger winter anomaly in H2O may only be attributed to stronger downward transport. For both models, the stronger downward transport is attributed to enhanced stratospheric polar winter jet during solar maximum. Future work will determine whether setting the lower boundary conditions of TIME-GCM with MERRA will improve the match between TIME-GCM and SD-WACCM. Also, with the TIME-GCM outputs, the influence of these MLT circulation changes on the ionospheric winter anomaly will be determined.

Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat

USDA-ARS?s Scientific Manuscript database

Cycles of whole genome duplication (WGD) and diploidization are hallmarks of eukaryotic genome evolution and speciation. Polyploid wheat (Triticum aestivum) has had a massive increase in genome size largely due to recent WGDs. How these processes may impact the dynamics of gene evolution was studied...

Multidimensional NMR analysis reveals truncated lignin structures in wood decayed by the brown rot basidiomycete Postia placenta

Treesearch

Daniel J. Yelle; Dongsheng Wei; John Ralph; Kenneth E. Hammel

2011-01-01

Lignocellulose biodegradation, an essential step in terrestrial carbon cycling, generally involves removal of the recalcitrant lignin barrier that otherwise prevents infiltration by microbial polysaccharide hydrolases. However, fungi that cause brown rot of wood, a major route for biomass recycling in coniferous forests, utilize wood polysaccharides efficiently while...

Using Long-Term Time-Lapse Imaging of Mammalian Cell Cycle Progression for Laboratory Instruction and Analysis

ERIC Educational Resources Information Center

Hinchcliffe, Edward H.

2005-01-01

Cinemicrography--the capture of moving cellular sequences through the microscope--has been influential in revealing the dynamic nature of cellular behavior. One of the more dramatic cellular events is mitosis, the division of sister chromatids into two daughter cells. Mitosis has been extensively studied in a variety of organisms, both…

Academic Self-Concept and Achievement in Polish Primary Schools: Cross-Lagged Modelling and Gender-Specific Effects

ERIC Educational Resources Information Center

Grygiel, Pawel; Modzelewski, Michal; Pisarek, Jolanta

2017-01-01

This study reports relationships between general academic self-concept and achievement in grade 3 and grade 5. Gender-specific effects were investigated using a longitudinal, two-cycle, 3-year autoregressive cross-lagged panel design in a large, representative sample of Polish primary school pupils (N = 4,226). Analysis revealed (a) reciprocal…

Synteny analysis in Rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials

USDA-ARS?s Scientific Manuscript database

Mutations often accompany DNA replication. Since there may be fewer cell cycles per year in the germlines of long-lived than short-lived angiosperms, the genomes of long-lived angiosperms may be diverging more slowly than those of short-lived angiosperms. Here we test this hypothesis. We first const...

The microbiome of Brazilian mangrove sediments as revealed by metagenomics.

PubMed

Andreote, Fernando Dini; Jiménez, Diego Javier; Chaves, Diego; Dias, Armando Cavalcante Franco; Luvizotto, Danice Mazzer; Dini-Andreote, Francisco; Fasanella, Cristiane Cipola; Lopez, Maryeimy Varon; Baena, Sandra; Taketani, Rodrigo Gouvêa; de Melo, Itamar Soares

2012-01-01

Here we embark in a deep metagenomic survey that revealed the taxonomic and potential metabolic pathways aspects of mangrove sediment microbiology. The extraction of DNA from sediment samples and the direct application of pyrosequencing resulted in approximately 215 Mb of data from four distinct mangrove areas (BrMgv01 to 04) in Brazil. The taxonomic approaches applied revealed the dominance of Deltaproteobacteria and Gammaproteobacteria in the samples. Paired statistical analysis showed higher proportions of specific taxonomic groups in each dataset. The metabolic reconstruction indicated the possible occurrence of processes modulated by the prevailing conditions found in mangrove sediments. In terms of carbon cycling, the sequences indicated the prevalence of genes involved in the metabolism of methane, formaldehyde, and carbon dioxide. With respect to the nitrogen cycle, evidence for sequences associated with dissimilatory reduction of nitrate, nitrogen immobilization, and denitrification was detected. Sequences related to the production of adenylsulfate, sulfite, and H(2)S were relevant to the sulphur cycle. These data indicate that the microbial core involved in methane, nitrogen, and sulphur metabolism consists mainly of Burkholderiaceae, Planctomycetaceae, Rhodobacteraceae, and Desulfobacteraceae. Comparison of our data to datasets from soil and sea samples resulted in the allotment of the mangrove sediments between those samples. The results of this study add valuable data about the composition of microbial communities in mangroves and also shed light on possible transformations promoted by microbial organisms in mangrove sediments.

The Microbiome of Brazilian Mangrove Sediments as Revealed by Metagenomics

PubMed Central

Andreote, Fernando Dini; Jiménez, Diego Javier; Chaves, Diego; Dias, Armando Cavalcante Franco; Luvizotto, Danice Mazzer; Dini-Andreote, Francisco; Fasanella, Cristiane Cipola; Lopez, Maryeimy Varon; Baena, Sandra; Taketani, Rodrigo Gouvêa; de Melo, Itamar Soares

2012-01-01

Here we embark in a deep metagenomic survey that revealed the taxonomic and potential metabolic pathways aspects of mangrove sediment microbiology. The extraction of DNA from sediment samples and the direct application of pyrosequencing resulted in approximately 215 Mb of data from four distinct mangrove areas (BrMgv01 to 04) in Brazil. The taxonomic approaches applied revealed the dominance of Deltaproteobacteria and Gammaproteobacteria in the samples. Paired statistical analysis showed higher proportions of specific taxonomic groups in each dataset. The metabolic reconstruction indicated the possible occurrence of processes modulated by the prevailing conditions found in mangrove sediments. In terms of carbon cycling, the sequences indicated the prevalence of genes involved in the metabolism of methane, formaldehyde, and carbon dioxide. With respect to the nitrogen cycle, evidence for sequences associated with dissimilatory reduction of nitrate, nitrogen immobilization, and denitrification was detected. Sequences related to the production of adenylsulfate, sulfite, and H2S were relevant to the sulphur cycle. These data indicate that the microbial core involved in methane, nitrogen, and sulphur metabolism consists mainly of Burkholderiaceae, Planctomycetaceae, Rhodobacteraceae, and Desulfobacteraceae. Comparison of our data to datasets from soil and sea samples resulted in the allotment of the mangrove sediments between those samples. The results of this study add valuable data about the composition of microbial communities in mangroves and also shed light on possible transformations promoted by microbial organisms in mangrove sediments. PMID:22737213

A genotype network reveals homoplastic cycles of convergent evolution in influenza A (H3N2) haemagglutinin.

PubMed

Wagner, Andreas

2014-07-07

Networks of evolving genotypes can be constructed from the worldwide time-resolved genotyping of pathogens like influenza viruses. Such genotype networks are graphs where neighbouring vertices (viral strains) differ in a single nucleotide or amino acid. A rich trove of network analysis methods can help understand the evolutionary dynamics reflected in the structure of these networks. Here, I analyse a genotype network comprising hundreds of influenza A (H3N2) haemagglutinin genes. The network is rife with cycles that reflect non-random parallel or convergent (homoplastic) evolution. These cycles also show patterns of sequence change characteristic for strong and local evolutionary constraints, positive selection and mutation-limited evolution. Such cycles would not be visible on a phylogenetic tree, illustrating that genotype network analysis can complement phylogenetic analyses. The network also shows a distinct modular or community structure that reflects temporal more than spatial proximity of viral strains, where lowly connected bridge strains connect different modules. These and other organizational patterns illustrate that genotype networks can help us study evolution in action at an unprecedented level of resolution. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock

DOE PAGES

Bagnoud, Alexandre; Chourey, Karuna; Hettich, Robert L.; ...

2016-10-14

A significant fraction (~ 20%) of microbial life is found in the terrestrial deep subsurface, yet the metabolic processes extant in those environments are poorly understood. Here we show that H 2, injected into the Opalinus Clay formation in a borehole located 300 meters below the surface, fuels a community of microorganisms with interconnected metabolisms. Metagenomic binning and metaproteomic analysis reveal a complete carbon cycle, driven by autotrophic hydrogen oxidizers. Dead biomass from these organisms is a substrate for a fermenting bacterium that produces acetate as a product. In turn, complete oxidizer heterotrophic sulfate- reducing bacteria utilize acetate and oxidizemore » it to CO 2, closing the cycle. This metabolic reconstruction sheds light onto a hydrogen-driven carbon cycle, and a sunlight-independent ecosystem in the deep subsurface.« less

AS160 controls eukaryotic cell cycle and proliferation by regulating the CDK inhibitor p21.

PubMed

Gongpan, Pianchou; Lu, Yanting; Wang, Fang; Xu, Yuhui; Xiong, Wenyong

2016-07-02

AS160 (TBC1D4) has been implicated in multiple biological processes. However, the role and the mechanism of action of AS160 in the regulation of cell proliferation remain unclear. In this study, we demonstrated that AS160 knockdown led to blunted cell proliferation in multiple cell types, including fibroblasts and cancer cells. The results of cell cycle analysis showed that these cells were arrested in the G1 phase. Intriguingly, this inhibition of cell proliferation and the cell cycle arrest caused by AS160 depletion were glucose independent. Moreover, AS160 silencing led to a marked upregulation of the expression of the cyclin-dependent kinase inhibitor p21. Furthermore, whereas AS160 overexpression resulted in p21 downregulation and rescued the arrested cell cycle in AS160-depeleted cells, p21 silencing rescued the inhibited cell cycle and proliferation in the cells. Thus, our results demonstrated that AS160 regulates glucose-independent eukaryotic cell proliferation through p21-dependent control of the cell cycle, and thereby revealed a molecular mechanism of AS160 modulation of cell cycle and proliferation that is of general physiological significance.

DIGE-based protein expression analysis of B[a]P-exposed hepatoma cells reveals a complex stress response including alterations in oxidative stress, cell cycle control, and cytoskeleton motility at toxic and subacute concentrations.

PubMed

Dautel, Franziska; Kalkhof, Stefan; Trump, Saskia; Michaelson, Jacob; Beyer, Andreas; Lehmann, Irina; von Bergen, Martin

2011-02-04

Although the effects of high concentrations of the carcinogen benzo[a]pyrene (B[a]P) have been studied extensively, little is known about its effects at subacute toxic concentrations, which are typical for environmental pollutants. We exposed murine Hepa1c1c7 cells to a toxic concentration (5 μM) and a subacute concentration (50 nM) of B[a]P over a period of 2-24 h to differentiate between acute and pseudochronic effects and conducted a time-course analysis of B[a]P-influenced protein expression by DIGE. In total, a set of 120 spots were found to be significantly altered due to B[a]P exposure of which 112 were subsequently identified by mass spectrometry. Clustering and principal component analysis were conducted to identify sets of proteins responding in a concerted manner to the exposure. Our results indicate an immediate response to the contaminant at the protein level and demonstrate that B[a]P exposure alters the cellular response by disturbing proteins involved in oxidative stress, cell cycle regulation, apoptosis, and cytoskeleton organization. Furthermore, network analysis of protein-protein interactions revealed a complex network of interacting, B[a]P-regulated proteins mostly belonging to the cytoskeleton organization and several signal transduction pathways.

Application of Spectral Analysis Techniques in the Intercomparison of Aerosol Data: 1. an EOF Approach to the Spatial-Temporal Variability of Aerosol Optical Depth Using Multiple Remote Sensing Data Sets

NASA Technical Reports Server (NTRS)

Li, Jing; Carlson, Barbara E.; Lacis, Andrew A.

2013-01-01

Many remote sensing techniques and passive sensors have been developed to measure global aerosol properties. While instantaneous comparisons between pixel-level data often reveal quantitative differences, here we use Empirical Orthogonal Function (EOF) analysis, also known as Principal Component Analysis, to demonstrate that satellite-derived aerosol optical depth (AOD) data sets exhibit essentially the same spatial and temporal variability and are thus suitable for large-scale studies. Analysis results show that the first four EOF modes of AOD account for the bulk of the variance and agree well across the four data sets used in this study (i.e., Aqua MODIS, Terra MODIS, MISR, and SeaWiFS). Only SeaWiFS data over land have slightly different EOF patterns. Globally, the first two EOF modes show annual cycles and are mainly related to Sahara dust in the northern hemisphere and biomass burning in the southern hemisphere, respectively. After removing the mean seasonal cycle from the data, major aerosol sources, including biomass burning in South America and dust in West Africa, are revealed in the dominant modes due to the different interannual variability of aerosol emissions. The enhancement of biomass burning associated with El Niño over Indonesia and central South America is also captured with the EOF technique.

Nuclear orphan receptor TLX affects gene expression, proliferation and cell apoptosis in beta cells.

PubMed

Shi, Xiaoli; Xiong, Xiaokan; Dai, Zhe; Deng, Haohua; Sun, Li; Hu, Xuemei; Zhou, Feng; Xu, Yancheng

Nuclear orphan receptor TLX is an essential regulator of the growth of neural stem cells. However, its exact function in pancreatic islet cells is still unknown. In the present study, gene expression profiling analysis revealed that overexpression of TLX in beta cell line MIN6 causes suppression of 176 genes and upregulation of 49 genes, including a cadre of cell cycle, cell proliferation and cell death control genes, such as Btg2, Ddit3 and Gadd45a. We next examined the effects of TLX overexpression on proliferation, apoptosis and insulin secretion in MIN6 cells. Proliferation analysis using EdU assay showed that overexpression of TLX increased percentage of EdU-positive cells. Cell cycle and apoptosis analysis revealed that overexpression of TLX in MIN6 cells resulted in higher percentage of cells exiting G1 into S-phase, and a 58.8% decrease of cell apoptosis induced by 0.5 mM palmitate. Moreover, TLX overexpression did not cause impairment of insulin secretion. Together, we conclude that TLX is among factors capable of controlling beta cell proliferation and survival, which may serve as a target for the development of novel therapies for diabetes. Copyright © 2015 Elsevier Inc. All rights reserved.

TPhP exposure disturbs carbohydrate metabolism, lipid metabolism, and the DNA damage repair system in zebrafish liver

NASA Astrophysics Data System (ADS)

Du, Zhongkun; Zhang, Yan; Wang, Guowei; Peng, Jianbiao; Wang, Zunyao; Gao, Shixiang

2016-02-01

Triphenyl phosphate is a high production volume organophosphate flame retardant that has been detected in multiple environmental media at increasing concentrations. The environmental and health risks of triphenyl phosphate have drawn attention because of the multiplex toxicity of this chemical compound. However, few studies have paid close attention to the impacts of triphenyl phosphate on liver metabolism. We investigated hepatic histopathological, metabolomic and transcriptomic responses of zebrafish after exposure to 0.050 mg/L and 0.300 mg/L triphenyl phosphate for 7 days. Metabolomic analysis revealed significant changes in the contents of glucose, UDP-glucose, lactate, succinate, fumarate, choline, acetylcarnitine, and several fatty acids. Transcriptomic analysis revealed that related pathways, such as the glycosphingolipid biosynthesis, PPAR signaling pathway and fatty acid elongation, were significantly affected. These results suggest that triphenyl phosphate exposure markedly disturbs hepatic carbohydrate and lipid metabolism in zebrafish. Moreover, DNA replication, the cell cycle, and non-homologous end-joining and base excision repair were strongly affected, thus indicating that triphenyl phosphate hinders the DNA damage repair system in zebrafish liver cells. The present study provides a systematic analysis of the triphenyl phosphate-induced toxic effects in zebrafish liver and demonstrates that low concentrations of triphenyl phosphate affect normal metabolism and cell cycle.

TPhP exposure disturbs carbohydrate metabolism, lipid metabolism, and the DNA damage repair system in zebrafish liver

PubMed Central

Du, Zhongkun; Zhang, Yan; Wang, Guowei; Peng, Jianbiao; Wang, Zunyao; Gao, Shixiang

2016-01-01

Triphenyl phosphate is a high production volume organophosphate flame retardant that has been detected in multiple environmental media at increasing concentrations. The environmental and health risks of triphenyl phosphate have drawn attention because of the multiplex toxicity of this chemical compound. However, few studies have paid close attention to the impacts of triphenyl phosphate on liver metabolism. We investigated hepatic histopathological, metabolomic and transcriptomic responses of zebrafish after exposure to 0.050 mg/L and 0.300 mg/L triphenyl phosphate for 7 days. Metabolomic analysis revealed significant changes in the contents of glucose, UDP-glucose, lactate, succinate, fumarate, choline, acetylcarnitine, and several fatty acids. Transcriptomic analysis revealed that related pathways, such as the glycosphingolipid biosynthesis, PPAR signaling pathway and fatty acid elongation, were significantly affected. These results suggest that triphenyl phosphate exposure markedly disturbs hepatic carbohydrate and lipid metabolism in zebrafish. Moreover, DNA replication, the cell cycle, and non-homologous end-joining and base excision repair were strongly affected, thus indicating that triphenyl phosphate hinders the DNA damage repair system in zebrafish liver cells. The present study provides a systematic analysis of the triphenyl phosphate-induced toxic effects in zebrafish liver and demonstrates that low concentrations of triphenyl phosphate affect normal metabolism and cell cycle. PMID:26898711

Evolution of the Lian River coastal basin in response to Quaternary marine transgressions in Southeast China

NASA Astrophysics Data System (ADS)

Tang, Yongjie; Zheng, Zhuo; Chen, Cong; Wang, Mengyuan; Chen, Bishan

2018-04-01

The coastal basin deposit in the Lian River plain is among the thickest Quaternary sequences along the southeastern coast of China. The clastic sediment accumulated in a variety of environmental settings including fluvial, channel, estuary/coastal and marine conditions. Detailed investigation of lithofacies, grain-size distributions, magnetic susceptibility, microfossils and chronology of marine core CN01, compared with regional cores, and combined with offshore seismic reflection profiles, has allowed us to correlate the spatial stratigraphy in the inner and outer plain and the seismic units. Grain size distribution analysis of core CN-01 through compositional data analysis and multivariate statistics were applied to clastic sedimentary facies and sedimentary cycles. Results show that these methods are able to derive a robust proxy information for the depositional environment of the Lian River plain. We have also been able to reconstruct deltaic evolution in response to marine transgressions. On the basis of dating results and chronostratigraphy, the estimated age of the onset of deposition in the Lian River coastal plain was more than 260 kyr BP. Three transgressive sedimentary cycles revealed in many regional cores support this age model. Detailed lithological and microfossil studies confirm that three marine (M3, M2 and M1) and three terrestrial (T3, T2 and T1) units can be distinguished. Spatial correlation between the inner plain, outer plain (typical cores characterized by marine transgression cycles) and offshore seismic reflectors reveals coherent sedimentary sequences. Two major boundaries (unconformity and erosion surfaces) can be recognized in the seismic profiles, and these correspond to weathered reddish and/or variegated clay in the study core, suggesting that Quaternary sediment changes on the Lian River plain were largely controlled by sea-level variations and coastline shift during glacial/interglacial cycles.

SB225002 Induces Cell Death and Cell Cycle Arrest in Acute Lymphoblastic Leukemia Cells through the Activation of GLIPR1

PubMed Central

Leal, Paulo C.; Bhasin, Manoj K.; Zenatti, Priscila Pini; Nunes, Ricardo J.; Yunes, Rosendo A.; Nowill, Alexandre E.; Libermann, Towia A.; Zerbini, Luiz Fernando; Yunes, José Andrés

2015-01-01

Acute Lymphoblastic Leukemia (ALL) is the most frequent childhood malignancy. In the effort to find new anti-leukemic agents, we evaluated the small drug SB225002 (N-(2-hydroxy-4-nitrophenyl)-N’-(2-bromophenyl)urea). Although initially described as a selective antagonist of CXCR2, later studies have identified other cellular targets for SB225002, with potential medicinal use in cancer. We found that SB225002 has a significant pro-apoptotic effect against both B- and T-ALL cell lines. Cell cycle analysis demonstrated that treatment with SB225002 induces G2-M cell cycle arrest. Transcriptional profiling revealed that SB225002-mediated apoptosis triggered a transcriptional program typical of tubulin binding agents. Network analysis revealed the activation of genes linked to the JUN and p53 pathways and inhibition of genes linked to the TNF pathway. Early cellular effects activated by SB225002 included the up-regulation of GLIPR1, a p53-target gene shown to have pro-apoptotic activities in prostate and bladder cancer. Silencing of GLIPR1 in B- and T-ALL cell lines resulted in increased resistance to SB225002. Although SB225002 promoted ROS increase in ALL cells, antioxidant N-Acetyl Cysteine pre-treatment only modestly attenuated cell death, implying that the pro-apoptotic effects of SB225002 are not exclusively mediated by ROS. Moreover, GLIPR1 silencing resulted in increased ROS levels both in untreated and SB225002-treated cells. In conclusion, SB225002 induces cell cycle arrest and apoptosis in different B- and T-ALL cell lines. Inhibition of tubulin function with concurrent activation of the p53 pathway, in particular, its downstream target GLIPR1, seems to underlie the anti-leukemic effect of SB225002. PMID:26302043

Silkworm Pupa Protein Hydrolysate Induces Mitochondria-Dependent Apoptosis and S Phase Cell Cycle Arrest in Human Gastric Cancer SGC-7901 Cells.

PubMed

Li, Xiaotong; Xie, Hongqing; Chen, Yajie; Lang, Mingzi; Chen, Yuyin; Shi, Liangen

2018-03-28

Silkworm pupae ( Bombyx mori ) are a high-protein nutrition source consumed in China since more than 2 thousand years ago. Recent studies revealed that silkworm pupae have therapeutic benefits to treat many diseases. However, the ability of the compounds of silkworm pupae to inhibit tumourigenesis remains to be elucidated. Here, we separated the protein of silkworm pupae and performed alcalase hydrolysis. Silkworm pupa protein hydrolysate (SPPH) can specifically inhibit the proliferation and provoke abnormal morphologic features of human gastric cancer cells SGC-7901 in a dose- and time-dependent manner. Moreover, flow cytometry indicated that SPPH can induce apoptosis and arrest the cell-cycle in S phase. Furthermore, SPPH was shown to provoke accumulation of reactive oxygen species (ROS) and depolarization of mitochondrial membrane potential. Western blotting analysis indicated that SPPH inhibited Bcl-2 expression and promoted Bax expression, and subsequently induced apoptosis-inducing factor and cytochrome C release, which led to the activation of initiator caspase-9 and executioner caspase-3, cleavage of poly (ADP-ribose) polymerase (PARP), eventually caused cell apoptosis. Moreover, SPPH-induced S-phase arrest was mediated by up-regulating the expression of E2F1 and down-regulating those of cyclin E, CDK2 and cyclin A2. Transcriptome sequencing and gene set enrichment analysis (GSEA) also revealed that SPPH treatment could affect gene expression and pathway regulation related to tumourigenesis, apoptosis and cell cycle. In summary, our results suggest that SPPH could specifically suppress cell growth of SGC-7901 through an intrinsic apoptotic pathway, ROS accumulation and cell cycle arrest, and silkworm pupae have a potential to become a source of anticancer agents in the future.

Comparative transcriptome analysis reveals different molecular mechanisms of Bacillus coagulans 2-6 response to sodium lactate and calcium lactate during lactic acid production.

PubMed

Qin, Jiayang; Wang, Xiuwen; Wang, Landong; Zhu, Beibei; Zhang, Xiaohua; Yao, Qingshou; Xu, Ping

2015-01-01

Lactate production is enhanced by adding calcium carbonate or sodium hydroxide during fermentation. However, Bacillus coagulans 2-6 can produce more than 180 g/L L-lactic acid when calcium lactate is accumulated, but less than 120 g/L L-lactic acid when sodium lactate is formed. The molecular mechanisms by which B. coagulans responds to calcium lactate and sodium lactate remain unclear. In this study, comparative transcriptomic methods based on high-throughput RNA sequencing were applied to study gene expression changes in B. coagulans 2-6 cultured in non-stress, sodium lactate stress and calcium lactate stress conditions. Gene expression profiling identified 712 and 1213 significantly regulated genes in response to calcium lactate stress and sodium lactate stress, respectively. Gene ontology assignments of the differentially expressed genes were performed. KEGG pathway enrichment analysis revealed that 'ATP-binding cassette transporters' were significantly affected by calcium lactate stress, and 'amino sugar and nucleotide sugar metabolism' was significantly affected by sodium lactate stress. It was also found that lactate fermentation was less affected by calcium lactate stress than by sodium lactate stress. Sodium lactate stress had negative effect on the expression of 'glycolysis/gluconeogenesis' genes but positive effect on the expression of 'citrate cycle (TCA cycle)' genes. However, calcium lactate stress had positive influence on the expression of 'glycolysis/gluconeogenesis' genes and had minor influence on 'citrate cycle (TCA cycle)' genes. Thus, our findings offer new insights into the responses of B. coagulans to different lactate stresses. Notably, our RNA-seq dataset constitute a robust database for investigating the functions of genes induced by lactate stress in the future and identify potential targets for genetic engineering to further improve L-lactic acid production by B. coagulans.

Transcriptome Analysis of Polyhydroxybutyrate Cycle Mutants Reveals Discrete Loci Connecting Nitrogen Utilization and Carbon Storage in Sinorhizobium meliloti

PubMed Central

Nordeste, Ricardo

2017-01-01

ABSTRACT Polyhydroxybutyrate (PHB) and glycogen polymers are produced by bacteria as carbon storage compounds under unbalanced growth conditions. To gain insights into the transcriptional mechanisms controlling carbon storage in Sinorhizobium meliloti, we investigated the global transcriptomic response to the genetic disruption of key genes in PHB synthesis and degradation and in glycogen synthesis. Under both nitrogen-limited and balanced growth conditions, transcriptomic analysis was performed with genetic mutants deficient in PHB synthesis (phbA, phbB, phbAB, and phbC), PHB degradation (bdhA, phaZ, and acsA2), and glycogen synthesis (glgA1). Three distinct genomic regions of the pSymA megaplasmid exhibited altered expression in the wild type and the PHB cycle mutants that was not seen in the glycogen synthesis mutant. An Fnr family transcriptional motif was identified in the upstream regions of a cluster of genes showing similar transcriptional patterns across the mutants. This motif was found at the highest density in the genomic regions with the strongest transcriptional effect, and the presence of this motif upstream of genes in these regions was significantly correlated with decreased transcript abundance. Analysis of the genes in the pSymA regions revealed that they contain a genomic overrepresentation of Fnr family transcription factor-encoding genes. We hypothesize that these loci, containing mostly nitrogen utilization, denitrification, and nitrogen fixation genes, are regulated in response to the intracellular carbon/nitrogen balance. These results indicate a transcriptional regulatory association between intracellular carbon levels (mediated through the functionality of the PHB cycle) and the expression of nitrogen metabolism genes. IMPORTANCE The ability of bacteria to store carbon and energy as intracellular polymers uncouples cell growth and replication from nutrient uptake and provides flexibility in the use of resources as they are available to the cell. The impact of carbon storage on cellular metabolism would be reflected in global transcription patterns. By investigating the transcriptomic effects of genetically disrupting genes involved in the PHB carbon storage cycle, we revealed a relationship between intracellular carbon storage and nitrogen metabolism. This work demonstrates the utility of combining transcriptome sequencing with metabolic pathway mutations for identifying underlying gene regulatory mechanisms. Author Video: An author video summary of this article is available. PMID:28905000

Vertical Distribution of Bacterial Communities in the Indian Ocean as Revealed by Analyses of 16S rRNA and nasA Genes.

PubMed

Jiang, Xuexia; Jiao, Nianzhi

2016-09-01

Bacteria play an important role in the marine biogeochemical cycles. However, research on the bacterial community structure of the Indian Ocean is scarce, particularly within the vertical dimension. In this study, we investigated the bacterial diversity of the pelagic, mesopelagic and bathypelagic zones of the southwestern Indian Ocean (50.46°E, 37.71°S). The clone libraries constructed by 16S rRNA gene sequence revealed that most phylotypes retrieved from the Indian Ocean were highly divergent from those retrieved from other oceans. Vertical differences were observed based on the analysis of natural bacterial community populations derived from the 16S rRNA gene sequences. Based on the analysis of the nasA gene sequences from GenBank database, a pair of general primers was developed and used to amplify the bacterial nitrate-assimilating populations. Environmental factors play an important role in mediating the bacterial communities in the Indian Ocean revealed by canonical correlation analysis.

Mesocyclones in Central Europe as seen by radar

NASA Astrophysics Data System (ADS)

Wapler, Kathrin; Hengstebeck, Thomas; Groenemeijer, Pieter

2016-02-01

The occurrence and characteristics of mesocyclones in Central Europe as seen by radar are analysed. A three year analysis shows an annual and diurnal cycle with a wider maximum in the late afternoon/evening compared to the diurnal cycle of general thunderstorms. Analysis of F2 tornado events and over a hundred hail storms show the characteristics of the corresponding mesocyclones as seen by radar. For all of the six F2 tornadoes in the three-year period in Germany a corresponding mesocyclone could be detected in radar data. Furthermore the analysis reveals that about half of all hail storms in Germany are associated with a mesocyclone detected in radar data within 10 km and 10 min. Some mesocyclone attributes, e.g. depth and maximum shear, and of the associated convective cell, e.g. reflectivity related parameters VIL, VILD and echotop, have predictive skill for indicating the occurrence of hail. The mesocyclone detection algorithm may support the analysis and nowcasting of severe weather events and thus support the warning process.

Metagenomic analysis reveals a green sulfur bacterium as a potential coral symbiont.

PubMed

Cai, Lin; Zhou, Guowei; Tian, Ren-Mao; Tong, Haoya; Zhang, Weipeng; Sun, Jin; Ding, Wei; Wong, Yue Him; Xie, James Y; Qiu, Jian-Wen; Liu, Sheng; Huang, Hui; Qian, Pei-Yuan

2017-08-24

Coral reefs are ecologically significant habitats. Coral-algal symbiosis confers ecological success on coral reefs and coral-microbial symbiosis is also vital to coral reefs. However, current understanding of coral-microbial symbiosis on a genomic scale is largely unknown. Here we report a potential microbial symbiont in corals revealed by metagenomics-based genomic study. Microbial cells in coral were enriched for metagenomic analysis and a high-quality draft genome of "Candidatus Prosthecochloris korallensis" was recovered by metagenome assembly and genome binning. Phylogenetic analysis shows "Ca. P. korallensis" belongs to the Prosthecochloris clade and is clustered with two Prosthecochloris clones derived from Caribbean corals. Genomic analysis reveals "Ca. P. korallensis" has potentially important ecological functions including anoxygenic photosynthesis, carbon fixation via the reductive tricarboxylic acid (rTCA) cycle, nitrogen fixation, and sulfur oxidization. Core metabolic pathway analysis suggests "Ca. P. korallensis" is a green sulfur bacterium capable of photoautotrophy or mixotrophy. Potential host-microbial interaction reveals a symbiotic relationship: "Ca. P. korallensis" might provide organic and nitrogenous nutrients to its host and detoxify sulfide for the host; the host might provide "Ca. P. korallensis" with an anaerobic environment for survival, carbon dioxide and acetate for growth, and hydrogen sulfide as an electron donor for photosynthesis.

Inhibition of Human Cytomegalovirus Replication by Artemisinins: Effects Mediated through Cell Cycle Modulation

PubMed Central

Roy, Sujayita; He, Ran; Kapoor, Arun; Forman, Michael; Mazzone, Jennifer R.; Posner, Gary H.

2015-01-01

Artemisinin-derived monomers and dimers inhibit human cytomegalovirus (CMV) replication in human foreskin fibroblasts (HFFs). The monomer artesunate (AS) inhibits CMV at micromolar concentrations, while dimers inhibit CMV replication at nanomolar concentrations, without increased toxicity in HFFs. We report on the variable anti-CMV activity of AS compared to the consistent and reproducible CMV inhibition by dimer 606 and ganciclovir (GCV). Investigation of this phenomenon revealed that the anti-CMV activity of AS correlated with HFFs synchronized to the G0/G1 stage of the cell cycle. In contact-inhibited serum-starved HFFs or cells arrested at early/late G1 with specific checkpoint regulators, AS and dimer 606 efficiently inhibited CMV replication. However, in cycling HFFs, in which CMV replication was productive, virus inhibition by AS was significantly reduced, but inhibition by dimer 606 and GCV was maintained. Cell cycle analysis in noninfected HFFs revealed that AS induced early G1 arrest, while dimer 606 partially blocked cell cycle progression. In infected HFFs, AS and dimer 606 prevented the progression of cell cycle toward the G1/S checkpoint. AS reduced the expression of cyclin-dependent kinases (CDK) 2, 4, and 6 in noninfected cycling HFFs, while the effect of dimer 606 on these CDKs was moderate. Neither compound affected CDK expression in noninfected contact-inhibited HFFs. In CMV-infected cells, AS activity correlated with reduced CDK2 levels. CMV inhibition by AS and dimer 606 also correlated with hypophosphorylation (activity) of the retinoblastoma protein (pRb). AS activity was strongly associated with pRb hypophosphorylation, while its reduced anti-CMV activity was marked by pRb phosphorylation. Roscovitine, a CDK2 inhibitor, antagonized the anti-CMV activities of AS and dimer 606. These data suggest that cell cycle modulation through CDKs and pRb might play a role in the anti-CMV activities of artemisinins. Proteins involved in this modulation may be identified and targeted for CMV inhibition. PMID:25870074

Strong evidence for the influence of solar cycles on a Late Miocene lake system revealed by biotic and abiotic proxies

PubMed Central

Kern, A.K.; Harzhauser, M.; Piller, W.E.; Mandic, O.; Soliman, A.

2012-01-01

The Late Miocene paleogeography of central Europe and its climatic history are well studied with a resolution of c. 106 years. Small-scale climatic variations are yet unresolved. Observing past climatic change of short periods, however, would encourage the understanding of the modern climatic system. Therefore, past climate archives require a resolution on a decadal to millennial scale. To detect such a short-term evolution, a continuous 6-m-core of the Paleo-Lake Pannon was analyzed in 1-cm-sample distance to provide information as precise and regular as possible. Measurements of the natural gamma radiation and magnetic susceptibility combined with the total abundance of ostracod shells were used as proxies to estimate millennial- to centennial scale environmental changes during the mid-Tortonian warm period. Patterns emerged, but no indisputable age model can be provided for the core, due to the lack of paleomagnetic reversals and the lack of minerals suitable for absolute dating. Therefore, herein we propose another method to determine a hypothetic time frame for these deposits. Based on statistical processes, including Lomb–Scargle and REDFIT periodograms along with Wavelet spectra, several distinct cyclicities could be detected. Calculations considering established off-shore sedimentation rates of the Tortonian Vienna Basin revealed patterns resembling Holocene solar-cycle-records well. The comparison of filtered data of Miocene and Holocene records displays highly similar patterns and comparable modulations. A best-fit adjustment of sedimentation rate results in signals which fit to the lower and upper Gleissberg cycle, the de Vries cycle, the unnamed 500-year- and 1000-year-cycles, as well as the Hallstatt cycle. Each of these cycles has a distinct and unique expression in the investigated environmental proxies, reflecting a complex forcing-system. Hence, a single-proxy-analysis, as often performed on Holocene records, should be considered cautiously as it might fail to capture the full range of solar cycles. PMID:23564975

Continuous field measurements of δD in water vapor by open-path Fourier transform infrared spectrometry

NASA Astrophysics Data System (ADS)

Wang, Wei; Liu, Wenqing; Zhang, Tianshu

2012-12-01

The stable isotopes in atmospheric water vapor contain rich information on the hydrologic cycles and gaseous exchange processes between biosphere and atmosphere. About one-week field experiment was conducted to continuously measure the isotope composition of water vapor in ambient air using an open-path FTIR system. Mixing ratios of H2 16O and HD16O were measured simultaneously. Analysis of water vapor isotopes revealed that the variations of H2 16O and HD16O were highly related. Mixing ratios of both isotopes varied considerably on a daily timescale or between days, with no obvious diurnal cycle, whereas the deuterium isotopic [delta]D showed clear diel cycle. The results illustrated that the correlation between [delta]D and H2O mixing ratio was relatively weak, which was also demonstrated by the Keeling plot analysis with the whole data. Yet the further Keeling analysis on a daily timescale displayed more obvious linear relationship between [delta]D and the total H2O concentration. All daily isotopic values of evapotranspiration source were obtained, with the range between -113.93±10.25‰ and -245.63±17.61‰ over the observation period.

The nitrogen cycle in cryoconites: naturally occurring nitrification-denitrification granules on a glacier.

PubMed

Segawa, Takahiro; Ishii, Satoshi; Ohte, Nobuhito; Akiyoshi, Ayumi; Yamada, Akinori; Maruyama, Fumito; Li, Zhongqin; Hongoh, Yuichi; Takeuchi, Nozomu

2014-10-01

Cryoconites are microbial aggregates commonly found on glacier surfaces where they tend to take spherical, granular forms. While it has been postulated that the microbes in cryoconite granules play an important role in glacier ecosystems, information on their community structure is still limited, and their functions remain unclear. Here, we present evidence for the occurrence of nitrogen cycling in cryoconite granules on a glacier in Central Asia. We detected marker genes for nitrogen fixation, nitrification and denitrification in cryoconite granules by digital polymerase chain reaction (PCR), while digital reverse transcription PCR analysis revealed that only marker genes for nitrification and denitrification were abundantly transcribed. Analysis of isotope ratios also indicated the occurrence of nitrification; nitrate in the meltwater on the glacier surface was of biological origin, while nitrate in the snow was of atmospheric origin. The predominant nitrifiers on this glacier belonged to the order Nitrosomonadales, as suggested by amoA sequences and 16S ribosomal RNA pyrosequencing analysis. Our results suggest that the intense carbon and nitrogen cycles by nitrifiers, denitrifiers and cyanobacteria support abundant and active microbes on the Asian glacier. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Global gene expression analysis combined with a genomics approach for the identification of signal transduction networks involved in postnatal mouse myocardial proliferation and development.

PubMed

Wang, Ruoxin; Su, Chao; Wang, Xinting; Fu, Qiang; Gao, Xingjie; Zhang, Chunyan; Yang, Jie; Yang, Xi; Wei, Minxin

2018-01-01

Mammalian cardiomyocytes may permanently lose their ability to proliferate after birth. Therefore, studying the proliferation and growth arrest of cardiomyocytes during the postnatal period may enhance the current understanding regarding this molecular mechanism. The present study identified the differentially expressed genes in hearts obtained from 24 h‑old mice, which contain proliferative cardiomyocytes; 7‑day‑old mice, in which the cardiomyocytes are undergoing a proliferative burst; and 10‑week‑old mice, which contain growth‑arrested cardiomyocytes, using global gene expression analysis. Furthermore, myocardial proliferation and growth arrest were analyzed from numerous perspectives, including Gene Ontology annotation, cluster analysis, pathway enrichment and network construction. The results of a Gene Ontology analysis indicated that, with increasing age, enriched gene function was not only associated with cell cycle, cell division and mitosis, but was also associated with metabolic processes and protein synthesis. In the pathway analysis, 'cell cycle', proliferation pathways, such as the 'PI3K‑AKT signaling pathway', and 'metabolic pathways' were well represented. Notably, the cluster analysis revealed that bone morphogenetic protein (BMP)1, BMP10, cyclin E2, E2F transcription factor 1 and insulin like growth factor 1 exhibited increased expression in hearts obtained from 7‑day‑old mice. In addition, the signal transduction pathway associated with the cell cycle was identified. The present study primarily focused on genes with altered expression, including downregulated anaphase promoting complex subunit 1, cell division cycle (CDC20), cyclin dependent kinase 1, MYC proto-oncogene, bHLH transcription factor and CDC25C, and upregulated growth arrest and DNA damage inducible α in 10-week group, which may serve important roles in postnatal myocardial cell cycle arrest. In conclusion, these data may provide important information regarding myocardial proliferation and development.

Initial and steady-state Ru growth by atomic layer deposition studied by in situ Angle Resolved X-ray Photoelectron Spectroscopy

NASA Astrophysics Data System (ADS)

Egorov, Konstantin V.; Lebedinskii, Yury Yu.; Soloviev, Anatoly A.; Chouprik, Anastasia A.; Azarov, Alexander Yu.; Markeev, Andrey M.

2017-10-01

The clear substrate-dependent growth and delayed film continuity are essential challenges of Ru atomic layer deposition (ALD) demanding adequate and versatile approaches for their study. Here, we report on the application of in situ Angle Resolved X-ray Phototelectron Spectroscopy (ARXPS) for investigation of initial and steady-state ALD growth of Ru using Ru(EtCp)2 and O2 as precursors. Using ARXPS surface analysis technique we determine such parameters of Ru ALD initial growth as incubation period, fractional coverage and the thickness of islands/film depending on the substrate chemical state, governed by the presence/absence of NH3/Ar plasma pretreatment. It was demonstrated that NH3/Ar plasma pretreatment allows to obtain the lowest incubation period (∼7 ALD cycles) resulting in a continuous ultrathin (∼20 Å) and smooth Ru films after 70 ALD cycles. In situ XPS at UHV was used at steady state Ru growth for analysis of half-cycle reactions that revealed formation of RuOx (x ≈ 2) layer with thickness of ∼8 Å after O2 pulse (first half-cycle). It was also shown that oxygen of RuOx layer combusts Ru(EtCp)2 ligands in the second half-cycle reaction and the observed Ru growth of ∼0.34 Å per cycle is in a good agreement with the amount of oxygen in the RuOx layer.

Long- and Short-Term Processes Indicated by the Displacement of the Chamber Roofs in the Monumental Wieliczka Salt Mine / Długo- i krótkotrwałe procesy sygnalizowane przemieszczeniami stropu komór w zabytkowej kopalni soli wieliczka

NASA Astrophysics Data System (ADS)

Kortas, Grzegorz

2013-03-01

This paper presents several processes that are characteristic for the salt rock mass, which have been found upon analysis of observations of the chamber roof displacements in the monumental Wieliczka Salt Mine. Those processes are revealed in different time frames and they range from short- to long-term ones. A regular long-term increase or decrease of creeping rate in the chamber roof is expressed by power function of time. It was found that an annual component of that process consists in the season cycle, marked by increased displacement rates in the summer and reduced ones in the winter. The seasonal changes in air humidity are the cause of those cycles. A rock slip cycle is observed in some chambers during several months. In those periods, we can identify displacements that happen when internal static and dynamic friction is overcome. In 2007-2009, single signals from large-area rock-mass movements were recorded in several chambers. They were probably associated with the change of geo-mechanical conditions in northern region of rock mass after a leak had been plugged in the cross-corridor Mina. The results of our analysis have revealed new cognitive components contributing to the description of rock behaviour in specific geological and mining conditions of Miocene salt deposits.

Genomic insights into metabolic versatility of a lithotrophic sulfur-oxidizing diazotrophic Alphaproteobacterium Azospirillum thiophilum.

PubMed

Orlova, Maria V; Tarlachkov, Sergey V; Dubinina, Galina A; Belousova, Elena V; Tutukina, Maria N; Grabovich, Margarita Y

2016-12-01

Diazotrophic Alphaproteobacteria of the genus Azospirillum are usually organotrophs, although some strains of Azospirillum lipoferum are capable of hydrogen-dependent autotrophic growth. Azospirillum thiophilum strain was isolated from a mineral sulfide spring, a biotope highly unusual for azospirilla. Here, the metabolic pathways utilized by A. thiophilum were revealed based on comprehensive analysis of its genomic organization, together with physiological and biochemical approaches. The A. thiophilum genome contained all the genes encoding the enzymes of carbon metabolism via glycolysis, tricarboxylic acid cycle and glyoxylate cycle. Genes for a complete set of enzymes responsible for autotrophic growth, with an active Calvin-Benson-Bassham cycle, were also revealed, and activity of the key enzymes was determined. Microaerobic chemolithoautotrophic growth of A. thiophilum was detected in the presence of thiosulfate and molecular hydrogen, being in line with the discovery of the genes encoding the two enzymes involved in dissimilatory thiosulfate oxidation, the Sox-complex and thiosulfate dehydrogenase and Ni-Fe hydrogenases. Azospirillum thiophilum utilizes methanol and formate, producing CO 2 that can further be metabolized via the Calvin cycle. Finally, it is capable of anaerobic respiration, using tetrathionate as a terminal electron acceptor. Such metabolic versatility is of great importance for adaptation of A. thiophilum to constantly changing physicochemical environment. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

Zentgraf, Florian; Baum, Elias; Dreizler, Andreas

Planar particle image velocimetry (PIV) and tomographic PIV (TPIV) measurements are utilized to analyze turbulent statistical theory quantities and the instantaneous turbulence within a single-cylinder optical engine. Measurements are performed during the intake and mid-compression stroke at 800 and 1500 RPM. TPIV facilitates the evaluation of spatially resolved Reynolds stress tensor (RST) distributions, anisotropic Reynolds stress invariants, and instantaneous turbulent vortical structures. The RST analysis describes distributions of individual velocity fluctuation components that arise from unsteady turbulent flow behavior as well as cycle-to-cycle variability (CCV). A conditional analysis, for which instantaneous PIV images are sampled by their tumble center location,more » reveals that CCV and turbulence have similar contributions to RST distributions at the mean tumble center, but turbulence is dominant in regions peripheral to the tumble center. Analysis of the anisotropic Reynolds stress invariants reveals the spatial distribution of axisymmetric expansion, axisymmetric contraction, and 3D isotropy within the cylinder. Findings indicate that the mid-compression flow exhibits a higher tendency toward 3D isotropy than the intake flow. A novel post-processing algorithm is utilized to classify the geometry of instantaneous turbulent vortical structures and evaluate their frequency of occurrence within the cylinder. Findings are coupled with statistical theory quantities to provide a comprehensive understanding of the distribution of turbulent velocity components, the distribution of anisotropic states of turbulence, and compare the turbulent vortical flow distribution that is theoretically expected to what is experimentally observed. The analyses reveal requisites of important turbulent flow quantities and discern their sensitivity to the local flow topography and engine operation.« less

An Ambystoma mexicanum EST sequencing project: analysis of 17,352 expressed sequence tags from embryonic and regenerating blastema cDNA libraries

PubMed Central

Habermann, Bianca; Bebin, Anne-Gaelle; Herklotz, Stephan; Volkmer, Michael; Eckelt, Kay; Pehlke, Kerstin; Epperlein, Hans Henning; Schackert, Hans Konrad; Wiebe, Glenis; Tanaka, Elly M

2004-01-01

Background The ambystomatid salamander, Ambystoma mexicanum (axolotl), is an important model organism in evolutionary and regeneration research but relatively little sequence information has so far been available. This is a major limitation for molecular studies on caudate development, regeneration and evolution. To address this lack of sequence information we have generated an expressed sequence tag (EST) database for A. mexicanum. Results Two cDNA libraries, one made from stage 18-22 embryos and the other from day-6 regenerating tail blastemas, generated 17,352 sequences. From the sequenced ESTs, 6,377 contigs were assembled that probably represent 25% of the expressed genes in this organism. Sequence comparison revealed significant homology to entries in the NCBI non-redundant database. Further examination of this gene set revealed the presence of genes involved in important cell and developmental processes, including cell proliferation, cell differentiation and cell-cell communication. On the basis of these data, we have performed phylogenetic analysis of key cell-cycle regulators. Interestingly, while cell-cycle proteins such as the cyclin B family display expected evolutionary relationships, the cyclin-dependent kinase inhibitor 1 gene family shows an unusual evolutionary behavior among the amphibians. Conclusions Our analysis reveals the importance of a comprehensive sequence set from a representative of the Caudata and illustrates that the EST sequence database is a rich source of molecular, developmental and regeneration studies. To aid in data mining, the ESTs have been organized into an easily searchable database that is freely available online. PMID:15345051

Natural variability of tropical upper stratospheric ozone inferred from the Atmosphere Explorer backscatter ultraviolet experiment

NASA Technical Reports Server (NTRS)

Frederick, J. E.; Abrams, R. B.; Dasgupta, R.; Guenther, B.

1981-01-01

Analysis of backscattered ultraviolet radiances observed at tropical latitudes by the Atmosphere Explorer-E satellite reveals both annual and semiannual cycles in upper stratospheric ozone. The annual variation dominates the signal at wavelengths which sense ozone primarily above 45 km while below this, to the lowest altitude sensed, 35 km, the semiannual component has comparable amplitude. Comparison of radiance measurements taken with the same instrument at solar minimum during 1976 and solar maximum in 1979 show no significant differences. This suggests that variations in upper stratospheric ozone over the solar cycle are small, although the data presently available do not allow a definite conclusion.

Seismic sensitivity to sub-surface solar activity from 18 yr of GOLF/SoHO observations

NASA Astrophysics Data System (ADS)

Salabert, D.; García, R. A.; Turck-Chièze, S.

2015-06-01

Solar activity has significantly changed over the last two Schwabe cycles. After a long and deep minimum at the end of Cycle 23, the weaker activity of Cycle 24 contrasts with the previous cycles. In this work, the response of the solar acoustic oscillations to solar activity is used in order to provide insights into the structural and magnetic changes in the sub-surface layers of the Sun during this on-going unusual period of low activity. We analyze 18 yr of continuous observations of the solar acoustic oscillations collected by the Sun-as-a-star GOLF instrument on board the SoHO spacecraft. From the fitted mode frequencies, the temporal variability of the frequency shifts of the radial, dipolar, and quadrupolar modes are studied for different frequency ranges that are sensitive to different layers in the solar sub-surface interior. The low-frequency modes show nearly unchanged frequency shifts between Cycles 23 and 24, with a time evolving signature of the quasi-biennial oscillation, which is particularly visible for the quadrupole component revealing the presence of a complex magnetic structure. The modes at higher frequencies show frequency shifts that are 30% smaller during Cycle 24, which is in agreement with the decrease observed in the surface activity between Cycles 23 and 24. The analysis of 18 yr of GOLF oscillations indicates that the structural and magnetic changes responsible for the frequency shifts remained comparable between Cycle 23 and Cycle 24 in the deeper sub-surface layers below 1400 km as revealed by the low-frequency modes. The frequency shifts of the higher-frequency modes, sensitive to shallower regions, show that Cycle 24 is magnetically weaker in the upper layers of Sun. Appendices are available in electronic form at http://www.aanda.orgThe following 68 GOLF frequency tables are available and Table A.1 is also available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/578/A137

Circadian Clock Synchronization of the Cell Cycle in Zebrafish Occurs through a Gating Mechanism Rather Than a Period-phase Locking Process.

PubMed

Laranjeiro, Ricardo; Tamai, T Katherine; Letton, William; Hamilton, Noémie; Whitmore, David

2018-04-01

Studies from a number of model systems have shown that the circadian clock controls expression of key cell cycle checkpoints, thus providing permissive or inhibitory windows in which specific cell cycle events can occur. However, a major question remains: Is the clock actually regulating the cell cycle through such a gating mechanism or, alternatively, is there a coupling process that controls the speed of cell cycle progression? Using our light-responsive zebrafish cell lines, we address this issue directly by synchronizing the cell cycle in culture simply by changing the entraining light-dark (LD) cycle in the incubator without the need for pharmacological intervention. Our results show that the cell cycle rapidly reentrains to a shifted LD cycle within 36 h, with changes in p21 expression and subsequent S phase timing occurring within the first few hours of resetting. Reentrainment of mitosis appears to lag S phase resetting by 1 circadian cycle. The range of entrainment of the zebrafish clock to differing LD cycles is large, from 16 to 32 hour periods. We exploited this feature to explore cell cycle entrainment at both the population and single cell levels. At the population level, cell cycle length is shortened or lengthened under corresponding T-cycles, suggesting that a 1:1 coupling mechanism is capable of either speeding up or slowing down the cell cycle. However, analysis at the single cell level reveals that this, in fact, is not true and that a gating mechanism is the fundamental method of timed cell cycle regulation in zebrafish. Cell cycle length at the single cell level is virtually unaltered with varying T-cycles.

Circadian Clock Synchronization of the Cell Cycle in Zebrafish Occurs through a Gating Mechanism Rather Than a Period-phase Locking Process

PubMed Central

Tamai, T. Katherine; Letton, William; Hamilton, Noémie; Whitmore, David

2018-01-01

Studies from a number of model systems have shown that the circadian clock controls expression of key cell cycle checkpoints, thus providing permissive or inhibitory windows in which specific cell cycle events can occur. However, a major question remains: Is the clock actually regulating the cell cycle through such a gating mechanism or, alternatively, is there a coupling process that controls the speed of cell cycle progression? Using our light-responsive zebrafish cell lines, we address this issue directly by synchronizing the cell cycle in culture simply by changing the entraining light-dark (LD) cycle in the incubator without the need for pharmacological intervention. Our results show that the cell cycle rapidly reentrains to a shifted LD cycle within 36 h, with changes in p21 expression and subsequent S phase timing occurring within the first few hours of resetting. Reentrainment of mitosis appears to lag S phase resetting by 1 circadian cycle. The range of entrainment of the zebrafish clock to differing LD cycles is large, from 16 to 32 hour periods. We exploited this feature to explore cell cycle entrainment at both the population and single cell levels. At the population level, cell cycle length is shortened or lengthened under corresponding T-cycles, suggesting that a 1:1 coupling mechanism is capable of either speeding up or slowing down the cell cycle. However, analysis at the single cell level reveals that this, in fact, is not true and that a gating mechanism is the fundamental method of timed cell cycle regulation in zebrafish. Cell cycle length at the single cell level is virtually unaltered with varying T-cycles. PMID:29444612

Do Women's Voices Provide Cues of the Likelihood of Ovulation? The Importance of Sampling Regime

PubMed Central

Fischer, Julia; Semple, Stuart; Fickenscher, Gisela; Jürgens, Rebecca; Kruse, Eberhard; Heistermann, Michael; Amir, Ofer

2011-01-01

The human voice provides a rich source of information about individual attributes such as body size, developmental stability and emotional state. Moreover, there is evidence that female voice characteristics change across the menstrual cycle. A previous study reported that women speak with higher fundamental frequency (F0) in the high-fertility compared to the low-fertility phase. To gain further insights into the mechanisms underlying this variation in perceived attractiveness and the relationship between vocal quality and the timing of ovulation, we combined hormone measurements and acoustic analyses, to characterize voice changes on a day-to-day basis throughout the menstrual cycle. Voice characteristics were measured from free speech as well as sustained vowels. In addition, we asked men to rate vocal attractiveness from selected samples. The free speech samples revealed marginally significant variation in F0 with an increase prior to and a distinct drop during ovulation. Overall variation throughout the cycle, however, precluded unequivocal identification of the period with the highest conception risk. The analysis of vowel samples revealed a significant increase in degree of unvoiceness and noise-to-harmonic ratio during menstruation, possibly related to an increase in tissue water content. Neither estrogen nor progestogen levels predicted the observed changes in acoustic characteristics. The perceptual experiments revealed a preference by males for voice samples recorded during the pre-ovulatory period compared to other periods in the cycle. While overall we confirm earlier findings in that women speak with a higher and more variable fundamental frequency just prior to ovulation, the present study highlights the importance of taking the full range of variation into account before drawing conclusions about the value of these cues for the detection of ovulation. PMID:21957453

Unravelling the potential of a new uracil phosphoribosyltransferase (UPRT) from Arabidopsis thaliana in sensitizing HeLa cells towards 5-fluorouracil.

PubMed

Narayanan, Sharmila; Sanpui, Pallab; Sahoo, Lingaraj; Ghosh, Siddhartha Sankar

2016-10-01

In silico studies with uracil phosphoribosyltransferase from Arabidopsis thaliana (AtUPRT) revealed its lower binding energies for uracil and 5-fluorouracil (5-FU) as compared to those of bacterial UPRT indicating the prospective of AtUPRT in gene therapy implications. Hence, AtUPRT was cloned and stably expressed in cervical cancer cells (HeLa) to investigate the effect of prodrug 5-FU on these transfected cancer cells. The treatment of AtUPRT-expressing HeLa (HeLa-UPP) cells with 5-FU for 72h resulted in significant decrease in cell viability. Moreover, 5-FU was observed to induce apoptosis and perturb mitochondrial membrane potential in HeLa-UPP cells. While cell cycle analysis revealed significant S-phase arrest as a result of 5-FU treatment in HeLa-UPP cells, quantitative gene expression analysis demonstrated simultaneous upregulation of important cell cycle related genes, cyclin D1 and p21. The survival fractions of non-transfected, vector-transfected and AtUPRT-transfected HeLa cells, following 5-FU treatment, were calculated to be 0.425, 0.366 and 0.227, respectively. Copyright © 2016 Elsevier B.V. All rights reserved.

The expression of the clock gene cycle has rhythmic pattern and is affected by photoperiod in the moth Sesamia nonagrioides.

PubMed

Kontogiannatos, Dimitrios; Gkouvitsas, Theodoros; Kourti, Anna

2017-06-01

To obtain clues to the link between the molecular mechanism of circadian and photoperiod clocks, we have cloned the circadian clock gene cycle (Sncyc) in the corn stalk borer, Sesamia nonagrioides, which undergoes facultative diapause controlled by photoperiod. Sequence analysis revealed a high degree of conservation among insects for this gene. SnCYC consists of 667 amino acids and structural analysis showed that it contains a BCTR domain in its C-terminal in addition to the common domains found in Drosophila CYC, i.e. bHLH, PAS-A, PAS-B domains. The results revealed that the sequence of Sncyc showed a similarity to that of its mammalian orthologue, Bmal1. We also investigated the expression patterns of Sncyc in the brain of larvae growing under long-day 16L: 8D (LD), constant darkness (DD) and short-day 10L: 14D (SD) conditions using qRT-PCR assays. The mRNAs of Sncyc expression was rhythmic in LD, DD and SD cycles. Also, it is remarkable that the photoperiodic conditions affect the expression patterns and/or amplitudes of circadian clock gene Sncyc. This gene is associated with diapause in S. nonagrioides, because under SD (diapause conditions) the photoperiodic signal altered mRNA accumulation. Sequence and expression analysis of cyc in S. nonagrioides shows interesting differences compared to Drosophila where this gene does not oscillate or change in expression patterns in response to photoperiod, suggesting that this species is an interesting new model to study the molecular control of insect circadian and photoperiodic clocks. Copyright © 2017 Elsevier Inc. All rights reserved.

Influence of the 11-year solar cycle on the effects of the equatorial quasi-biennial oscillation, manifesting in the extratropical northern atmosphere

NASA Astrophysics Data System (ADS)

Sitnov, S. A.

2009-01-01

Using the longest and most reliable ozonesonde data sets grouped for four regions (Japan, Europe, as well as temperate and polar latitudes of Canada) the comparative analysis of regional responses of ozone, temperature, horizontal wind, tropopause and surface pressure on the equatorial quasi-biennial oscillation (QBO effects), manifesting in opposite phases of the 11-year solar cycle (11-yr SC) was carried out. The impact of solar cycle is found to be the strongest at the Canadian Arctic, near one of two climatological centres of polar vortex, where in solar maximum conditions the QBO signals in ozone and temperature have much larger amplitudes, embrace greater range of heights, and are maximized much higher than those in solar minimum conditions. The strengthening of the temperature QBO effect during solar maxima can explain why correlation between the 11-yr SC and polar winter stratospheric temperature is reversed in the opposite QBO phases. At the border of polar vortex the 11-yr SC also modulates the QBO effect in zonal wind, strengthening the quasi-biennial modulation of polar vortex during solar maxima that is associated with strong negative correlation between stratospheric QBO signals in zonal wind and temperature. Above Japan the QBO effects of ozone, temperature, and zonal wind, manifesting in solar maxima reveal the downward phase dynamics, reminding similar feature of the zonal wind in the equatorial stratosphere. Above Europe, the QBO effects in solar maxima reveal more similarity with those above Japan, while in solar minima with the effects obtained at the Canadian middle-latitude stations. It is revealed that the 11-yr SC influences regional QBO effects in tropopause height, tropopause temperature and surface pressure. The influence most distinctly manifest itself in tropopause characteristics above Japan. The results of the accompanying analysis of the QBO reference time series testify that in the period of 1965-2006 above 50-hPa level the duration of the QBO cycle in solar maxima is 1-3 months longer than in solar minima. The differences are more distinct at higher levels, but they are diminished with lengthening of the period.

Phosphorylation of mitogen-activated protein kinase (MAPK) is required for cytokinesis and progression of cell cycle in tobacco BY-2 cells.

PubMed

Ma, Zhaowu; Yu, Guanghui

2010-02-15

The role of mitogen-activated protein kinase (MAPK) in plant cytokinesis remains largely uncharacterized. To elucidate its role, tobacco Bright Yellow-2 (BY-2) cells have been synchronized using a two-step procedure, and the different phases of the cell cycle identified by Histone 4 gene expression and the mitotic index. MAPK expression was analyzed by semi-quantitative (SQ) RT-PCR and protein gel blot analysis for phosphorylated MAPK during cell cycle progression. The SQ RT-PCR analysis indicated that MAPK expression is lower in mitosis than in interphase (G1, G2 and S). However, the amount of phosphorylated MAPK remained stable throughout the cell cycle, indicating that MAPK activity is predominantly regulated at the post-translational level and that phosphorylation of MAPK plays an important role in mitosis. Application of the specific MAPK phosphorylation inhibitor U0126 revealed that while U0126 treatment decreases the phosphorylation of MAPK and the progression from telophase to early cytokinesis is significantly inhibited. The formation of the phragmoplast is also negatively affected at this stage. These results demonstrate that MAPK phosphorylation is involved in the formation of the cell plate within the phragmoplast during cytokinesis and that MAPK predominantly functions during the cytokinesis stage of the cell cycle in tobacco BY-2 cells. Copyright 2009 Elsevier GmbH. All rights reserved.

Using mental mapping to unpack perceived cycling risk.

PubMed

Manton, Richard; Rau, Henrike; Fahy, Frances; Sheahan, Jerome; Clifford, Eoghan

2016-03-01

Cycling is the most energy-efficient mode of transport and can bring extensive environmental, social and economic benefits. Research has highlighted negative perceptions of safety as a major barrier to the growth of cycling. Understanding these perceptions through the application of novel place-sensitive methodological tools such as mental mapping could inform measures to increase cyclist numbers and consequently improve cyclist safety. Key steps to achieving this include: (a) the design of infrastructure to reduce actual risks and (b) targeted work on improving safety perceptions among current and future cyclists. This study combines mental mapping, a stated-preference survey and a transport infrastructure inventory to unpack perceptions of cycling risk and to reveal both overlaps and discrepancies between perceived and actual characteristics of the physical environment. Participants translate mentally mapped cycle routes onto hard-copy base-maps, colour-coding road sections according to risk, while a transport infrastructure inventory captures the objective cycling environment. These qualitative and quantitative data are matched using Geographic Information Systems and exported to statistical analysis software to model the individual and (infra)structural determinants of perceived cycling risk. This method was applied to cycling conditions in Galway City (Ireland). Participants' (n=104) mental maps delivered data-rich perceived safety observations (n=484) and initial comparison with locations of cycling collisions suggests some alignment between perception and reality, particularly relating to danger at roundabouts. Attributing individual and (infra)structural characteristics to each observation, a Generalised Linear Mixed Model statistical analysis identified segregated infrastructure, road width, the number of vehicles as well as gender and cycling experience as significant, and interactions were found between individual and infrastructural variables. The paper concludes that mental mapping is a highly useful tool for assessing perceptions of cycling risk with a strong visual aspect and significant potential for public participation. This distinguishes it from more traditional cycling safety assessment tools that focus solely on the technical assessment of cycling infrastructure. Further development of online mapping tools is recommended as part of bicycle suitability measures to engage cyclists and the general public and to inform 'soft' and 'hard' cycling policy responses. Copyright © 2015 Elsevier Ltd. All rights reserved.

The combined effect of age and basal follicle-stimulating hormone on the cost of a live birth at assisted reproductive technology.

PubMed

Henne, Melinda B; Stegmann, Barbara J; Neithardt, Adrienne B; Catherino, William H; Armstrong, Alicia Y; Kao, Tzu-Cheg; Segars, James H

2008-01-01

To predict the cost of a delivery following assisted reproductive technologies (ART). Cost analysis based on retrospective chart analysis. University-based ART program. Women aged >or=26 and

Prediction of solar activity from solar background magnetic field variations in cycles 21-23

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

Shepherd, Simon J.; Zharkov, Sergei I.; Zharkova, Valentina V., E-mail: s.j.shepherd@brad.ac.uk, E-mail: s.zharkov@hull.ac.uk, E-mail: valentina.zharkova@northumbria.ac.uk

2014-11-01

A comprehensive spectral analysis of both the solar background magnetic field (SBMF) in cycles 21-23 and the sunspot magnetic field in cycle 23 reported in our recent paper showed the presence of two principal components (PCs) of SBMF having opposite polarity, e.g., originating in the northern and southern hemispheres, respectively. Over a duration of one solar cycle, both waves are found to travel with an increasing phase shift toward the northern hemisphere in odd cycles 21 and 23 and to the southern hemisphere in even cycle 22. These waves were linked to solar dynamo waves assumed to form in differentmore » layers of the solar interior. In this paper, for the first time, the PCs of SBMF in cycles 21-23 are analyzed with the symbolic regression technique using Hamiltonian principles, allowing us to uncover the underlying mathematical laws governing these complex waves in the SBMF presented by PCs and to extrapolate these PCs to cycles 24-26. The PCs predicted for cycle 24 very closely fit (with an accuracy better than 98%) the PCs derived from the SBMF observations in this cycle. This approach also predicts a strong reduction of the SBMF in cycles 25 and 26 and, thus, a reduction of the resulting solar activity. This decrease is accompanied by an increasing phase shift between the two predicted PCs (magnetic waves) in cycle 25 leading to their full separation into the opposite hemispheres in cycle 26. The variations of the modulus summary of the two PCs in SBMF reveals a remarkable resemblance to the average number of sunspots in cycles 21-24 and to predictions of reduced sunspot numbers compared to cycle 24: 80% in cycle 25 and 40% in cycle 26.« less

Effect of Board Thickness on Sn-Ag-Cu Joint Interconnect Mechanical Shock Performance

NASA Astrophysics Data System (ADS)

Lee, Tae-Kyu; Xie, Weidong

2014-12-01

The mechanical stability of solder joints with Sn-Ag-Cu alloy joints on various board thicknesses was investigated with a high G level shock environment. A test vehicle with three different board thicknesses was used for board drop shock performance tests. These vehicles have three different strain and shock level condition couples per board, and are used to identify the joint stability and failure modes based on the board responses. The results revealed that joint stability is sensitive to board thickness. The board drop shock test showed that the first failure location shifts from the corner location near the standoff to the center with increased board thickness due to the shock wave response. From analysis of the thickness variation and failure cycle number, the strain rate during the pulse strain cycle is the dominant factor, which defines the life cycle number per board thickness, and not the maximum strain value. The failure location shift and the shock performance differentiation are discussed from the perspective of maximum principal strain, cycle frequency and strain rate per cycle.

A spectro-interferometric view of l Carinae's modulated pulsations

NASA Astrophysics Data System (ADS)

Anderson, Richard I.; Mérand, Antoine; Kervella, Pierre; Breitfelder, Joanne; Eyer, Laurent; Gallenne, Alexandre

Classical Cepheids are radially pulsating stars that enable important tests of stellar evolution and play a crucial role in the calibration of the local Hubble constant. l Carinae is a particularly well-known distance calibrator, being the closest long-period (P ~ 35.5 d) Cepheid and subtending the largest angular diameter. We have carried out an unprecedented observing program to investigate whether recently discovered cycle-to-cycle changes (modulations) of l Carinae's radial velocity (RV) variability are mirrored by its variability in angular size. To this end, we have secured a fully contemporaneous dataset of high-precision RVs and high-precision angular diameters. Here we provide a concise summary of our project and report preliminary results. We confirm the modulated nature of the RV variability and find tentative evidence of cycle-to-cycle differences in l Car's maximal angular diameter. Our analysis is exploring the limits of state-of-the-art instrumentation and reveals additional complexity in the pulsations of Cepheids. If confirmed, our result suggests a previously unknown pulsation cycle dependence of projection factors required for determining Cepheid distances via the Baade-Wesselink technique.

Identification of Cell Cycle-regulated Genes in Fission YeastD⃞

PubMed Central

Peng, Xu; Karuturi, R. Krishna Murthy; Miller, Lance D.; Lin, Kui; Jia, Yonghui; Kondu, Pinar; Wang, Long; Wong, Lim-Soon; Liu, Edison T.; Balasubramanian, Mohan K.; Liu, Jianhua

2005-01-01

Cell cycle progression is both regulated and accompanied by periodic changes in the expression levels of a large number of genes. To investigate cell cycle-regulated transcriptional programs in the fission yeast Schizosaccharomyces pombe, we developed a whole-genome oligonucleotide-based DNA microarray. Microarray analysis of both wild-type and cdc25 mutant cell cultures was performed to identify transcripts whose levels oscillated during the cell cycle. Using an unsupervised algorithm, we identified 747 genes that met the criteria for cell cycle-regulated expression. Peaks of gene expression were found to be distributed throughout the entire cell cycle. Furthermore, we found that four promoter motifs exhibited strong association with cell cycle phase-specific expression. Examination of the regulation of MCB motif-containing genes through the perturbation of DNA synthesis control/MCB-binding factor (DSC/MBF)-mediated transcription in arrested synchronous cdc10 mutant cell cultures revealed a subset of functional targets of the DSC/MBF transcription factor complex, as well as certain gene promoter requirements. Finally, we compared our data with those for the budding yeast Saccharomyces cerevisiae and found ∼140 genes that are cell cycle regulated in both yeasts, suggesting that these genes may play an evolutionarily conserved role in regulation of cell cycle-specific processes. Our complete data sets are available at http://giscompute.gis.a-star.edu.sg/~gisljh/CDC. PMID:15616197

Degradation analysis of a Ni-based layered positive-electrode active material cycled at elevated temperatures studied by scanning transmission electron microscopy and electron energy-loss spectroscopy

NASA Astrophysics Data System (ADS)

Kojima, Y.; Muto, S.; Tatsumi, K.; Kondo, H.; Oka, H.; Horibuchi, K.; Ukyo, Y.

We investigate the local structural changes in a positive electrode of a lithium ion secondary battery (LiNi 0.8Co 0.15Al 0.05O 2 (NCA) as the active material) associated with charge-discharge cycling at elevated temperatures by scanning transmission electron microscopy (STEM) and electron energy-loss spectroscopy (EELS). STEM-EELS spectral imaging reveals the evolution of a NiO-like phase localized near the surface and grain boundary regions after many cycles. The amounts of capacity fading and resistance increase are discussed based on the results of the semiquantitative estimation of NiO-like and other product phases. We also identify the chemical state of lithium in the NiO-like phase substituting for Ni.

Light and lunar cycle as cues to diel migration of a sound-scattering layer

NASA Astrophysics Data System (ADS)

Benoit-Bird, Kelly J.; Au, Whitlow W. L.

2001-05-01

The Hawaiian mesopelagic boundary community is an island-associated midwater scattering layer comprised of small fishes, shrimps, and squids that undergoes diel vertical as well as horizontal migrations. It has been hypothesized that light levels are an important cue or trigger for vertical migration and presumably, horizontal migration. The migration pattern of the scattering layer was measured over complete lunar cycles while the incident light levels were recorded. Due to differences in the rise and set times of the moon and cloud cover, light and lunar cycle were not completely coupled, allowing separation of the light effects of moon phase and other cues associated with lunar cycle. Four calibrated echosounder moorings were deployed with approximately even spacing, perpendicular to the leeward coast of Oahu. Moorings were deployed for one complete lunar cycle at each of three locations, recording 10 echoes every 15 min. Light sensors measured the nocturnal light intensity at 30-s intervals. Statistical analysis revealed significant effects of both light and other lunar cycle cues. Overall, the effect size was very low considering the light transmission characteristics of the subtropical Pacific, making measurement from stationary acoustic platforms critical.

Influence of temperature on the aging behavior of 18650-type lithium ion cells: A comprehensive approach combining electrochemical characterization and post-mortem analysis

NASA Astrophysics Data System (ADS)

Friesen, Alex; Mönnighoff, Xaver; Börner, Markus; Haetge, Jan; Schappacher, Falko M.; Winter, Martin

2017-02-01

The understanding of the aging behavior of lithium ion batteries in automotive and energy storage applications is essential for the acceptance of the technology. Therefore, aging experiments were conducted on commercial 18650-type state-of-the-art cells to determine the influence of the temperature during electrochemical cycling on the aging behavior of the different cell components. The cells, based on Li(Ni0.5Co0.2Mn0.3)O2 (NCM532)/graphite, were aged at 20 °C and 45 °C to different states of health. The electrochemical performance of the investigated cells shows remarkable differences depending on the cycling temperature. At contrast to the expected behavior, the cells cycled at 45 °C show a better electrochemical performance over lifetime than the cells cycled at 20 °C. Comprehensive post-mortem analyses revealed the main aging mechanisms, showing a complex interaction between electrodes and electrolyte. The main aging mechanisms of the cells cycled at 45 °C differ strongly at contrast to cells cycled at 20 °C. A strong correlation between the formed SEI, the electrolyte composition and the electrochemical performance over lifetime was observed.

Effect of light-dark cycles on hydrogen and poly-β-hydroxybutyrate production by a photoheterotrophic culture and Rhodobacter capsulatus using a dark fermentation effluent as substrate.

PubMed

Montiel Corona, Virginia; Le Borgne, Sylvie; Revah, Sergio; Morales, Marcia

2017-02-01

A Rhodobacter capsulatus strain and a photoheterotrophic culture (IZT) were cultivated to produce hydrogen under different light-dark cycles. A dark fermentation effluent (DFE) was used as substrate. It was found that IZT culture had an average cumulative hydrogen production (Paccum H 2 ) of 1300±43mLH 2 L -1 under continuous illumination and light-dark cycles of 30 or 60min. In contrast, R. capsulatus reduced its Paccum H 2 by 20% under 30:30min light-dark cycles, but tripled its poly-β-hydroxybutyrate (PHB) content (308±2mgPHB gdw -1 ) compared to continuous illumination. The highest PHB content by IZT culture was 178±10mgPHB gdw -1 under 15:15min light-dark cycles. PCR-DGGE analysis revealed that the IZT culture was mainly composed of Rhodopseudomonas palustris identified with high nucleotide similarity (99%). The evaluated cultures might be used for hydrogen and PHB production. They might provide energy savings by using light-dark cycles and DFE valorization. Copyright © 2016 Elsevier Ltd. All rights reserved.

A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells.

PubMed

Ly, Tony; Ahmad, Yasmeen; Shlien, Adam; Soroka, Dominique; Mills, Allie; Emanuele, Michael J; Stratton, Michael R; Lamond, Angus I

2014-01-01

Technological advances have enabled the analysis of cellular protein and RNA levels with unprecedented depth and sensitivity, allowing for an unbiased re-evaluation of gene regulation during fundamental biological processes. Here, we have chronicled the dynamics of protein and mRNA expression levels across a minimally perturbed cell cycle in human myeloid leukemia cells using centrifugal elutriation combined with mass spectrometry-based proteomics and RNA-Seq, avoiding artificial synchronization procedures. We identify myeloid-specific gene expression and variations in protein abundance, isoform expression and phosphorylation at different cell cycle stages. We dissect the relationship between protein and mRNA levels for both bulk gene expression and for over ∼6000 genes individually across the cell cycle, revealing complex, gene-specific patterns. This data set, one of the deepest surveys to date of gene expression in human cells, is presented in an online, searchable database, the Encyclopedia of Proteome Dynamics (http://www.peptracker.com/epd/). DOI: http://dx.doi.org/10.7554/eLife.01630.001.

Modelling urea-cycle disorder citrullinemia type 1 with disease-specific iPSCs.

PubMed

Yoshitoshi-Uebayashi, Elena Yukie; Toyoda, Taro; Yasuda, Katsutaro; Kotaka, Maki; Nomoto, Keiko; Okita, Keisuke; Yasuchika, Kentaro; Okamoto, Shinya; Takubo, Noriyuki; Nishikubo, Toshiya; Soga, Tomoyoshi; Uemoto, Shinji; Osafune, Kenji

2017-05-06

Citrullinemia type 1 (CTLN1) is a urea cycle disorder (UCD) caused by mutations of the ASS1 gene, which is responsible for production of the enzyme argininosuccinate synthetase (ASS), and classically presented as life-threatening hyperammonemia in newborns. Therapeutic options are limited, and neurological sequelae may persist. To understand the pathophysiology and find novel treatments, induced pluripotent stem cells (iPSCs) were generated from a CTLN1 patient and differentiated into hepatocyte-like cells (HLCs). CTLN1-HLCs have lower ureagenesis, recapitulating part of the patient's phenotype. l-arginine, an amino acid clinically used for UCD treatment, improved this phenotype in vitro. Metabolome analysis revealed an increase in tricarboxylic acid (TCA) cycle metabolites in CTLN1, suggesting a connection between CTLN1 and the TCA cycle. This CTLN1-iPSC model improves the understanding of CTLN1 pathophysiology and can be used to pursue new therapeutic approaches. Copyright © 2017 Elsevier Inc. All rights reserved.

A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells

PubMed Central

Ly, Tony; Ahmad, Yasmeen; Shlien, Adam; Soroka, Dominique; Mills, Allie; Emanuele, Michael J; Stratton, Michael R; Lamond, Angus I

2014-01-01

Technological advances have enabled the analysis of cellular protein and RNA levels with unprecedented depth and sensitivity, allowing for an unbiased re-evaluation of gene regulation during fundamental biological processes. Here, we have chronicled the dynamics of protein and mRNA expression levels across a minimally perturbed cell cycle in human myeloid leukemia cells using centrifugal elutriation combined with mass spectrometry-based proteomics and RNA-Seq, avoiding artificial synchronization procedures. We identify myeloid-specific gene expression and variations in protein abundance, isoform expression and phosphorylation at different cell cycle stages. We dissect the relationship between protein and mRNA levels for both bulk gene expression and for over ∼6000 genes individually across the cell cycle, revealing complex, gene-specific patterns. This data set, one of the deepest surveys to date of gene expression in human cells, is presented in an online, searchable database, the Encyclopedia of Proteome Dynamics (http://www.peptracker.com/epd/). DOI: http://dx.doi.org/10.7554/eLife.01630.001 PMID:24596151

Sirt3 promotes the urea cycle and fatty acid oxidation during dietary restriction

PubMed Central

Hallows, William C.; Yu, Wei; Smith, Brian C.; Devries, Mark K.; Ellinger, James J.; Someya, Shinichi; Shortreed, Michael R.; Prolla, Tomas; Markley, John L.; Smith, Lloyd M.; Zhao, Shimin; Guan, Kun-Liang; Denu, John M.

2011-01-01

Summary Emerging evidence suggests that protein acetylation is a broad-ranging regulatory mechanism. Here we utilize acetyl-peptide arrays and metabolomic analyses to identify substrates of mitochondrial deacetylase Sirt3. We identified ornithine transcarbamoylase (OTC) from the urea cycle, and enzymes involved in β-oxidation. Metabolomic analyses of fasted mice lacking Sirt3 (sirt3−/−) revealed alterations in β-oxidation and the urea cycle. Biochemical analysis demonstrated that Sirt3 directly deacetylates OTC and stimulates its activity. Mice under caloric restriction (CR) increased Sirt3 protein levels, leading to deacetylation and stimulation of OTC activity. In contrast, sirt3−/− mice failed to deacetylate OTC in response to CR. Inability to stimulate OTC under CR led to a failure to reduce orotic acid levels, a known outcome of OTC deficiency. Thus, Sirt3 directly regulates OTC activity and promotes the urea cycle during CR, and the results suggest that under low energy input, Sirt3 modulates mitochondria by promoting amino-acid catabolism and β-oxidation. PMID:21255725

Biochemical effects of veterinary antibiotics on proliferation and cell cycle arrest of human HEK293 cells.

PubMed

Kim, Hyeon Young; Kim, Ki-Tae; Kim, Sang Don

2012-08-01

The purpose of this study was to examine the effects of veterinary antibiotics, including amoxicillin (AMX), chlortetracycline (CTC) and tylosin (TYL), on the biochemical mechanism of human embryonic kidney cells (HEK293). CTC and TYL inhibited HEK293 cell proliferation, in both time- and dose-dependent manners, and changed the cell morphology; whereas, AMX showed no cytotoxic effects. The cell cycle analysis of CTC and TYL revealed G1-arrest in HEK293 cells. Western blot analysis also showed that CTC and TYL affected the activation of DNA damage responsive proteins, as well as cell cycle regulatory proteins, such as p53, p21(Waf1/Cip1) and Rb protein, which are crucial in the G1-S transition. The activation of p21(Waf1/Cip1) was significantly up-regulated over time, but there was no change in the level of CDK2 expression. The results of this study suggest that veterinary antibiotics, even at low level concentrations on continuous exposure, can potentially risk the development of human cells.

Seasonal Patterns in Microbial Community Composition in Denitrifying Bioreactors Treating Subsurface Agricultural Drainage.

PubMed

Porter, Matthew D; Andrus, J Malia; Bartolerio, Nicholas A; Rodriguez, Luis F; Zhang, Yuanhui; Zilles, Julie L; Kent, Angela D

2015-10-01

Denitrifying bioreactors, consisting of water flow control structures and a woodchip-filled trench, are a promising approach for removing nitrate from agricultural subsurface or tile drainage systems. To better understand the seasonal dynamics and the ecological drivers of the microbial communities responsible for denitrification in these bioreactors, we employed microbial community "fingerprinting" techniques in a time-series examination of three denitrifying bioreactors over 2 years, looking at bacteria, fungi, and the denitrifier functional group responsible for the final step of complete denitrification. Our analysis revealed that microbial community composition responds to depth and seasonal variation in moisture content and inundation of the bioreactor media, as well as temperature. Using a geostatistical analysis approach, we observed recurring temporal patterns in bacterial and denitrifying bacterial community composition in these bioreactors, consistent with annual cycling. The fungal communities were more stable, having longer temporal autocorrelations, and did not show significant annual cycling. These results suggest a recurring seasonal cycle in the denitrifying bioreactor microbial community, likely due to seasonal variation in moisture content.

Na2.5Fe1.75(SO4)3/Ketjen/rGO: An advanced cathode composite for sodium ion batteries

NASA Astrophysics Data System (ADS)

Goñi, A.; Iturrondobeitia, A.; Gil de Muro, I.; Lezama, L.; Rojo, T.

2017-11-01

An advanced cathode composite Na2.5Fe1.75(SO4)3/Ketjen/rGO for sodium ion batteries has been prepared, joining together the excellent electrochemical properties of the three components: off stoichiometric iron sulfate alluaudite, Ketjen Black carbon and reduced graphene oxide (rGO). This electrode material has been exhaustively characterized by XRD, thermogravimetric analysis, Raman spectroscopy and SEM and TEM microscopy. The study has demonstrated that a high quality electrode material has been designed containing a porous sulfate core properly coated by interweaved rGO fibers and Ketjen Black nanoparticles. The electrochemical study has revealed an excellent performance providing specific capacities close to the theoretical one at 1C. Additionally, this composite has shown a very good rate capability and a great cycling stability for at least 200 cycles maintaining a coulombic efficiency of 96%. The post mortem analysis, which includes EPR and XPS measurements, has demonstrated that the carbonaceous coating on the composite generates a stable and protective SEI layer over the active material guaranteeing a successful performance during a long cycle life.

Thickness effects of yttria-doped ceria interlayers on solid oxide fuel cells

NASA Astrophysics Data System (ADS)

Fan, Zeng; An, Jihwan; Iancu, Andrei; Prinz, Fritz B.

2012-11-01

Determining the optimal thickness range of the interlayed yttria-doped ceria (YDC) films promises to further enhance the performance of solid oxide fuel cells (SOFCs) at low operating temperatures. The YDC interlayers are fabricated by the atomic layer deposition (ALD) method with one super cycle of the YDC deposition consisting of 6 ceria deposition cycles and one yttria deposition cycle. YDC films of various numbers of ALD super cycles, ranging from 2 to 35, are interlayered into bulk fuel cells with a 200 um thick yttria-stabilized zirconia (YSZ) electrolyte. Measurements and analysis of the linear sweep voltammetry of these fuel cells reveal that the performance of the given cells is maximized at 10 super cycles. Auger elemental mapping and X-ray photoelectron spectroscopy (XPS) techniques are employed to determine the film completeness, and they verify 10 super cycles of YDC to be the critical thickness point. This optimal YDC interlayer condition (6Ce1Y × 10 super cycles) is applied to the case of micro fuel cells as well, and the average performance enhancement factor is 1.4 at operating temperatures of 400 and 450 °C. A power density of 1.04 W cm-2 at 500 °C is also achieved with the optimal YDC recipe.

Physiology and Endocrinology of the Ovarian Cycle in Macaques

PubMed Central

Weinbauer, Gerhard F.; Niehoff, Marc; Niehaus, Michael; Srivastav, Shiela; Fuchs, Antje; Van Esch, Eric; Cline, J. Mark

2009-01-01

Macaques provide excellent models for preclinical testing and safety assessment of female reproductive toxicants. Currently, cynomolgus monkeys are the predominant species for (reproductive) toxicity testing. Marmosets and rhesus monkeys are being used occasionally. The authors provide a brief review on physiology and endocrinology of the cynomolgus monkey ovarian cycle, practical guidance on assessment and monitoring of ovarian cyclicity, and new data on effects of social housing on ovarian cyclicity in toxicological studies. In macaques, cycle monitoring is achieved using daily vaginal smears for menstruation combined with cycle-timed frequent sampling for steroid and peptide hormone analysis. Owing to requirements of frequent and timed blood sampling, it is not recommended to incorporate these special evaluations into a general toxicity study design. Marmosets lack external signs of ovarian cyclicity, and cycle monitoring is done by regular determinations of progesterone. Cynomolgus and marmoset monkeys do not exhibit seasonal variations in ovarian activity, whereas such annual rhythm is pronounced in rhesus monkeys. Studies on pair- and group-housed cynomolgus monkeys revealed transient alterations in the duration and endocrinology of the ovarian cycle followed by return to normal cyclicity after approximately six months. This effect is avoided if the animals had contact with each other prior to mingling. These experiments also demonstrated that synchronization of ovarian cycles did not occur. PMID:20852722

Senescence-associated microRNAs target cell cycle regulatory genes in normal human lung fibroblasts.

PubMed

Markopoulos, Georgios S; Roupakia, Eugenia; Tokamani, Maria; Vartholomatos, George; Tzavaras, Theodore; Hatziapostolou, Maria; Fackelmayer, Frank O; Sandaltzopoulos, Raphael; Polytarchou, Christos; Kolettas, Evangelos

2017-10-01

Senescence recapitulates the ageing process at the cell level. A senescent cell stops dividing and exits the cell cycle. MicroRNAs (miRNAs) acting as master regulators of transcription, have been implicated in senescence. In the current study we investigated and compared the expression of miRNAs in young versus senescent human fibroblasts (HDFs), and analysed the role of mRNAs expressed in replicative senescent HFL-1 HDFs. Cell cycle analysis confirmed that HDFs accumulated in G 1 /S cell cycle phase. Nanostring analysis of isolated miRNAs from young and senescent HFL-1 showed that a distinct set of 15 miRNAs were significantly up-regulated in senescent cells including hsa-let-7d-5p, hsa-let-7e-5p, hsa-miR-23a-3p, hsa-miR-34a-5p, hsa-miR-122-5p, hsa-miR-125a-3p, hsa-miR-125a-5p, hsa-miR-125b-5p, hsa-miR-181a-5p, hsa-miR-221-3p, hsa-miR-222-3p, hsa-miR-503-5p, hsa-miR-574-3p, hsa-miR-574-5p and hsa-miR-4454. Importantly, pathway analysis of miRNA target genes down-regulated during replicative senescence in a public RNA-seq data set revealed a significant high number of genes regulating cell cycle progression, both G 1 /S and G 2 /M cell cycle phase transitions and telomere maintenance. The reduced expression of selected miRNA targets, upon replicative and oxidative-stress induced senescence, such as the cell cycle effectors E2F1, CcnE, Cdc6, CcnB1 and Cdc25C was verified at the protein and/or RNA levels. Induction of G1/S cell cycle phase arrest and down-regulation of cell cycle effectors correlated with the up-regulation of miR-221 upon both replicative and oxidative stress-induced senescence. Transient expression of miR-221/222 in HDFs promoted the accumulation of HDFs in G1/S cell cycle phase. We propose that miRNAs up-regulated during replicative senescence may act in concert to induce cell cycle phase arrest and telomere erosion, establishing a senescent phenotype. Copyright © 2017 Elsevier Inc. All rights reserved.

SU-E-J-227: Breathing Pattern Consistency and Reproducibility: Comparative Analysis for Supine and Prone Body Positioning

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

Laugeman, E; Weiss, E; Chen, S

2014-06-01

Purpose: Evaluate and compare the cycle-to-cycle consistency of breathing patterns and their reproducibility over the course of treatment, for supine and prone positioning. Methods: Respiratory traces from 25 patients were recorded for sequential supine/prone 4DCT scans acquired prior to treatment, and during the course of the treatment (weekly or bi-weekly). For each breathing cycle, the average(AVE), end-of-exhale(EoE) and end-of-inhale( EoI) locations were identified using in-house developed software. In addition, the mean values and variations for the above quantities were computed for each breathing trace. F-tests were used to compare the cycle-to-cycle consistency of all pairs of sequential supine and pronemore » scans. Analysis of variances was also performed using population means for AVE, EoE and EoI to quantify differences between the reproducibility of prone and supine respiration traces over the treatment course. Results: Consistency: Cycle-to-cycle variations are less in prone than supine in the pre-treatment and during-treatment scans for AVE, EoE and EoI points, for the majority of patients (differences significant at p<0.05). The few cases where the respiratory pattern had more variability in prone appeared to be random events. Reproducibility: The reproducibility of breathing patterns (supine and prone) improved as treatment progressed, perhaps due to patients becoming more comfortable with the procedure. However, variability in supine position continued to remain significantly larger than in prone (p<0.05), as indicated by the variance analysis of population means for the pretreatment and subsequent during-treatment scans. Conclusions: Prone positioning stabilizes breathing patterns in most subjects investigated in this study. Importantly, a parallel analysis of the same group of patients revealed a tendency towards increasing motion amplitude of tumor targets in prone position regardless of their size or location; thus, the choice for body positioning during radiation therapy will have to consider the clinical relevance of the two opposing trends - breathing consistency and motion amplitude.« less

A year in the life of a thrombolite: comparative metatranscriptomics reveals dynamic metabolic changes over diel and seasonal cycles.

PubMed

Louyakis, Artemis S; Gourlé, Hadrien; Casaburi, Giorgio; Bonjawo, Rachelle M E; Duscher, Alexandrea A; Foster, Jamie S

2018-02-01

Microbialites are one of the oldest known ecosystems on Earth and the coordinated metabolisms and activities of these mineral-depositing communities have had a profound impact on the habitability of the planet. Despite efforts to understand the diversity and metabolic potential of these systems, there has not been a systematic molecular analysis of the transcriptional changes that occur within a living microbialite over time. In this study, we generated metatranscriptomic libraries from actively growing thrombolites, a type of microbialite, throughout diel and seasonal cycles and observed dynamic shifts in the population and metabolic transcriptional activity. The most transcribed genes in all seasons were associated with photosynthesis, but only transcripts associated with photosystem II exhibited diel cycling. Photosystem I transcripts were constitutively expressed at all time points including midnight and sunrise. Transcripts associated with nitrogen fixation, methanogenesis and dissimilatory sulfate reduction exhibited diel cycling, and variability between seasons. Networking analysis of the metatranscriptomes showed correlated expression patterns helping to elucidate how metabolic interactions are coordinated within the thrombolite community. These findings have identified distinctive temporal patterns within the thrombolites and will serve an important foundation to understand the mechanisms by which these communities form and respond to changes in their environment. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Rapid Cdc13 turnover and telomere length homeostasis are controlled by Cdk1-mediated phosphorylation of Cdc13.

PubMed

Tseng, Shun-Fu; Shen, Zih-Jie; Tsai, Hung-Ji; Lin, Yi-Hsuan; Teng, Shu-Chun

2009-06-01

Budding yeast telomerase is mainly activated by Tel1/Mec1 (yeast ATM/ATR) on Cdc13 from late S to G2 phase of the cell cycle. Here, we demonstrated that the telomerase-recruitment domain of Cdc13 is also phosphorylated by Cdk1 at the same cell cycle stage as the Tel1/Mec1-dependent regulation. Phosphor-specific gel analysis demonstrated that Cdk1 phosphorylates residues 308 and 336 of Cdc13. The residue T308 of Cdc13 is critical for efficient Mec1-mediated S306 phosphorylation in vitro. Phenotypic analysis in vivo revealed that the mutations in the Cdc13 S/TP motifs phosphorylated by Cdk1 caused cell cycle delay and telomere shortening and these phenotypes could be partially restored by the replacement with a negative charge residue. In the absence of Ku or Tel1, Cdk1-mediated phosphorylation of Cdc13 showed no effect on telomere length maintenance. Moreover, this Cdk1-mediated phosphorylation was required to promote the regular turnover of Cdc13. Together these results demonstrate that Cdk1 phosphorylates the telomerase recruitment domain of Cdc13, thereby preserves optimal function and expression level of Cdc13 for precise telomere replication and cell cycle progression.

Comparative analysis of waste-to-energy alternatives for a low-capacity power plant in Brazil.

PubMed

Ferreira, Elzimar Tadeu de F; Balestieri, José Antonio P

2018-03-01

The Brazilian National Solid Waste Policy has been implemented with some difficulty, especially in convincing the different actors of society about the importance of conscious awareness among every citizen and businesses concerning adequate solid waste disposal and recycling. Technologies for recovering energy from municipal solid waste were considered in National Solid Waste Policy (NSWP), given that their technical and environmental viability is ensured, being the landfill biogas burning in internal combustion engines and solid waste incineration suggested options. In the present work, an analysis of current technologies and a collection of basic data on electricity generation using biogas from waste/liquid effluents is presented, as well as an assessment of the installation of a facility that harnesses biogas from waste or liquid effluents for producing electricity. Two combined cycle concepts were evaluated with capacity in the range 4-11 MW, gas turbine burning landfill biogas and an incinerator that burns solid waste hybrid cycle, and a solid waste gasification system to burn syngas in gas turbines. A comparative analysis of them demonstrated that the cycle with gasification from solid waste has proved to be technically more appealing than the hybrid cycle integrated with incineration because of its greater efficiency and considering the initially defined guidelines for electricity generation. The economic analysis does not reveal significant attractive values; however, this is not a significant penalty to the project given the fact that this is a pilot low-capacity facility, which is intended to be constructed to demonstrate appropriate technologies of energy recovery from solid waste.

Modeling East Asian Dust and Its Radiative Feedbacks in CAM4-BAM

NASA Astrophysics Data System (ADS)

Xie, Xiaoning; Liu, Xiaodong; Che, Huizheng; Xie, Xiaoxun; Wang, Hongli; Li, Jiandong; Shi, Zhengguo; Liu, Yangang

2018-01-01

East Asian dust and its radiative feedbacks are analyzed by the use of the fourth version of the Community Atmosphere Model (CAM4) with a bulk aerosol model parameterization (BAM) for the dust size distribution (CAM4-BAM). Two numerical experiments are conducted and intercompared: one with (Active) and one without (Passive) the radiative effects of dust aerosols. This CAM4-BAM captures the main spatial distribution of the dust aerosol optical depth (AOD) and the dust surface concentrations over East Asia, with positive correlations with the local observational data on annual and seasonal means. A comparative analysis of the Active and Passive experiments reveals that consideration of the dust-radiation interaction can significantly reduce dust emissions, loading, transport, and dry and wet depositions over East Asia, which is opposite to the enhanced dust cycle over North Africa. Further analysis of the contrasting dust-radiation feedbacks between North Africa and East Asia shows that over North Africa, the dust radiative forcing significantly increases the surface temperature and 10 m wind speed, whereas it decreases the surface temperature and the surface wind speeds over East Asia. These contrasting radiative effects, in turn, result in distinct dust cycle changes over these two regions. Mechanistic analysis reveals that the radiative contrasts between East Asia and North Africa are mainly due to the differences in their regional surface albedo, dust vertical distribution, and size distribution.

Real time myocardial contrast echocardiography during supine bicycle stress and continuous infusion of contrast agent. Cutoff values for myocardial contrast replenishment discriminating abnormal myocardial perfusion.

PubMed

Miszalski-Jamka, Tomasz; Kuntz-Hehner, Stefanie; Schmidt, Harald; Hammerstingl, Christoph; Tiemann, Klaus; Ghanem, Alexander; Troatz, Clemens; Lüderitz, Berndt; Omran, Heyder

2007-07-01

Myocardial contrast echocardiography (MCE) is a new imaging modality for diagnosing coronary artery disease (CAD). The aim of our study was to evaluate feasibility of qualitative myocardial contrast replenishment (RP) assessment during supine bicycle stress MCE and find out cutoff values for such analysis, which could allow accurate detection of CAD. Forty-four consecutive patients, scheduled for coronary angiography (CA) underwent supine bicycle stress two-dimensional echocardiography (2DE). During the same session, MCE was performed at peak stress and post stress. Ultrasound contrast agent (SonoVue) was administered in continuous mode using an infusion pump (BR-INF 100, Bracco Research). Seventeen-segment model of left ventricle was used in analysis. MCE was assessed off-line in terms of myocardial contrast opacification and RP. RP was evaluated on the basis of the number of cardiac cycles required to refill the segment with contrast after its prior destruction with high-power frames. Determination of cutoff values for RP assessment was performed by means of reference intervals and receiver operating characteristic analysis. Quantitative CA was carried out using CAAS system. MCE could be assessed in 42 patients. CA revealed CAD in 25 patients. Calculated cutoff values for RP-analysis (peak-stress RP >3 cardiac cycles and difference between peak stress and post stress RP >0 cardiac cycles) provided sensitive (88%) and accurate (88%) detection of CAD. Sensitivity and accuracy of 2DE were 76% and 79%, respectively. Qualitative RP-analysis based on the number of cardiac cycles required to refill myocardium with contrast is feasible during supine bicycle stress MCE and enables accurate detection of CAD.

Manufacture of low carbon astroloy turbine disk shapes by hot isostatic pressing. Volume 2, project 1

NASA Technical Reports Server (NTRS)

Eng, R. D.; Evans, D. J.

1979-01-01

The performance of a hot isotatic pressed disk installed in an experimental engine and exposed to realistic operating conditions in a 150-hour engine test and a 1000 cycle endurance test is documented. Post test analysis, based on visual, fluorescent penetrant and dimensional inspection, revealed no defects in the disk and indicated that the disk performed satisfactorily.

New insights on ecosystem mercury cycling revealed by stable isotopes of mercury in water flowing from a headwater peatland catchment

Treesearch

Glenn E. Woerndle; Martin Tsz-Ki Tsui; Stephen D. Sebestyen; Joel D. Blum; Xiangping Nie; Randall K. Kolka

2018-01-01

Stable isotope compositions of mercury (Hg) were measured in the outlet stream and in soil cores at different landscape positions in a 9.7-ha boreal upland-peatland catchment. An acidic permanganate/persulfate digestion procedure was validated for water samples with high dissolved organic matter (DOM) concentrations through Hg spike addition analysis. We report a...

Direct effects of temperature on forest nitrogen cycling revealed through analysis of long-term watershed records

Treesearch

E.N. Jack Brookshire; Stefan Gerber; Jackson R. Webster; James M. Vose; Wayne T. Swank

2010-01-01

The microbial conversion of organic nitrogen (N) to plant available forms is a critical determinant of plant growth and carbon sequestration in forests worldwide. In temperate zones, microbial activity is coupled to variations in temperature, yet at the ecosystem level, microbial N mineralization seems to play a minor role in determining patterns of N loss. Rather, N...

Controlled initiation of chromosomal replication in Escherichia coli requires functional Hda protein.

PubMed

Camara, Johanna Eltz; Skarstad, Kirsten; Crooke, Elliott

2003-05-01

Regulatory inactivation of DnaA helps ensure that the Escherichia coli chromosome is replicated only once per cell cycle, through accelerated hydrolysis of active replication initiator ATP-DnaA to inactive ADP-DnaA. Analysis of deltahda strains revealed that the regulatory inactivation of DnaA component Hda is necessary for maintaining controlled initiation but not for cell growth or viability.

Muscle biopsies from human muscle diseases with myopathic pathology reveal common alterations in mitochondrial function.

PubMed

Sunitha, Balaraju; Gayathri, Narayanappa; Kumar, Manish; Keshava Prasad, Thottethodi Subrahmanya; Nalini, Atchayaram; Padmanabhan, Balasundaram; Srinivas Bharath, Muchukunte Mukunda

2016-07-01

Muscle diseases are clinically and genetically heterogeneous and manifest as dystrophic, inflammatory and myopathic pathologies, among others. Our previous study on the cardiotoxin mouse model of myodegeneration and inflammation linked muscle pathology with mitochondrial damage and oxidative stress. In this study, we investigated whether human muscle diseases display mitochondrial changes. Muscle biopsies from muscle disease patients, represented by dysferlinopathy (dysfy) (dystrophic pathology; n = 43), polymyositis (PM) (inflammatory pathology; n = 24), and distal myopathy with rimmed vacuoles (DMRV) (distal myopathy; n = 31) were analyzed. Mitochondrial damage (ragged blue and COX-deficient fibers) was revealed in dysfy, PM, and DMRV cases by enzyme histochemistry (SDH and COX-SDH), electron microscopy (vacuolation and altered cristae) and biochemical assays (significantly increased ADP/ATP ratio). Proteomic analysis of muscle mitochondria from all three muscle diseases by isobaric tag for relative and absolute quantitation labeling and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis demonstrated down-regulation of electron transport chain (ETC) complex subunits, assembly factors and Krebs cycle enzymes. Interestingly, 80 of the under-expressed proteins were common among the three pathologies. Assay of ETC and Krebs cycle enzyme activities validated the MS data. Mitochondrial proteins from muscle pathologies also displayed higher tryptophan (Trp) oxidation and the same was corroborated in the cardiotoxin model. Molecular modeling predicted Trp oxidation to alter the local structure of mitochondrial proteins. Our data highlight mitochondrial alterations in muscle pathologies, represented by morphological changes, altered mitochondrial proteome and protein oxidation, thereby establishing the role of mitochondrial damage in human muscle diseases. We investigated whether human muscle diseases display mitochondrial changes. Muscle biopsies from dysferlinopathy (Dysfy), polymyositis (PM), and distal myopathy with rimmed vacuoles (DMRV) displayed morphological and biochemical evidences of mitochondrial dysfunction. Proteomic analysis revealed down-regulation of electron transport chain (ETC) subunits, assembly factors, and tricarboxylic acid (TCA) cycle enzymes, with 80 proteins common among the three pathologies. Mitochondrial proteins from muscle pathologies also displayed higher Trp oxidation that could alter the local structure. Cover image for this issue: doi: 10.1111/jnc.13324. © 2016 International Society for Neurochemistry.

Improving the Performance at Elevated Temperature of High Voltage Graphite/LiNi 0.5Mn 1.5O 4 Cells with Added Lithium Catechol Dimethyl Borate

DOE PAGES

Dong, Yingnan; Demeaux, Julien; Zhang, Yuzi; ...

2016-12-13

Performance of LiNi 0.5Mn 1.5O 4/graphite cells cycled to 4.8 V at 55°C with the 1.2 M LiPF 6 in EC/EMC (3/7, STD electrolyte) with and without added lithium catechol dimethyl borate (LiCDMB) has been investigated. The incorporation of 0.5 wt% LiCDMB to the STD electrolyte results in an improved capacity retention and coulombic efficiency upon cycling at 55°C. Ex-situ analysis of the electrode surfaces via a combination of SEM, TEM, and XPS reveals that oxidation of LiCDMB at high potential results in the deposition of a passivation layer on the electrode surface, preventing transition metal ion dissolution from themore » cathode and subsequent deposition on the anode. NMR investigations of the bulk electrolyte stored at 85°C reveals that added LiCDMB prevents the thermal decomposition of LiPF 6.« less

Improving the Performance at Elevated Temperature of High Voltage Graphite/LiNi 0.5Mn 1.5O 4 Cells with Added Lithium Catechol Dimethyl Borate

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

Dong, Yingnan; Demeaux, Julien; Zhang, Yuzi

Performance of LiNi 0.5Mn 1.5O 4/graphite cells cycled to 4.8 V at 55°C with the 1.2 M LiPF 6 in EC/EMC (3/7, STD electrolyte) with and without added lithium catechol dimethyl borate (LiCDMB) has been investigated. The incorporation of 0.5 wt% LiCDMB to the STD electrolyte results in an improved capacity retention and coulombic efficiency upon cycling at 55°C. Ex-situ analysis of the electrode surfaces via a combination of SEM, TEM, and XPS reveals that oxidation of LiCDMB at high potential results in the deposition of a passivation layer on the electrode surface, preventing transition metal ion dissolution from themore » cathode and subsequent deposition on the anode. NMR investigations of the bulk electrolyte stored at 85°C reveals that added LiCDMB prevents the thermal decomposition of LiPF 6.« less

Effect of oxygen minimum zone formation on communities of marine protists

PubMed Central

Orsi, William; Song, Young C; Hallam, Steven; Edgcomb, Virginia

2012-01-01

Changes in ocean temperature and circulation patterns compounded by human activities are leading to oxygen minimum zone (OMZ) expansion with concomitant alteration in nutrient and climate active trace gas cycling. Here, we report the response of microbial eukaryote populations to seasonal changes in water column oxygen-deficiency using Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island British Columbia, as a model ecosystem. We combine small subunit ribosomal RNA gene sequencing approaches with multivariate statistical methods to reveal shifts in operational taxonomic units during successive stages of seasonal stratification and renewal. A meta-analysis is used to identify common and unique patterns of community composition between Saanich Inlet and the anoxic/sulfidic Cariaco Basin (Venezuela) and Framvaren Fjord (Norway) to show shared and unique responses of microbial eukaryotes to oxygen and sulfide in these three environments. Our analyses also reveal temporal fluctuations in rare populations of microbial eukaryotes, particularly anaerobic ciliates, that may be of significant importance to the biogeochemical cycling of methane in OMZs. PMID:22402396

Imaging the fate of histone Cse4 reveals de novo replacement in S phase and subsequent stable residence at centromeres

PubMed Central

Wisniewski, Jan; Hajj, Bassam; Chen, Jiji; Mizuguchi, Gaku; Xiao, Hua; Wei, Debbie; Dahan, Maxime; Wu, Carl

2014-01-01

The budding yeast centromere contains Cse4, a specialized histone H3 variant. Fluorescence pulse-chase analysis of an internally tagged Cse4 reveals that it is replaced with newly synthesized molecules in S phase, remaining stably associated with centromeres thereafter. In contrast, C-terminally-tagged Cse4 is functionally impaired, showing slow cell growth, cell lethality at elevated temperatures, and extra-centromeric nuclear accumulation. Recent studies using such strains gave conflicting findings regarding the centromeric abundance and cell cycle dynamics of Cse4. Our findings indicate that internally tagged Cse4 is a better reporter of the biology of this histone variant. Furthermore, the size of centromeric Cse4 clusters was precisely mapped with a new 3D-PALM method, revealing substantial compaction during anaphase. Cse4-specific chaperone Scm3 displays steady-state, stoichiometric co-localization with Cse4 at centromeres throughout the cell cycle, while undergoing exchange with a nuclear pool. These findings suggest that a stable Cse4 nucleosome is maintained by dynamic chaperone-in-residence Scm3. DOI: http://dx.doi.org/10.7554/eLife.02203.001 PMID:24844245

Trophic Mode-Dependent Proteomic Analysis Reveals Functional Significance of Light-Independent Chlorophyll Synthesis in Synechocystis sp. PCC 6803.

PubMed

Fang, Longfa; Ge, Haitao; Huang, Xiahe; Liu, Ye; Lu, Min; Wang, Jinlong; Chen, Weiyang; Xu, Wu; Wang, Yingchun

2017-01-09

The photosynthetic model organism Synechocystis sp. PCC 6803 can grow in different trophic modes, depending on the availability of light and exogenous organic carbon source. However, how the protein profile changes to facilitate the cells differentially propagate in different modes has not been comprehensively investigated. Using isobaric labeling-based quantitative proteomics, we simultaneously identified and quantified 45% Synechocystis proteome across four different trophic modes, i.e., autotrophic, heterotrophic, photoheterotrophic, and mixotrophic modes. Among the 155 proteins that are differentially expressed across four trophic modes, proteins involved in nitrogen assimilation and light-independent chlorophyll synthesis are dramatically upregulated in the mixotrophic mode, concomitant with a dramatic increase of P II phosphorylation that senses carbon and nitrogen assimilation status. Moreover, functional study using a mutant defective in light-independent chlorophyll synthesis revealed that this pathway is important for chlorophyll accumulation under a cycled light/dark illumination regime, a condition mimicking day/night cycles in certain natural habitats. Collectively, these results provide the most comprehensive information on trophic mode-dependent protein expression in cyanobacterium, and reveal the functional significance of light-independent chlorophyll synthesis in trophic growth. Copyright © 2017 The Author. Published by Elsevier Inc. All rights reserved.

High Concentration of Melatonin Regulates Leaf Development by Suppressing Cell Proliferation and Endoreduplication in Arabidopsis.

PubMed

Wang, Qiannan; An, Bang; Shi, Haitao; Luo, Hongli; He, Chaozu

2017-05-05

N -acetyl-5-methoxytryptamine (Melatonin), as a crucial messenger in plants, functions in adjusting biological rhythms, stress tolerance, plant growth and development. Several studies have shown the retardation effect of exogenous melatonin treatment on plant growth and development. However, the in vivo role of melatonin in regulating plant leaf growth and the underlying mechanism are still unclear. In this study, we found that high concentration of melatonin suppressed leaf growth in Arabidopsis by reducing both cell size and cell number. Further kinetic analysis of the fifth leaves showed that melatonin remarkably inhibited cell division rate. Additionally, flow cytometic analysis indicated that melatonin negatively regulated endoreduplication during leaf development. Consistently, the expression analysis revealed that melatonin regulated the transcriptional levels of key genes of cell cycle and ribosome. Taken together, this study suggests that high concentration of melatonin negatively regulated the leaf growth and development in Arabidopsis , through modulation of endoreduplication and the transcripts of cell cycle and ribosomal key genes.

High Concentration of Melatonin Regulates Leaf Development by Suppressing Cell Proliferation and Endoreduplication in Arabidopsis

PubMed Central

Wang, Qiannan; An, Bang; Shi, Haitao; Luo, Hongli; He, Chaozu

2017-01-01

N-acetyl-5-methoxytryptamine (Melatonin), as a crucial messenger in plants, functions in adjusting biological rhythms, stress tolerance, plant growth and development. Several studies have shown the retardation effect of exogenous melatonin treatment on plant growth and development. However, the in vivo role of melatonin in regulating plant leaf growth and the underlying mechanism are still unclear. In this study, we found that high concentration of melatonin suppressed leaf growth in Arabidopsis by reducing both cell size and cell number. Further kinetic analysis of the fifth leaves showed that melatonin remarkably inhibited cell division rate. Additionally, flow cytometic analysis indicated that melatonin negatively regulated endoreduplication during leaf development. Consistently, the expression analysis revealed that melatonin regulated the transcriptional levels of key genes of cell cycle and ribosome. Taken together, this study suggests that high concentration of melatonin negatively regulated the leaf growth and development in Arabidopsis, through modulation of endoreduplication and the transcripts of cell cycle and ribosomal key genes. PMID:28475148

Analysis of the weekly cycle in the atmosphere near Moscow

NASA Astrophysics Data System (ADS)

Gruzdev, A. N.

2013-03-01

Using the spectral method and the method of grouping by days of week, we analyzed the weekly cycles by standard air sounding data obtained at the Dolgoprudny station near Moscow and by the results of measurements of NO2 content in the stratosphere and the atmospheric boundary layer at the Zvenigorod Research Station of the Obukhov Institute of Atmospheric Physics, Russian Academy of Sciences, in 1990-2010. We revealed weekly cycles of the NO2 content in the vertical column of the stratosphere, temperature, geopotential, meridional wind velocity in the troposphere and lower stratosphere, and the tropopause height in the warm half of the year (mid-April to mid-October). The weekly variations in temperature in the troposphere are positive in the first half of the week and negative in the second half, and the variations in temperature in the tropopause layer and in the lower stratosphere are opposite in sign to the tropospheric variations. The weekly cycle of the tropopause height is approximately in phase with the cycle of tropospheric temperature, and the weekly cycle of the NO2 content in the stratospheric column is opposite in phase to the cycle of the tropopause height. Weekly variations were also observed in the total ozone content over Moscow. This finding was confirmed by calculations based on regression relationships between the vertical distribution of ozone and tropopause height. Conceptual mechanisms of weekly cycles were proposed.

Menstrual cycle variation in women's preferences for the scent of symmetrical men.

PubMed Central

Gangestad, S W; Thornhill, R

1998-01-01

Evidence suggests that female sexual preferences change across the menstrual cycle. Women's extra-pair copulations tend to occur in their most fertile period, whereas their intra-pair copulations tend to be more evenly spread out across the cycle. This pattern is consistent with women preferentially seeking men who evidence phenotypic markers of genetic benefits just before and during ovulation. This study examined whether women's olfactory preferences for men's scent would tend to favour the scent of more symmetrical men, most notably during the women's fertile period. College women sniffed and rated the attractiveness of the scent of 41 T-shirts worn over a period of two nights by different men. Results indicated that normally cycling (non-pill using) women near the peak fertility of their cycle tended to prefer the scent of shirts worn by symmetrical men. Normally ovulating women at low fertility within their cycle, and women using a contraceptive pill, showed no significant preference for either symmetrical or asymmetrical men's scent. A separate analysis revealed that, within the set of normally cycling women, individual women's preference for symmetry correlated with their probability of conception, given the actuarial value associated with the day of the cycle they reported at the time they smelled the shirts. Potential sexual selection processes and proximate mechanisms accounting for these findings are discussed. PMID:9633114

Cell cycle, differentiation and tissue-independent expression of ribosomal protein L37.

PubMed

Su, S; Bird, R C

1995-09-15

A unique human cDNA (hG1.16) that encodes a mRNA of 450 nucleotides was isolated from a subtractive library derived from HeLa cells. The relative expression level of hG1.16 during different cell-cycle phases was determined by Northern-blot analysis of cells synchronized by double-thymidine block and serum deprivation/refeeding. hG1.16 was constitutively expressed during all phases of the cell cycle, including the quiescent phase when even most constitutively expressed genes experience some suppression of expression. The expression level of hG1.16 did not change during terminal differentiation of myoblasts to myotubes, during which cells become permanently post-mitotic. Examination of other tissues revealed that the relative expression level of hG1.16 was constitutive in all embryonic mouse tissues examined, including brain, eye, heart, kidney, liver, lung and skeletal muscle. This was unusual in that expression was not down-modulated during differentiation and did not vary appreciably between tissue types. Analysis by inter-species Northern-blot analysis revealed that hG1.16 was highly conserved among all vertebrates studied (from fish to humans but not in insects). DNA sequence analysis of hG1.16 revealed a high level of similarity to rat ribosomal protein L37, identifying hG1.16 as a new member of this multigene family. The deduced amino acid sequence of hG1.16 was identical to rat ribosomal protein L37 that contained 97 amino acids, many of which are highly positively charged (15 arginine and 14 lysine residues with a predicted M(r) of 11,065). hG1.16 protein has a single C2-C2 zinc-finger-like motif which is also present in rat ribosomal protein L37. Using primers designed from the sequence of hG1.16, unique bovine and rat cDNAs were also isolated by 5'-rapid-amplification of cDNA ends. DNA sequences of bovine and rat G1.16, clones were 92.8% and 92.2% similar to human G1.16 while the deduced amino acid sequences derived from bovine and rat cDNAs each differed by a single amino acid from the sequence of hG1.16 and the published rat L37 sequence. Southern-blot analysis revealed that hG1.16 exists in multiple copies in human, rat and mouse genomes. These G1.16 clones encode unique human, rat and bovine members of the ribosomal protein L37 gene family, which are constitutively expressed even during transitions from quiescence to active cell proliferation or terminal differentiation, in all tissues and all vertebrates investigated.

Spatial methods for deriving crop rotation history

NASA Astrophysics Data System (ADS)

Mueller-Warrant, George W.; Trippe, Kristin M.; Whittaker, Gerald W.; Anderson, Nicole P.; Sullivan, Clare S.

2017-08-01

Benefits of converting 11 years of remote sensing classification data into cropping history of agricultural fields included measuring lengths of rotation cycles and identifying specific sequences of intervening crops grown between final years of old grass seed stands and establishment of new ones. Spatial and non-spatial methods were complementary. Individual-year classification errors were often correctable in spreadsheet-based non-spatial analysis, whereas their presence in spatial data generally led to exclusion of fields from further analysis. Markov-model testing of non-spatial data revealed that year-to-year cropping sequences did not match average frequencies for transitions among crops grown in western Oregon, implying that rotations into new grass seed stands were influenced by growers' desires to achieve specific objectives. Moran's I spatial analysis of length of time between consecutive grass seed stands revealed that clustering of fields was relatively uncommon, with high and low value clusters only accounting for 7.1 and 6.2% of fields.

Impact of neoadjuvant chemotherapy and postoperative adjuvant chemotherapy cycles on survival of patients with advanced-stage ovarian cancer

PubMed Central

Chung, Young Shin; Kim, Yun-Ji; Lee, Inha; Nam, Eun Ji; Kim, Sunghoon; Kim, Sang Wun; Kim, Young Tae

2017-01-01

Background There is currently no consensus regarding the optimal number of chemotherapy cycles to be administered before and after interval debulking surgery (IDS) in patients with advanced ovarian cancer. This study aimed to evaluate the impact of the number of neoadjuvant chemotherapy (NAC) and postoperative adjuvant chemotherapy (POAC) cycles on the survival of patients with advanced ovarian cancer undergoing NAC/IDS/POAC. Methods We retrospectively reviewed data from 203 patients who underwent NAC/IDS/POAC at Yonsei Cancer Hospital between 2006 and 2016. All patients underwent taxane plus carboplatin chemotherapy for NAC and POAC. The patient outcomes were analyzed according to the number of NAC, POAC, and total chemotherapy (NAC+POAC) cycles. Results Patients who received fewer than 6 cycles of total chemotherapy (n = 8) had poorer progression-free survival (PFS) and overall survival (OS) than those completing at least 6 cycles (p = 0.005 and p<0.001, respectively). Among patients who completed at least 6 cycles of total chemotherapy (n = 189), Kaplan-Meier analysis revealed no significant difference in either PFS or OS according to the number of NAC cycles (1–3 vs. ≥4; p = 0.136 and p = 0.267, respectively). Among patients who experienced complete remission after 3 cycles of POAC (n = 98), the addition of further POAC cycles did not improve the PFS or OS (3 vs. ≥4; p = 0.641 and p = 0.104, respectively). Conclusion IDS after 4 cycles of NAC may be a safe and effective option when completing 6 cycles of total chemotherapy. Furthermore, the addition of more than 3 cycles of POAC does not appear to influence the survival of patients achieving completion remission after 3 cycles of POAC. PMID:28873393

Impact of neoadjuvant chemotherapy and postoperative adjuvant chemotherapy cycles on survival of patients with advanced-stage ovarian cancer.

PubMed

Chung, Young Shin; Kim, Yun-Ji; Lee, Inha; Lee, Jung-Yun; Nam, Eun Ji; Kim, Sunghoon; Kim, Sang Wun; Kim, Young Tae

2017-01-01

There is currently no consensus regarding the optimal number of chemotherapy cycles to be administered before and after interval debulking surgery (IDS) in patients with advanced ovarian cancer. This study aimed to evaluate the impact of the number of neoadjuvant chemotherapy (NAC) and postoperative adjuvant chemotherapy (POAC) cycles on the survival of patients with advanced ovarian cancer undergoing NAC/IDS/POAC. We retrospectively reviewed data from 203 patients who underwent NAC/IDS/POAC at Yonsei Cancer Hospital between 2006 and 2016. All patients underwent taxane plus carboplatin chemotherapy for NAC and POAC. The patient outcomes were analyzed according to the number of NAC, POAC, and total chemotherapy (NAC+POAC) cycles. Patients who received fewer than 6 cycles of total chemotherapy (n = 8) had poorer progression-free survival (PFS) and overall survival (OS) than those completing at least 6 cycles (p = 0.005 and p<0.001, respectively). Among patients who completed at least 6 cycles of total chemotherapy (n = 189), Kaplan-Meier analysis revealed no significant difference in either PFS or OS according to the number of NAC cycles (1-3 vs. ≥4; p = 0.136 and p = 0.267, respectively). Among patients who experienced complete remission after 3 cycles of POAC (n = 98), the addition of further POAC cycles did not improve the PFS or OS (3 vs. ≥4; p = 0.641 and p = 0.104, respectively). IDS after 4 cycles of NAC may be a safe and effective option when completing 6 cycles of total chemotherapy. Furthermore, the addition of more than 3 cycles of POAC does not appear to influence the survival of patients achieving completion remission after 3 cycles of POAC.

How Hinge Positioning in Cross-Country Ski Bindings Affect Exercise Efficiency, Cycle Characteristics and Muscle Coordination during Submaximal Roller Skiing

PubMed Central

Bolger, Conor M.; Sandbakk, Øyvind; Ettema, Gertjan; Federolf, Peter

2016-01-01

The purposes of the current study were to 1) test if the hinge position in the binding of skating skis has an effect on gross efficiency or cycle characteristics and 2) investigate whether hinge positioning affects synergistic components of the muscle activation in six lower leg muscles. Eleven male skiers performed three 4-min sessions at moderate intensity while cross-country ski-skating and using a klapskate binding. Three different positions were tested for the binding’s hinge, ranging from the front of the first distal phalange to the metatarsal-phalangeal joint. Gross efficiency and cycle characteristics were determined, and the electromyographic (EMG) signals of six lower limb muscles were collected. EMG signals were wavelet transformed, normalized, joined into a multi-dimensional vector, and submitted to a principle component analysis (PCA). Our results did not reveal any changes to gross efficiency or cycle characteristics when altering the hinge position. However, our EMG analysis found small but significant effects of hinge positioning on muscle coordinative patterns (P < 0.05). The changed patterns in muscle activation are in alignment with previously described mechanisms that explain the effects of hinge positioning in speed-skating klapskates. Finally, the within-subject results of the EMG analysis suggested that in addition to the between-subject effects, further forms of muscle coordination patterns appear to be employed by some, but not all participants. PMID:27203597

Numerical analysis of the hemodynamic effect of plaque ulceration in the stenotic carotid artery bifurcation

NASA Astrophysics Data System (ADS)

Wong, Emily Y.; Milner, Jaques S.; Steinman, David A.; Poepping, Tamie L.; Holdsworth, David W.

2009-02-01

The presence of ulceration in carotid artery plaque is an independent risk factor for thromboembolic stroke. However, the associated pathophysiological mechanisms - in particular the mechanisms related to the local hemodynamics in the carotid artery bifurcation - are not well understood. We investigated the effect of carotid plaque ulceration on the local time-varying three-dimensional flow field using computational fluid dynamics (CFD) models of a stenosed carotid bifurcation geometry, with and without the presence of ulceration. CFD analysis of each model was performed with a spatial finite element discretization of over 150,000 quadratic tetrahedral elements and a temporal discretization of 4800 timesteps per cardiac cycle, to adequately resolve the flow field and pulsatile flow, respectively. Pulsatile flow simulations were iterated for five cardiac cycles to allow for cycle-to-cycle analysis following the damping of initial transients in the solution. Comparison between models revealed differences in flow patterns induced by flow exiting from the region of the ulcer cavity, in particular, to the shape, orientation and helicity of the high velocity jet through the stenosis. The stenotic jet in both models exhibited oscillatory motion, but produced higher levels of phase-ensembled turbulence intensity in the ulcerated model. In addition, enhanced out-of-plane recirculation and helical flow was observed in the ulcerated model. These preliminary results suggest that local fluid behaviour may contribute to the thrombogenic risk associated with plaque ulcerations in the stenotic carotid artery bifurcation.

Identification of multiple dmrt1s in catfish: localization, dimorphic expression pattern, changes during testicular cycle and after methyltestosterone treatment.

PubMed

Raghuveer, K; Senthilkumaran, B

2009-05-01

The double sex and mab-3 related (DM) transcription factor 1 (dmrt1) plays an important role in testicular differentiation. Here, we report cloning of multiple dmrt1s, a full-length and two alternative spliced forms from adult catfish (Clarias gariepinus) testis, which encode predicted proteins of 287 (dmrt1a), 253 (dmrt1b) and 233 (dmrt1c) amino acid residues respectively. Interestingly, dmrt1c lacks the majority of the DM domain. Multiple dmrt1s (dmrt1a and dmrt1c) were obtained from Clarias batrachus as well. Tissue distribution (transcript and protein) of catfish dmrt1 revealed exclusive expression in testis. Semi-quantitative RT-PCR revealed the presence of multiple dmrt1s with high levels of dmrt1a in adult testis but not in ovary. Real-time RT-PCR analysis during testicular cycle showed higher levels of dmrt1 transcripts in preparatory and pre-spawning when compared with spawning and post-spawning phases. Immunocytochemical and immunofluorescence localization revealed the presence of catfish Dmrt1 protein in spermatogonia and spermatocytes, which indicates plausible role in spermatogenesis. Histological analysis indicated initiation of gonadal sex differentiation in catfish around 40-50 days after hatching. The potential role for dmrt1 in testicular differentiation is evident from its stage-dependent elevated expression in developing testis. Furthermore, dimorphic expressions of dmrt1s were evident at different stages of gonadal development or recrudescence in catfish. Treatment of methyl testosterone (MT) during early stages of gonadal sex differentiation resulted in adult males. Interestingly, we also obtained MT-treated fishes having ova-testis gonads. Analysis of dmrt1, sox9a, foxl2 and cyp19a1 expression patterns in MT-treated gonads revealed tissue-specific pattern. These results together suggest that multiple dmrt1s are testis-specific markers in catfish.

Identification of Methanogenic archaea in the Hyporheic Sediment of Sitka Stream

PubMed Central

Buriánková, Iva; Brablcová, Lenka; Mach, Václav; Dvořák, Petr; Chaudhary, Prem Prashant; Rulík, Martin

2013-01-01

Methanogenic archaea produce methane as a metabolic product under anoxic conditions and they play a crucial role in the global methane cycle. In this study molecular diversity of methanogenic archaea in the hyporheic sediment of the lowland stream Sitka (Olomouc, Czech Republic) was analyzed by PCR amplification, cloning and sequencing analysis of the methyl coenzyme M reductase alpha subunit (mcrA) gene. Sequencing analysis of 60 clones revealed 24 different mcrA phylotypes from hyporheic sedimentary layers to a depth of 50 cm. Phylotypes were affiliated with Methanomicrobiales, Methanosarcinales and Methanobacteriales orders. Only one phylotype remains unclassified. The majority of the phylotypes showed higher affiliation with uncultured methanogens than with known methanogenic species. The presence of relatively rich assemblage of methanogenic archaea confirmed that methanogens may be an important component of hyporheic microbial communities and may affect CH4 cycling in rivers. PMID:24278322

Fiat lux! Phylogeny and bioinformatics shed light on GABA functions in plants.

PubMed

Renault, Hugues

2013-06-01

The non-protein amino acid γ-aminobutyric acid (GABA) accumulates in plants in response to a wide variety of environmental cues. Recent data point toward an involvement of GABA in tricarboxylic acid (TCA) cycle activity and respiration, especially in stressed roots. To gain further insights into potential GABA functions in plants, phylogenetic and bioinformatic approaches were undertaken. Phylogenetic reconstruction of the GABA transaminase (GABA-T) protein family revealed the monophyletic nature of plant GABA-Ts. However, this analysis also pointed to the common origin of several plant aminotransferases families, which were found more similar to plant GABA-Ts than yeast and human GABA-Ts. A computational analysis of AtGABA-T co-expressed genes was performed in roots and in stress conditions. This second approach uncovered a strong connection between GABA metabolism and glyoxylate cycle during stress. Both in silico analyses open new perspectives and hypotheses for GABA metabolic functions in plants.

Fiat lux!

PubMed Central

Renault, Hugues

2013-01-01

The non-protein amino acid γ-aminobutyric acid (GABA) accumulates in plants in response to a wide variety of environmental cues. Recent data point toward an involvement of GABA in tricarboxylic acid (TCA) cycle activity and respiration, especially in stressed roots. To gain further insights into potential GABA functions in plants, phylogenetic and bioinformatic approaches were undertaken. Phylogenetic reconstruction of the GABA transaminase (GABA-T) protein family revealed the monophyletic nature of plant GABA-Ts. However, this analysis also pointed to the common origin of several plant aminotransferases families, which were found more similar to plant GABA-Ts than yeast and human GABA-Ts. A computational analysis of AtGABA-T co-expressed genes was performed in roots and in stress conditions. This second approach uncovered a strong connection between GABA metabolism and glyoxylate cycle during stress. Both in silico analyses open new perspectives and hypotheses for GABA metabolic functions in plants. PMID:23518583

The long non-coding RNA HOTAIR promotes the proliferation of serous ovarian cancer cells through the regulation of cell cycle arrest and apoptosis

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

Qiu, Jun-jun; Department of Obstetrics and Gynecology of Shanghai Medical College, Fudan University, 138 Yixueyuan Road, Shanghai 200032; Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, 413 Zhaozhou Road, Shanghai 200011

HOX transcript antisense RNA (HOTAIR) is a well-known long non-coding RNA (lncRNA) whose dysregulation correlates with poor prognosis and malignant progression in many forms of cancer. Here, we investigate the expression pattern, clinical significance, and biological function of HOTAIR in serous ovarian cancer (SOC). Clinically, we found that HOTAIR levels were overexpressed in SOC tissues compared with normal controls and that HOTAIR overexpression was correlated with an advanced FIGO stage and a high histological grade. Multivariate analysis revealed that HOTAIR is an independent prognostic factor for predicting overall survival in SOC patients. We demonstrated that HOTAIR silencing inhibited A2780 andmore » OVCA429 SOC cell proliferation in vitro and that the anti-proliferative effects of HOTAIR silencing also occurred in vivo. Further investigation into the mechanisms responsible for the growth inhibitory effects by HOTAIR silencing revealed that its knockdown resulted in the induction of cell cycle arrest and apoptosis through certain cell cycle-related and apoptosis-related proteins. Together, these results highlight a critical role of HOTAIR in SOC cell proliferation and contribute to a better understanding of the importance of dysregulated lncRNAs in SOC progression. - Highlights: • HOTAIR overexpression correlates with an aggressive tumour phenotype and a poor prognosis in SOC. • HOTAIR promotes SOC cell proliferation both in vitro and in vivo. • The proliferative role of HOTAIR is associated with regulation of the cell cycle and apoptosis.« less

Genome-Wide Studies Reveal that H3K4me3 Modification in Bivalent Genes Is Dynamically Regulated during the Pluripotent Cell Cycle and Stabilized upon Differentiation.

PubMed

Grandy, Rodrigo A; Whitfield, Troy W; Wu, Hai; Fitzgerald, Mark P; VanOudenhove, Jennifer J; Zaidi, Sayyed K; Montecino, Martin A; Lian, Jane B; van Wijnen, André J; Stein, Janet L; Stein, Gary S

2016-02-15

Stem cell phenotypes are reflected by posttranslational histone modifications, and this chromatin-related memory must be mitotically inherited to maintain cell identity through proliferative expansion. In human embryonic stem cells (hESCs), bivalent genes with both activating (H3K4me3) and repressive (H3K27me3) histone modifications are essential to sustain pluripotency. Yet, the molecular mechanisms by which this epigenetic landscape is transferred to progeny cells remain to be established. By mapping genomic enrichment of H3K4me3/H3K27me3 in pure populations of hESCs in G2, mitotic, and G1 phases of the cell cycle, we found striking variations in the levels of H3K4me3 through the G2-M-G1 transition. Analysis of a representative set of bivalent genes revealed that chromatin modifiers involved in H3K4 methylation/demethylation are recruited to bivalent gene promoters in a cell cycle-dependent fashion. Interestingly, bivalent genes enriched with H3K4me3 exclusively during mitosis undergo the strongest upregulation after induction of differentiation. Furthermore, the histone modification signature of genes that remain bivalent in differentiated cells resolves into a cell cycle-independent pattern after lineage commitment. These results establish a new dimension of chromatin regulation important in the maintenance of pluripotency. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Genome-Wide Studies Reveal that H3K4me3 Modification in Bivalent Genes Is Dynamically Regulated during the Pluripotent Cell Cycle and Stabilized upon Differentiation

PubMed Central

Grandy, Rodrigo A.; Whitfield, Troy W.; Wu, Hai; Fitzgerald, Mark P.; VanOudenhove, Jennifer J.; Zaidi, Sayyed K.; Montecino, Martin A.; Lian, Jane B.; van Wijnen, André J.; Stein, Janet L.

2015-01-01

Stem cell phenotypes are reflected by posttranslational histone modifications, and this chromatin-related memory must be mitotically inherited to maintain cell identity through proliferative expansion. In human embryonic stem cells (hESCs), bivalent genes with both activating (H3K4me3) and repressive (H3K27me3) histone modifications are essential to sustain pluripotency. Yet, the molecular mechanisms by which this epigenetic landscape is transferred to progeny cells remain to be established. By mapping genomic enrichment of H3K4me3/H3K27me3 in pure populations of hESCs in G2, mitotic, and G1 phases of the cell cycle, we found striking variations in the levels of H3K4me3 through the G2-M-G1 transition. Analysis of a representative set of bivalent genes revealed that chromatin modifiers involved in H3K4 methylation/demethylation are recruited to bivalent gene promoters in a cell cycle-dependent fashion. Interestingly, bivalent genes enriched with H3K4me3 exclusively during mitosis undergo the strongest upregulation after induction of differentiation. Furthermore, the histone modification signature of genes that remain bivalent in differentiated cells resolves into a cell cycle-independent pattern after lineage commitment. These results establish a new dimension of chromatin regulation important in the maintenance of pluripotency. PMID:26644406

Can You Ride a Bicycle? The Ability to Ride a Bicycle Prevents Reduced Social Function in Older Adults With Mobility Limitation

PubMed Central

Sakurai, Ryota; Kawai, Hisashi; Yoshida, Hideyo; Fukaya, Taro; Suzuki, Hiroyuki; Kim, Hunkyung; Hirano, Hirohiko; Ihara, Kazushige; Obuchi, Shuichi; Fujiwara, Yoshinori

2016-01-01

Background The health benefits of bicycling in older adults with mobility limitation (ML) are unclear. We investigated ML and functional capacity of older cyclists by evaluating their instrumental activities of daily living (IADL), intellectual activity, and social function. Methods On the basis of interviews, 614 community-dwelling older adults (after excluding 63 participants who never cycled) were classified as cyclists with ML, cyclists without ML, non-cyclists with ML (who ceased bicycling due to physical difficulties), or non-cyclists without ML (who ceased bicycling for other reasons). A cyclist was defined as a person who cycled at least a few times per month, and ML was defined as difficulty walking 1 km or climbing stairs without using a handrail. Functional capacity and physical ability were evaluated by standardized tests. Results Regular cycling was documented in 399 participants, and 74 of them (18.5%) had ML; among non-cyclists, 49 had ML, and 166 did not. Logistic regression analysis for evaluating the relationship between bicycling and functional capacity revealed that non-cyclists with ML were more likely to have reduced IADL and social function compared to cyclists with ML. However, logistic regression analysis also revealed that the risk of bicycle-related falls was significantly associated with ML among older cyclists. Conclusions The ability and opportunity to bicycle may prevent reduced IADL and social function in older adults with ML, although older adults with ML have a higher risk of falls during bicycling. It is important to develop a safe environment for bicycling for older adults. PMID:26902165

Differential gene expression profiling of endometrium during the mid-luteal phase of the estrous cycle between a repeat breeder (RB) and non-RB cows.

PubMed

Hayashi, Ken-Go; Hosoe, Misa; Kizaki, Keiichiro; Fujii, Shiori; Kanahara, Hiroko; Takahashi, Toru; Sakumoto, Ryosuke

2017-03-23

Repeat breeding directly affects reproductive efficiency in cattle due to an increase in services per conception and calving interval. This study aimed to investigate whether changes in endometrial gene expression profile are involved in repeat breeding in cows. Differential gene expression profiles of the endometrium were investigated during the mid-luteal phase of the estrous cycle between repeat breeder (RB) and non-RB cows using microarray analysis. The caruncular (CAR) and intercaruncular (ICAR) endometrium of both ipsilateral and contralateral uterine horns to the corpus luteum were collected from RB (inseminated at least three times but not pregnant) and non-RB cows on Day 15 of the estrous cycle (4 cows/group). Global gene expression profiles of these endometrial samples were analyzed with a 15 K custom-made oligo-microarray for cattle. Immunohistochemistry was performed to investigate the cellular localization of proteins of three identified transcripts in the endometrium. Microarray analysis revealed that 405 and 397 genes were differentially expressed in the CAR and ICAR of the ipsilateral uterine horn of RB, respectively when compared with non-RB cows. In the contralateral uterine horn, 443 and 257 differentially expressed genes were identified in the CAR and ICAR of RB, respectively when compared with non-RB cows. Gene ontology analysis revealed that genes involved in development and morphogenesis were mainly up-regulated in the CAR of RB cows. In the ICAR of both the ipsilateral and contralateral uterine horns, genes related to the metabolic process were predominantly enriched in the RB cows when compared with non-RB cows. In the analysis of the whole uterus (combining the data above four endometrial compartments), RB cows showed up-regulation of 37 genes including PRSS2, GSTA3 and PIPOX and down-regulation of 39 genes including CHGA, KRT35 and THBS4 when compared with non-RB cows. Immunohistochemistry revealed that CHGA, GSTA3 and PRSS2 proteins were localized in luminal and glandular epithelial cells and stroma of the endometrium. The present study showed that endometrial gene expression profiles are different between RB and non-RB cows. The identified candidate endometrial genes and functions in each endometrial compartment may contribute to bovine reproductive performance.

Cyclin C influences the timing of mitosis in fission yeast

PubMed Central

Banyai, Gabor; Szilagyi, Zsolt; Baraznenok, Vera; Khorosjutina, Olga; Gustafsson, Claes M.

2017-01-01

The multiprotein Mediator complex is required for the regulated transcription of nearly all RNA polymerase II–dependent genes. Mediator contains the Cdk8 regulatory subcomplex, which directs periodic transcription and influences cell cycle progression in fission yeast. Here we investigate the role of CycC, the cognate cyclin partner of Cdk8, in cell cycle control. Previous reports suggested that CycC interacts with other cellular Cdks, but a fusion of CycC to Cdk8 reported here did not cause any obvious cell cycle phenotypes. We find that Cdk8 and CycC interactions are stabilized within the Mediator complex and the activity of Cdk8-CycC is regulated by other Mediator components. Analysis of a mutant yeast strain reveals that CycC, together with Cdk8, primarily affects M-phase progression but mutations that release Cdk8 from CycC control also affect timing of entry into S phase. PMID:28515143

Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock.

PubMed

Bagnoud, Alexandre; Chourey, Karuna; Hettich, Robert L; de Bruijn, Ino; Andersson, Anders F; Leupin, Olivier X; Schwyn, Bernhard; Bernier-Latmani, Rizlan

2016-10-14

The Opalinus Clay formation will host geological nuclear waste repositories in Switzerland. It is expected that gas pressure will build-up due to hydrogen production from steel corrosion, jeopardizing the integrity of the engineered barriers. In an in situ experiment located in the Mont Terri Underground Rock Laboratory, we demonstrate that hydrogen is consumed by microorganisms, fuelling a microbial community. Metagenomic binning and metaproteomic analysis of this deep subsurface community reveals a carbon cycle driven by autotrophic hydrogen oxidizers belonging to novel genera. Necromass is then processed by fermenters, followed by complete oxidation to carbon dioxide by heterotrophic sulfate-reducing bacteria, which closes the cycle. This microbial metabolic web can be integrated in the design of geological repositories to reduce pressure build-up. This study shows that Opalinus Clay harbours the potential for chemolithoautotrophic-based system, and provides a model of microbial carbon cycle in deep subsurface environments where hydrogen and sulfate are present.

Functional profiles of orphan membrane transporters in the life cycle of the malaria parasite

PubMed Central

Kenthirapalan, Sanketha; Waters, Andrew P.; Matuschewski, Kai; Kooij, Taco W. A.

2016-01-01

Assigning function to orphan membrane transport proteins and prioritizing candidates for detailed biochemical characterization remain fundamental challenges and are particularly important for medically relevant pathogens, such as malaria parasites. Here we present a comprehensive genetic analysis of 35 orphan transport proteins of Plasmodium berghei during its life cycle in mice and Anopheles mosquitoes. Six genes, including four candidate aminophospholipid transporters, are refractory to gene deletion, indicative of essential functions. We generate and phenotypically characterize 29 mutant strains with deletions of individual transporter genes. Whereas seven genes appear to be dispensable under the experimental conditions tested, deletion of any of the 22 other genes leads to specific defects in life cycle progression in vivo and/or host transition. Our study provides growing support for a potential link between heavy metal homeostasis and host switching and reveals potential targets for rational design of new intervention strategies against malaria. PMID:26796412

Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock

PubMed Central

Bagnoud, Alexandre; Chourey, Karuna; Hettich, Robert L.; de Bruijn, Ino; Andersson, Anders F.; Leupin, Olivier X.; Schwyn, Bernhard; Bernier-Latmani, Rizlan

2016-01-01

The Opalinus Clay formation will host geological nuclear waste repositories in Switzerland. It is expected that gas pressure will build-up due to hydrogen production from steel corrosion, jeopardizing the integrity of the engineered barriers. In an in situ experiment located in the Mont Terri Underground Rock Laboratory, we demonstrate that hydrogen is consumed by microorganisms, fuelling a microbial community. Metagenomic binning and metaproteomic analysis of this deep subsurface community reveals a carbon cycle driven by autotrophic hydrogen oxidizers belonging to novel genera. Necromass is then processed by fermenters, followed by complete oxidation to carbon dioxide by heterotrophic sulfate-reducing bacteria, which closes the cycle. This microbial metabolic web can be integrated in the design of geological repositories to reduce pressure build-up. This study shows that Opalinus Clay harbours the potential for chemolithoautotrophic-based system, and provides a model of microbial carbon cycle in deep subsurface environments where hydrogen and sulfate are present. PMID:27739431

Genome and metagenome enabled analyses reveal new insight into the global biogeography and potential urea utilization in marine Thaumarchaeota.

NASA Astrophysics Data System (ADS)

Ahlgren, N.; Parada, A. E.; Fuhrman, J. A.

2016-02-01

Marine Thaumarchaea are an abundant, important group of marine microbial communities as they fix carbon, oxidize ammonium, and thus contribute to key N and C cycles in the oceans. From an enrichment culture, we have sequenced the complete genome of a new Thaumarchaeota strain, SPOT01. Analysis of this genome and other Thaumarchaeal genomes contributes new insight into its role in N cycling and clarifies the broader biogeography of marine Thaumarchaeal genera. Phylogenomics of Thaumarchaeota genomes reveal coherent separation into clusters roughly equivalent to the genus level, and SPOT01 represents a new genus of marine Thaumarchaea. Competitive fragment recruitment of globally distributed metagenomes from TARA, Ocean Sampling Day, and those generated from a station off California shows that the SPOT01 genus is often the most abundant genus, especially where total Thaumarchaea are most abundant in the overall community. The SPOT01 genome contains urease genes allowing it to use an alternative form of N. Genomic and metagenomic analysis also reveal that among planktonic genomes and populations, the urease genes in general are more frequently found in members of the SPOT01 genus and another genus dominant in deep waters, thus we predict these two genera contribute most significantly to urea utilization among marine Thaumarchaea. Recruitment also revealed broader biogeographic and ecological patterns of the putative genera. The SPOT01 genus was most abundant at colder temperatures (<16 C), reflective of its dominance at subpolar to polar latitudes (>45 degrees). The genus containing Nitrosopumilus maritimus had the highest temperature range, and the genus containing Candidatus Nitrosopelagicus brevis was typically most abundant at intermediate temperatures and intermediate latitudes ( 35-45 degrees). Together these genome and metagenome enabled analyses provide significant new insight into the ecology and biogeochemical contributions of marine archaea.

Body mass index is an independent risk factor for the development of endometrial polyps in patients undergoing in vitro fertilization.

PubMed

Onalan, Reside; Onalan, Gogsen; Tonguc, Esra; Ozdener, Tulin; Dogan, Muammer; Mollamahmutoglu, Leyla

2009-04-01

To determine the subgroup of patients in whom office hysteroscopy should be routinely performed before an in vitro fertilization (IVF) program. Retrospective cohort analysis. Tertiary education and research hospital. Two hundred twenty-three patients who underwent a uterine evaluation by office hysteroscopy before the IVF and embryo transfer cycle. The office hysteroscopy was performed in the follicular phase of the menstrual cycle before the IVF cycle. The office findings: number of polyps, number of multiple polyps, and polyp size. Patients with polycystic ovary syndrome (PCOS) had a higher number of endometrial polyps, but the difference was not statistically significant (28.9% vs. 18.3%). When comparing the patients according to BMI, patients with BMI >or=30 had a statistically significantly higher number of endometrial polyps versus BMI <30 (52% vs. 15%). On the other hand, obesity was positively correlated with the occurrence of polyps, size of the polyps, and occurrence of multiple number of polyps in the correlation analysis. In addition, logistic regression analysis using age, obesity, duration of infertility, and estradiol levels revealed that obesity was an independent prognostic factor for the development of endometrial polyps. Office hysteroscopy should be performed in patients with BMI >or=30 because obesity may act as an initiator for the pathogenesis of endometrial polyps.

Laser cutting of various materials: Kerf width size analysis and life cycle assessment of cutting process

NASA Astrophysics Data System (ADS)

Yilbas, Bekir Sami; Shaukat, Mian Mobeen; Ashraf, Farhan

2017-08-01

Laser cutting of various materials including Ti-6Al-4V alloy, steel 304, Inconel 625, and alumina is carried out to assess the kerf width size variation along the cut section. The life cycle assessment is carried out to determine the environmental impact of the laser cutting in terms of the material waste during the cutting process. The kerf width size is formulated and predicted using the lump parameter analysis and it is measured from the experiments. The influence of laser output power and laser cutting speed on the kerf width size variation is analyzed using the analytical tools including scanning electron and optical microscopes. In the experiments, high pressure nitrogen assisting gas is used to prevent oxidation reactions in the cutting section. It is found that the kerf width size predicted from the lump parameter analysis agrees well with the experimental data. The kerf width size variation increases with increasing laser output power. However, this behavior reverses with increasing laser cutting speed. The life cycle assessment reveals that material selection for laser cutting is critical for the environmental protection point of view. Inconel 625 contributes the most to the environmental damages; however, recycling of the waste of the laser cutting reduces this contribution.

Thermoeconomic analysis of an integrated multi-effect desalination thermal vapor compression (MED-TVC) system with a trigeneration system using triple-pressure HRSG

NASA Astrophysics Data System (ADS)

Ghaebi, Hadi; Abbaspour, Ghader

2018-05-01

In this research, thermoeconomic analysis of a multi-effect desalination thermal vapor compression (MED-TVC) system integrated with a trigeneration system with a gas turbine prime mover is carried out. The integrated system comprises of a compressor, a combustion chamber, a gas turbine, a triple-pressure (low, medium and high pressures) heat recovery steam generator (HRSG) system, an absorption chiller cycle (ACC), and a multi-effect desalination (MED) system. Low pressure steam produced in the HRSG is used to drive absorption chiller cycle, medium pressure is used in desalination system and high pressure superheated steam is used for heating purposes. For thermodynamic and thermoeconomic analysis of the proposed integrated system, Engineering Equation Solver (EES) is used by employing mass, energy, exergy, and cost balance equations for each component of system. The results of the modeling showed that with the new design, the exergy efficiency in the base design will increase to 57.5%. In addition, thermoeconomic analysis revealed that the net power, heating, fresh water and cooling have the highest production cost, respectively.

Transcriptomic analysis reveals metabolic switches and surface remodeling as key processes for stage transition in Trypanosoma cruzi

PubMed Central

Greif, Gonzalo; Rodriguez, Matias; Alvarez-Valin, Fernando

2017-01-01

American trypanosomiasis is a chronic and endemic disease which affects millions of people. Trypanosoma cruzi, its causative agent, has a life cycle that involves complex morphological and functional transitions, as well as a variety of environmental conditions. This requires a tight regulation of gene expression, which is achieved mainly by post-transcriptional regulation. In this work we conducted an RNAseq analysis of the three major life cycle stages of T. cruzi: amastigotes, epimastigotes and trypomastigotes. This analysis allowed us to delineate specific transcriptomic profiling for each stage, and also to identify those biological processes of major relevance in each state. Stage specific expression profiling evidenced the plasticity of T. cruzi to adapt quickly to different conditions, with particular focus on membrane remodeling and metabolic shifts along the life cycle. Epimastigotes, which replicate in the gut of insect vectors, showed higher expression of genes related to energy metabolism, mainly Krebs cycle, respiratory chain and oxidative phosphorylation related genes, and anabolism related genes associated to nucleotide and steroid biosynthesis; also, a general down-regulation of surface glycoprotein coding genes was seen at this stage. Trypomastigotes, living extracellularly in the bloodstream of mammals, express a plethora of surface proteins and signaling genes involved in invasion and evasion of immune response. Amastigotes mostly express membrane transporters and genes involved in regulation of cell cycle, and also express a specific subset of surface glycoprotein coding genes. In addition, these results allowed us to improve the annotation of the Dm28c genome, identifying new ORFs and set the stage for construction of networks of co-expression, which can give clues about coded proteins of unknown functions. PMID:28286708

Comparative long-term trend analysis of daily weather conditions with daily pollen concentrations in Brussels, Belgium

NASA Astrophysics Data System (ADS)

Bruffaerts, Nicolas; De Smedt, Tom; Delcloo, Andy; Simons, Koen; Hoebeke, Lucie; Verstraeten, Caroline; Van Nieuwenhuyse, An; Packeu, Ann; Hendrickx, Marijke

2018-03-01

A clear rise in seasonal and annual temperatures, a gradual increase of total radiation, and a relative trend of change in seasonal precipitation have been observed for the last four decades in Brussels (Belgium). These local modifications may have a direct and indirect public health impact by altering the timing and intensity of allergenic pollen seasons. In this study, we assessed the statistical correlations (Spearman's test) between pollen concentration and meteorological conditions by using long-term daily datasets of 11 pollen types (8 trees and 3 herbaceous plants) and 10 meteorological parameters observed in Brussels between 1982 and 2015. Furthermore, we analyzed the rate of change in the annual cycle of the same selected pollen types by the Mann-Kendall test. We revealed an overall trend of increase in daily airborne tree pollen (except for the European beech tree) and an overall trend of decrease in daily airborne pollen from herbaceous plants (except for Urticaceae). These results revealed an earlier onset of the flowering period for birch, oak, ash, plane, grasses, and Urticaceae. Finally, the rates of change in pollen annual cycles were shown to be associated with the rates of change in the annual cycles of several meteorological parameters such as temperature, radiation, humidity, and rainfall.

[Effect of the estrous cycle stage on sensitivity to pheromone 2,5-dimethylpyrazine in the house mouse Mus musculus].

PubMed

Daev, E V; Dukel'skaia, A V; Kazarova, V E; Fil'kina, Ia A

2007-01-01

Frequency of cytogenetic disturbances was estimated in mitotically dividing bone marrow cells of CBA strain female mice after the 24-h long action of pheromone 2,5-dimethylpyrazine (2,5-DMP). The stage of the estrous cycle of each animal was taken into account at the moment of the end of the pheromone action. The analysis was performed using the anatelophase method that allows evaluating frequencies of various types of disturbances--bridges, fragments, delayed chromosomes. The spontaneous level of the mitotic disturbances revealed by the anatelophase method in animals of the control group amounts to 5.4 %. Action of pheromone 2,5-dimethylpyrasine induced the mitosis disturbances detected in the dividing bone marrow cells at the anaphase-telophase stage in the females at the di- + postestrus stage. The corresponding frequency of disturbances after the pheromone action was equal to 9.2%. In the female in estrus, the mitotic disturbance level amounted 6.7%, which did not differ statistically significantly from control. It is suggested that differences in the female mouse hormonal state at different estrous cycle stages affect sensitivity to olfactory signals. Mechanisms of the revealed effect and significance of the differences in sensitivity to pheromone for reproductive processes are discussed.

Comparative long-term trend analysis of daily weather conditions with daily pollen concentrations in Brussels, Belgium.

PubMed

Bruffaerts, Nicolas; De Smedt, Tom; Delcloo, Andy; Simons, Koen; Hoebeke, Lucie; Verstraeten, Caroline; Van Nieuwenhuyse, An; Packeu, Ann; Hendrickx, Marijke

2018-03-01

A clear rise in seasonal and annual temperatures, a gradual increase of total radiation, and a relative trend of change in seasonal precipitation have been observed for the last four decades in Brussels (Belgium). These local modifications may have a direct and indirect public health impact by altering the timing and intensity of allergenic pollen seasons. In this study, we assessed the statistical correlations (Spearman's test) between pollen concentration and meteorological conditions by using long-term daily datasets of 11 pollen types (8 trees and 3 herbaceous plants) and 10 meteorological parameters observed in Brussels between 1982 and 2015. Furthermore, we analyzed the rate of change in the annual cycle of the same selected pollen types by the Mann-Kendall test. We revealed an overall trend of increase in daily airborne tree pollen (except for the European beech tree) and an overall trend of decrease in daily airborne pollen from herbaceous plants (except for Urticaceae). These results revealed an earlier onset of the flowering period for birch, oak, ash, plane, grasses, and Urticaceae. Finally, the rates of change in pollen annual cycles were shown to be associated with the rates of change in the annual cycles of several meteorological parameters such as temperature, radiation, humidity, and rainfall.

Gene structure, expression, and DNA methylation characteristics of sea cucumber cyclin B gene during aestivation.

PubMed

Zhu, Aijun; Chen, Muyan; Zhang, Xiumei; Storey, Kenneth B

2016-12-05

The sea cucumber, Apostichopus japonicus, is a good model for studying environmentally-induced aestivation by a marine invertebrate. One of the central requirements of aestivation is the repression of energy-expensive cellular processes such as cell cycle progression. The present study identified the gene structure of the cell cycle regulator, cyclin B, and detected the expression levels of this gene over three stages of the annual aestivation-arousal cycle. Furthermore, the DNA methylation characteristics of cyclin B were analyzed in non-aestivation and deep-aestivation stages of sea cucumbers. We found that the cyclin B promoter contains a CpG island, three CCAAT-boxes and three cell cycle gene homology regions (CHRs). Application of qRT-PCR analysis showed significant downregulation of cyclin B transcript levels during deep-aestivation in comparison with non-aestivation in both intestine and longitudinal muscle, and these returned to basal levels after arousal from aestivation. Methylation analysis of the cyclin B core promoter revealed that its methylation level showed significant differences between non-aestivation and deep-aestivation stages (p<0.05) and interestingly, a positive correlation between Cyclin B transcripts expression and methylation levels of the core promoter was also observed. Our findings suggest that cell cycle progression may be reversibly arrested during aestivation as indicated by the changes in cyclin B expression levels and we propose that DNA methylation is one of the regulatory mechanisms involved in cyclin B transcriptional variation. Copyright © 2016 Elsevier B.V. All rights reserved.

International business cycle synchronization since the 1870s: Evidence from a novel network approach

NASA Astrophysics Data System (ADS)

Antonakakis, Nikolaos; Gogas, Periklis; Papadimitriou, Theophilos; Sarantitis, Georgios Antonios

2016-04-01

In this study, we examine the issue of business cycle synchronization from a historical perspective in 27 developed and developing countries. Based on a novel complex network approach, the Threshold-Minimum Dominating Set (T-MDS), our results reveal heterogeneous patterns of international business cycle synchronization during fundamental globalization periods since the 1870s. In particular, the proposed methodology reveals that worldwide business cycles de-coupled during the Gold Standard, though they were synchronized during the Great Depression. The Bretton Woods era was associated with a lower degree of synchronization as compared to that during the Great Depression, while worldwide business cycle synchronization increased to unprecedented levels during the latest period of floating exchange rates and the Great Recession.

Effect of brushing and thermocycling on the shade and surface roughness of CAD-CAM ceramic restorations.

PubMed

Yuan, Judy Chia-Chun; Barão, Valentim Adelino Ricardo; Wee, Alvin G; Alfaro, Maria F; Afshari, Fatemeh S; Sukotjo, Cortino

2017-09-29

The effects of toothbrushing (B) and thermocycling (TC) on the surface texture of different materials with various fabrication processes have been investigated. However, studies of computer-aided design and computer-aided manufacturing (CAD-CAM) ceramic restorations are limited. The purpose of this in vitro study was to evaluate the effect of B and TC on the color stability and surface roughness of extrinsically characterized and glazed CAD-CAM ceramic restorations. Lithium disilicate CAD ceramic (n=90) and zirconia ceramic (n=90) were studied. All specimens were crystallized/sintered, characterized, and glazed following the manufacturer's recommendation. The specimens were divided into 9 different groups: B, TC, and a combination of B plus TC (B+TC). Brushing was performed at 50 000, 100 000, and 150 000 cycles, simulating an oral environment of 5, 10, and 15 years. Thermocycling was performed at 6000, 12 000, and 18 000 cycles, simulating an oral environment of 5, 10, and 15 years. Brushing plus TC was performed with the combination of the 50 000 cycles of B, then 6000 cycles of TC, and 10 000 cycles of B, then 12 000 cycles of TC, and 15 000 cycles of B, then 18 000 cycles of TC. The color and surface roughness of each specimen were measured before and after all interventions with simulated cycles. Color differences (ΔE) and surface roughness (ΔR a ) data were analyzed using 2-way ANOVA, followed by the least significant difference test (α=.05). The correlation between ΔE and ΔR a was statistically analyzed using the Pearson correlation analysis. Within the lithium disilicate CAD groups, intervention did not result in any significant differences in color change (P>.05). Within the zirconia groups, a 15-year clinical simulation revealed significantly higher ΔE values than a simulated 5-year exposure (P=.017). Increased simulated cycles showed significantly higher R a values for all groups. Within the zirconia groups, B revealed significantly smoother surfaces than TC (P<.001) and B+TC interventions (P<.001). For the zirconia, simulating B+TC for15 years revealed significantly higher R a values than the groups of B+TC for 5 years (P<.001) and B+TC for 10 years (P=.003). No correlation (lithium disilicate CAD, r=.079; P=.462; zirconia, r=.001; P=.989) was found between the color change and surface roughness. For both lithium disilicate CAD and zirconia, color changes were below the selected clinical perceptible threshold (ΔE=2.6) after all intervention and simulated cycles. All mean surface roughness measurements were below 0.2 μm. Generally, the surface of both lithium disilicate CAD and zirconia became rougher. No correlation was found between color difference and surface roughness for either material. Published by Elsevier Inc.

Negative correlation between rates of molecular evolution and flowering cycles in temperate woody bamboos revealed by plastid phylogenomics.

PubMed

Ma, Peng-Fei; Vorontsova, Maria S; Nanjarisoa, Olinirina Prisca; Razanatsoa, Jacqueline; Guo, Zhen-Hua; Haevermans, Thomas; Li, De-Zhu

2017-12-21

Heterogeneous rates of molecular evolution are universal across the tree of life, posing challenges for phylogenetic inference. The temperate woody bamboos (tribe Arundinarieae, Poaceae) are noted for their extremely slow molecular evolutionary rates, supposedly caused by their mysterious monocarpic reproduction. However, the correlation between substitution rates and flowering cycles has not been formally tested. Here we present 15 newly sequenced plastid genomes of temperate woody bamboos, including the first genomes ever sequenced from Madagascar representatives. A data matrix of 46 plastid genomes representing all 12 lineages of Arundinarieae was assembled for phylogenetic and molecular evolutionary analyses. We conducted phylogenetic analyses using different sequences (e.g., coding and noncoding) combined with different data partitioning schemes, revealing conflicting relationships involving internodes among several lineages. A great difference in branch lengths were observed among the major lineages, and topological inconsistency could be attributed to long-branch attraction (LBA). Using clock model-fitting by maximum likelihood and Bayesian approaches, we furthermore demonstrated extensive rate variation among these major lineages. Rate accelerations mainly occurred for the isolated lineages with limited species diversification, totaling 11 rate shifts during the tribe's evolution. Using linear regression analysis, we found a negative correlation between rates of molecular evolution and flowering cycles for Arundinarieae, notwithstanding that the correlation maybe insignificant when taking the phylogenetic structure into account. Using the temperate woody bamboos as an example, we found further evidence that rate heterogeneity is universal in plants, suggesting that this will pose a challenge for phylogenetic reconstruction of bamboos. The bamboos with longer flowering cycles tend to evolve more slowly than those with shorter flowering cycles, in accordance with a putative generation time effect.

Aryl hydrocarbon receptor (AHR) is a potential tumour suppressor in pituitary adenomas.

PubMed

Formosa, R; Borg, J; Vassallo, J

2017-08-01

Pituitary adenomas (PA) represent the largest group of intracranial neoplasms and yet the molecular mechanisms driving this disease remain largely unknown. The aim of this study was to use a high-throughput screening method to identify molecular pathways that may be playing a significant and consistent role in PA. RNA profiling using microarrays on eight local PAs identified the aryl hydrocarbon receptor (AHR) signalling pathway as a key canonical pathway downregulated in all PA types. This was confirmed by real-time PCR in 31 tumours. The AHR has been shown to regulate cell cycle progression in various cell types; however, its role in pituitary tissue has never been investigated. In order to validate the role of AHR in PA behaviour, further functional studies were undertaken. Over-expression of AHR in GH3 cells revealed a tumour suppressor potential independent of exogenous ligand activation by benzo α-pyrene (BαP). Cell cycle analysis and quantitative PCR of cell cycle regulator genes revealed that both unstimulated and BαP-stimulated AHR reduced E2F-driven transcription and altered expression of cell cycle regulator genes, thus increasing the percentage of cells in G 0 /G 1 phase and slowing the proliferation rate of GH3 cells. Co-immunoprecipitation confirmed the interaction between AHR and retinoblastoma (Rb1) protein supporting this as a functional mechanism for the observed reduction. Endogenous Ahr reduction using silencing RNA confirmed the tumour suppressive function of the Ahr. These data support a mechanistic pathway for the putative tumour suppressive role of AHR specifically in PA, possibly through its role as a cell cycle co-regulator, even in the absence of exogenous ligands. © 2017 The authors.

Aryl hydrocarbon receptor (AHR) is a potential tumour suppressor in pituitary adenomas

PubMed Central

Formosa, R; Borg, J

2017-01-01

Pituitary adenomas (PA) represent the largest group of intracranial neoplasms and yet the molecular mechanisms driving this disease remain largely unknown. The aim of this study was to use a high-throughput screening method to identify molecular pathways that may be playing a significant and consistent role in PA. RNA profiling using microarrays on eight local PAs identified the aryl hydrocarbon receptor (AHR) signalling pathway as a key canonical pathway downregulated in all PA types. This was confirmed by real-time PCR in 31 tumours. The AHR has been shown to regulate cell cycle progression in various cell types; however, its role in pituitary tissue has never been investigated. In order to validate the role of AHR in PA behaviour, further functional studies were undertaken. Over-expression of AHR in GH3 cells revealed a tumour suppressor potential independent of exogenous ligand activation by benzo α-pyrene (BαP). Cell cycle analysis and quantitative PCR of cell cycle regulator genes revealed that both unstimulated and BαP-stimulated AHR reduced E2F-driven transcription and altered expression of cell cycle regulator genes, thus increasing the percentage of cells in G0/G1 phase and slowing the proliferation rate of GH3 cells. Co-immunoprecipitation confirmed the interaction between AHR and retinoblastoma (Rb1) protein supporting this as a functional mechanism for the observed reduction. Endogenous Ahr reduction using silencing RNA confirmed the tumour suppressive function of the Ahr. These data support a mechanistic pathway for the putative tumour suppressive role of AHR specifically in PA, possibly through its role as a cell cycle co-regulator, even in the absence of exogenous ligands. PMID:28649092

Rapamycin impairs metabolism-secretion coupling in rat pancreatic islets by suppressing carbohydrate metabolism.

PubMed

Shimodahira, Makiko; Fujimoto, Shimpei; Mukai, Eri; Nakamura, Yasuhiko; Nishi, Yuichi; Sasaki, Mayumi; Sato, Yuichi; Sato, Hiroki; Hosokawa, Masaya; Nagashima, Kazuaki; Seino, Yutaka; Inagaki, Nobuya

2010-01-01

Rapamycin, an immunosuppressant used in human transplantation, impairs beta-cell function, but the mechanism is unclear. Chronic (24 h) exposure to rapamycin concentration dependently suppressed 16.7 mM glucose-induced insulin release from islets (1.65+/-0.06, 30 nM rapamycin versus 2.35+/-0.11 ng/islet per 30 min, control, n=30, P<0.01) without affecting insulin and DNA contents. Rapamycin also decreased alpha-ketoisocaproate-induced insulin release, suggesting reduced mitochondrial carbohydrate metabolism. ATP content in the presence of 16.7 mM glucose was significantly reduced in rapamycin-treated islets (13.42+/-0.47, rapamycin versus 16.04+/-0.46 pmol/islet, control, n=30, P<0.01). Glucose oxidation, which indicates the velocity of metabolism in the Krebs cycle, was decreased by rapamycin in the presence of 16.7 mM glucose (30.1+/-2.7, rapamycin versus 42.2+/-3.3 pmol/islet per 90 min, control, n=9, P<0.01). Immunoblotting revealed that the expression of complex I, III, IV, and V was not affected by rapamycin. Mitochondrial ATP production indicated that the respiratory chain downstream of complex II was not affected, but that carbohydrate metabolism in the Krebs cycle was reduced by rapamycin. Analysis of enzymes in the Krebs cycle revealed that activity of alpha-ketoglutarate dehydrogenase (KGDH), which catalyzes one of the slowest reactions in the Krebs cycle, was reduced by rapamycin (10.08+/-0.82, rapamycin versus 13.82+/-0.84 nmol/mg mitochondrial protein per min, control, n=5, P<0.01). Considered together, these findings indicate that rapamycin suppresses high glucose-induced insulin secretion from pancreatic islets by reducing mitochondrial ATP production through suppression of carbohydrate metabolism in the Krebs cycle, together with reduced KGDH activity.

Helicobacter pylori Induced Phosphatidylinositol-3-OH Kinase/mTOR Activation Increases Hypoxia Inducible Factor-1α to Promote Loss of Cyclin D1 and G0/G1 Cell Cycle Arrest in Human Gastric Cells.

PubMed

Canales, Jimena; Valenzuela, Manuel; Bravo, Jimena; Cerda-Opazo, Paulina; Jorquera, Carla; Toledo, Héctor; Bravo, Denisse; Quest, Andrew F G

2017-01-01

Helicobacter pylori ( H. pylori ) is a human gastric pathogen that has been linked to the development of several gastric pathologies, such as gastritis, peptic ulcer, and gastric cancer. In the gastric epithelium, the bacterium modifies many signaling pathways, resulting in contradictory responses that favor both proliferation and apoptosis. Consistent with such observations, H. pylori activates routes associated with cell cycle progression and cell cycle arrest. H. pylori infection also induces the hypoxia-induced factor HIF-1α, a transcription factor known to promote expression of genes that permit metabolic adaptation to the hypoxic environment in tumors and angiogenesis. Recently, however, also roles for HIF-1α in the repair of damaged DNA and inhibition of gene expression were described. Here, we investigated signaling pathways induced by H. pylori in gastric cells that favor HIF-1α expression and the consequences thereof in infected cells. Our results revealed that H. pylori promoted PI3K/mTOR-dependent HIF-1α induction, HIF-1α translocation to the nucleus, and activity as a transcription factor as evidenced using a reporter assay. Surprisingly, however, transcription of known HIF-1α effector genes evaluated by qPCR analysis, revealed either no change (LDHA and GAPDH), statistically insignificant increases SLC2A1 (GLUT-1) or greatly enhance transcription (VEGFA), but in an HIF-1α-independent manner, as quantified by PCR analysis in cells with shRNA-mediated silencing of HIF-1α. Instead, HIF-1α knockdown facilitated G1/S progression and increased Cyclin D1 protein half-life, via a post-translational pathway. Taken together, these findings link H. pylori -induced PI3K-mTOR activation to HIF-1α induced G0/G1 cell cycle arrest by a Cyclin D1-dependent mechanism. Thus, HIF-1α is identified here as a mediator between survival and cell cycle arrest signaling activated by H. pylori infection.

Integrated analysis of rice transcriptomic and metabolomic responses to elevated night temperatures identifies sensitivity- and tolerance-related profiles.

PubMed

Glaubitz, Ulrike; Li, Xia; Schaedel, Sandra; Erban, Alexander; Sulpice, Ronan; Kopka, Joachim; Hincha, Dirk K; Zuther, Ellen

2017-01-01

Transcript and metabolite profiling were performed on leaves from six rice cultivars under high night temperature (HNT) condition. Six genes were identified as central for HNT response encoding proteins involved in transcription regulation, signal transduction, protein-protein interactions, jasmonate response and the biosynthesis of secondary metabolites. Sensitive cultivars showed specific changes in transcript abundance including abiotic stress responses, changes of cell wall-related genes, of ABA signaling and secondary metabolism. Additionally, metabolite profiles revealed a highly activated TCA cycle under HNT and concomitantly increased levels in pathways branching off that could be corroborated by enzyme activity measurements. Integrated data analysis using clustering based on one-dimensional self-organizing maps identified two profiles highly correlated with HNT sensitivity. The sensitivity profile included genes of the functional bins abiotic stress, hormone metabolism, cell wall, signaling, redox state, transcription factors, secondary metabolites and defence genes. In the tolerance profile, similar bins were affected with slight differences in hormone metabolism and transcription factor responses. Metabolites of the two profiles revealed involvement of GABA signaling, thus providing a link to the TCA cycle status in sensitive cultivars and of myo-inositol as precursor for inositol phosphates linking jasmonate signaling to the HNT response specifically in tolerant cultivars. © 2016 John Wiley & Sons Ltd.

Comparison of Vehicle-Broadcasted Fuel Consumption Rates against Precise Fuel Measurements for Medium- and Heavy-Duty Vehicles and Engines

DOE PAGES

Pink, Alex; Ragatz, Adam; Wang, Lijuan; ...

2017-03-28

Vehicles continuously report real-time fuel consumption estimates over their data bus, known as the controller area network (CAN). However, the accuracy of these fueling estimates is uncertain to researchers who collect these data from any given vehicle. To assess the accuracy of these estimates, CAN-reported fuel consumption data are compared against fuel measurements from precise instrumentation. The data analyzed consisted of eight medium/heavy-duty vehicles and two medium-duty engines. Varying discrepancies between CAN fueling rates and the more accurate measurements emerged but without a vehicular trend-for some vehicles the CAN under-reported fuel consumption and for others the CAN over-reported fuel consumption.more » Furthermore, a qualitative real-time analysis revealed that the operating conditions under which these fueling discrepancies arose varied among vehicles. A drive cycle analysis revealed that while CAN fueling estimate accuracy differs for individual vehicles, that CAN estimates capture the relative fuel consumption differences between drive cycles within 4% for all vehicles and even more accurately for some vehicles. Furthermore, in situations where only CAN-reported data are available, CAN fueling estimates can provide relative fuel consumption trends but not accurate or precise fuel consumption rates.« less

Comparison of Vehicle-Broadcasted Fuel Consumption Rates against Precise Fuel Measurements for Medium- and Heavy-Duty Vehicles and Engines

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

Pink, Alex; Ragatz, Adam; Wang, Lijuan

Vehicles continuously report real-time fuel consumption estimates over their data bus, known as the controller area network (CAN). However, the accuracy of these fueling estimates is uncertain to researchers who collect these data from any given vehicle. To assess the accuracy of these estimates, CAN-reported fuel consumption data are compared against fuel measurements from precise instrumentation. The data analyzed consisted of eight medium/heavy-duty vehicles and two medium-duty engines. Varying discrepancies between CAN fueling rates and the more accurate measurements emerged but without a vehicular trend-for some vehicles the CAN under-reported fuel consumption and for others the CAN over-reported fuel consumption.more » Furthermore, a qualitative real-time analysis revealed that the operating conditions under which these fueling discrepancies arose varied among vehicles. A drive cycle analysis revealed that while CAN fueling estimate accuracy differs for individual vehicles, that CAN estimates capture the relative fuel consumption differences between drive cycles within 4% for all vehicles and even more accurately for some vehicles. Furthermore, in situations where only CAN-reported data are available, CAN fueling estimates can provide relative fuel consumption trends but not accurate or precise fuel consumption rates.« less

Successive chlorothalonil applications inhibit soil nitrification and discrepantly affect abundances of functional genes in soil nitrogen cycling.

PubMed

Teng, Ying; Zhang, Manyun; Yang, Guangmei; Wang, Jun; Christie, Peter; Luo, Yongming

2017-02-01

Broad-spectrum fungicide chlorothalonil (CTN) is successively applied into intensive agriculture soil. However, the impacts of successive CTN applications on soil nitrification and related microorganisms remain poorly understood. A microcosm study was conducted to reveal the effects of successive CTN applications on soil nitrification and functional genes involved in soil nitrogen (N) cycling. The CTN at the dosages of 5 mg kg -1 dry soil (RD) and 25 mg kg -1 dry soil (5RD) was successively applied into the test soil at 7-day intervals which resulted in the accumulations of CTN residues. After 28 days of incubation, CTN residues in the RD and 5RD treatments were 3.14 and 69.7 mg kg -1 dry soil respectively. Net nitrification rates in the RD and 5RD treatments were lower than that obtained from the blank control (CK). Real-time PCR analysis revealed that AOA and AOB amoA gene abundances were significantly decreased by CTN applications. Moreover, CTN applications also discrepantly decreased the abundances of functional genes involved in soil denitrification, with the exception of nosZ gene. Principal component analysis further supported the observation that successive CTN applications could result in enhanced ecological toxicity.

Elimination of active tad elements during the sexual phase of the Neurospora crassa life cycle.

PubMed

Anderson, C; Tang, Q; Kinsey, J A

2001-06-01

Tad is an active LINE-like retrotransposon isolated from the Adiopodoumé strain of Neurospora crassa. Extensive analysis of other Neurospora strains has revealed no other strain with active Tad, but all strains tested have multiple copies of defective Tad elements. We have examined the ability of Tad to survive during the sexual cycle of Neurospora and find that active Tad is rapidly eliminated. The characteristics of this elimination suggest that the repeat-induced point mutation (RIP) mechanism was responsible. By the use of transformation to switch the mating type of the Adiopodoumé strain we concluded that this strain is not defective in the RIP process. Analysis of defective Tad elements isolated from a variety of strains indicates that the major difference between these elements and active Tad is due to the presence of a large number of G-C to A-T transition mutations. This would be expected if the changes were due primarily to the RIP process. Mapping of a selection of defective Tad elements reveals that they are present on all of the chromosomes; however, many of the elements are not widely shared among strains. This suggests that repeated introduction and elimination of Tad elements has occurred. Mechanisms that might be responsible for this repeated introduction are discussed. Copyright 2001 Academic Press.

Systems analysis of ethanol production in the genetically engineered cyanobacterium Synechococcus sp. PCC 7002.

PubMed

Kopka, Joachim; Schmidt, Stefanie; Dethloff, Frederik; Pade, Nadin; Berendt, Susanne; Schottkowski, Marco; Martin, Nico; Dühring, Ulf; Kuchmina, Ekaterina; Enke, Heike; Kramer, Dan; Wilde, Annegret; Hagemann, Martin; Friedrich, Alexandra

2017-01-01

Future sustainable energy production can be achieved using mass cultures of photoautotrophic microorganisms, which are engineered to synthesize valuable products directly from CO 2 and sunlight. As cyanobacteria can be cultivated in large scale on non-arable land, these phototrophic bacteria have become attractive organisms for production of biofuels. Synechococcus sp. PCC 7002, one of the cyanobacterial model organisms, provides many attractive properties for biofuel production such as tolerance of seawater and high light intensities. Here, we performed a systems analysis of an engineered ethanol-producing strain of the cyanobacterium Synechococcus sp. PCC 7002, which was grown in artificial seawater medium over 30 days applying a 12:12 h day-night cycle. Biosynthesis of ethanol resulted in a final accumulation of 0.25% (v/v) ethanol, including ethanol lost due to evaporation. The cultivation experiment revealed three production phases. The highest production rate was observed in the initial phase when cells were actively growing. In phase II growth of the producer strain stopped, but ethanol production rate was still high. Phase III was characterized by a decrease of both ethanol production and optical density of the culture. Metabolomics revealed that the carbon drain due to ethanol diffusion from the cell resulted in the expected reduction of pyruvate-based intermediates. Carbon-saving strategies successfully compensated the decrease of central intermediates of carbon metabolism during the first phase of fermentation. However, during long-term ethanol production the producer strain showed clear indications of intracellular carbon limitation. Despite the decreased levels of glycolytic and tricarboxylic acid cycle intermediates, soluble sugars and even glycogen accumulated in the producer strain. The changes in carbon assimilation patterns are partly supported by proteome analysis, which detected decreased levels of many enzymes and also revealed the stress phenotype of ethanol-producing cells. Strategies towards improved ethanol production are discussed. Systems analysis of ethanol production in Synechococcus sp. PCC 7002 revealed initial compensation followed by increasing metabolic limitation due to excessive carbon drain from primary metabolism.

Economic cycles and their synchronization: Spectral analysis of macroeconomic series from Italy, The Netherlands, and the UK

NASA Astrophysics Data System (ADS)

Sella, Lisa; Vivaldo, Gianna; Ghil, Michael; Groth, Andreas

2010-05-01

The present work applies several advanced spectral methods (Ghil et al., Rev. Geophys., 2002) to the analysis of macroeconomic fluctuations in Italy, The Netherlands, and the United Kingdom. These methods provide valuable time-and-frequency-domain tools that complement traditional time-domain analysis, and are thus fairly well known by now in the geosciences and life sciences, but not yet widespread in quantitative economics. In particular, they enable the identification and characterization of nonlinear trends and dominant cycles --- including low-frequency and seasonal components --- that characterize the behavior of each time series. We explore five fundamental indicators of the real (i.e., non-monetary), aggregate economy --- namely gross domestic product (GDP), consumption, fixed investments, exports and imports --- in a univariate as well as multivariate setting. A single-channel analysis by means of three independent spectral methods --- singular spectrum analysis (SSA), the multi-taper method (MTM), and the maximum-entropy method (MEM) --- reveals very similar near-annual cycles, as well as several longer periodicities, in the macroeconomic indicators of all the countries analyzed. Since each indicator represents different features of an economic system, we combine them to infer if common oscillatory modes are present, either among different indicators within the same country or among the same indicators across different countries. Multichannel-SSA (M-SSA) reinforces the previous results, and shows that the common modes agree in character with solutions of a non-equilibrium dynamic model (NEDyM) that produces endogenous business cycles (Hallegatte et al., JEBO, 2008). The presence of these modes in NEDyM results from adjustment delays and other nonequilibrium effects that were added to a neoclassical Solow (Q. J. Econ., 1956) growth model. Their confirmation by the present analysis has important consequences for the net impact of natural disasters on the economy of a country: Hallegatte and Ghil (Ecol. Econ., 2008) have shown that the presence of business cycles modifies substantially this impact with respect to their impact on an economy in or near equilibrium. The present work concludes with a study of the synchronization of economic fluctuations, which follows a similar study of macroeconomic indicators for the United States, presented in a nearby poster. Since business cycles are not country-specific phenomena, but show common characteristics across countries, our aim is to uncover hidden global behavior across the European economies (cf. Mazzi and Savio, Macmillan, 2006).

Ovarian stimulation length, number of follicles higher than 17 mm and estradiol on the day of human chorionic gonadotropin administration are risk factors for multiple pregnancy in intrauterine insemination

PubMed Central

MELO, MARCO A.B.; SIMÓN, CARLOS; REMOHÍ, JOSÉ; PELLICER, ANTONIO; MESEGUER, MARCOS

2007-01-01

Aim:  The aim of the present study was to identify the risk factors, their prognostic value on multiple pregnancies (MP) prediction and their thresholds in women undergoing controlled ovarian hyperstimulation (COH) with follicle stimulating hormone (FSH) and intrauterine insemination (IUI). Methods:  A case‐control study was carried out by identifying in our database all the pregnancies reached by donor and conjugal IUI (DIUI and CIUI, respectively), and compared cycle features, patients’ characteristics and sperm analysis results between women achieving single pregnancy (SP) versus MP. The number of gestational sacs, follicular sizes and estradiol levels on the human chorionic gonadotropin (hCG) administration day, COH length and semen parameters were obtained from each cycle and compared. Student's t‐tests for mean comparisons, receiver–operator curve (ROC) analysis to determine the predictive value of each parameter on MP achievement and multiple regression analysis to determine single parameter influence were carried out. Results:  Women with MP in IUI stimulated cycles reached the adequate size of the dominant follicle (17 mm) significantly earlier than those achieving SP. Also, the mean follicles number, and estradiol levels on the hCG day were higher in the CIUI and DIUI MP group. Nevertheless, only ROC curve analysis revealed good prognostic value for estradiol and follicles higher than 17 mm. Multiple regression analysis confirmed these results. No feature of the basic sperm analysis, either in the ejaculate or in the prepared sample, was different or predictive of MP. When using donor sperm, different thresholds of follicle number, stimulation length and estradiol in the prediction of MP were noted, in comparison with CIUI. Conclusions:  MP in stimulated IUI cycles are closely associated to stimulation length, number of developed follicles higher than 17 mm on the day of hCG administration and estradiol levels. Also, estradiol has a good predictive value over MP in IUI stimulated cycles. The establishment of clinical thresholds will certainly help in the management of these couples to avoid undesired multiple pregnancies by canceling cycles or converting them into in vitro fertilization procedures. (Reprod Med Biol 2007; 6: 19–26) PMID:29699262

Extrinsic pseudocapacitve Li-ion storage of SnS anode via lithiation-induced structural optimization on cycling

NASA Astrophysics Data System (ADS)

Lian, Qingwang; Zhou, Gang; Liu, Jiatu; Wu, Chen; Wei, Weifeng; Chen, Libao; Li, Chengchao

2017-10-01

Here, we report a new enhanced extrinsic pseudocapacitve Li-ion storage mechanism via lithiation-induced structural optimization strategy. The flower-like C@SnS and bulk SnS exhibit initial capacity decay and subsequent increase of capacity on cycling. After a long-term lithiation/delithiation process, flower-like C@SnS and bulk SnS exhibit improved rate performance and reversible capacity in comparison with those of initial state. Moreover, a high capacity of 530 mAh g-1 is still remained even after 1550 cycles at a high current density of 5.0 A g-1 for flower-like C@SnS after pre-lithiation of 350 cycles. According to the comprehensive analysis of structural evolution and electrochemical performance, it demonstrates that SnS electrodes experience crystal size reduction and further amorphization on cycling, which enhances the reversibility of conversion reaction for SnS, leading to increasing capacity. On the other hand, surface-dominated extrinsic pseudocapacitive contribution results in enhanced rate performance because electrodes expose a large fraction of Li+ sites on surface or near-surface region with structural optimization on cycling. This study reveals that extrinsic pseudocapacitance of SnS can be stimulated via lithiation-induced structural optimization, which gives rise to high-rate and long-lived performances.

SPARC expression induces cell cycle arrest via STAT3 signaling pathway in medulloblastoma cells

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

Chetty, Chandramu; Dontula, Ranadheer; Ganji, Purnachandra Nagaraju

2012-01-13

Highlights: Black-Right-Pointing-Pointer Ectopic expression of SPARC impaired cell proliferation in medulloblastoma cells. Black-Right-Pointing-Pointer SPARC expression induces STAT3 mediated cell cycle arrest in medulloblastoma cells. Black-Right-Pointing-Pointer SPARC expression significantly inhibited pre-established tumor growth in nude-mice. -- Abstract: Dynamic cell interaction with ECM components has profound influence in cancer progression. SPARC is a component of the ECM, impairs the proliferation of different cell types and modulates tumor cell aggressive features. We previously reported that SPARC expression significantly impairs medulloblastoma tumor growth in vivo. In this study, we demonstrate that expression of SPARC inhibits medulloblastoma cell proliferation. MTT assay indicated a dose-dependent reductionmore » in tumor cell proliferation in adenoviral mediated expression of SPARC full length cDNA (Ad-DsRed-SP) in D425 and UW228 cells. Flow cytometric analysis showed that Ad-DsRed-SP-infected cells accumulate in the G2/M phase of cell cycle. Further, immunoblot and immunoprecipitation analyses revealed that SPARC induced G2/M cell cycle arrest was mediated through inhibition of the Cyclin-B-regulated signaling pathway involving p21 and Cdc2 expression. Additionally, expression of SPARC decreased STAT3 phosphorylation at Tyr-705; constitutively active STAT3 expression reversed SPARC induced G2/M arrest. Ad-DsRed-SP significantly inhibited the pre-established orthotopic tumor growth and tumor volume in nude-mice. Immunohistochemical analysis of tumor sections from mice treated with Ad-DsRed-SP showed decreased immunoreactivity for pSTAT3 and increased immunoreactivity for p21 compared to tumor section from mice treated with mock and Ad-DsRed. Taken together our studies further reveal that STAT3 plays a key role in SPARC induced G2/M arrest in medulloblastoma cells. These new findings provide a molecular basis for the mechanistic understanding of the effects of SPARC on medulloblastoma tumor cell proliferation.« less

Comparative Transcriptome Analysis Reveals Different Molecular Mechanisms of Bacillus coagulans 2-6 Response to Sodium Lactate and Calcium Lactate during Lactic Acid Production

PubMed Central

Qin, Jiayang; Wang, Xiuwen; Wang, Landong; Zhu, Beibei; Zhang, Xiaohua; Yao, Qingshou; Xu, Ping

2015-01-01

Lactate production is enhanced by adding calcium carbonate or sodium hydroxide during fermentation. However, Bacillus coagulans 2-6 can produce more than 180 g/L L-lactic acid when calcium lactate is accumulated, but less than 120 g/L L-lactic acid when sodium lactate is formed. The molecular mechanisms by which B. coagulans responds to calcium lactate and sodium lactate remain unclear. In this study, comparative transcriptomic methods based on high-throughput RNA sequencing were applied to study gene expression changes in B. coagulans 2-6 cultured in non-stress, sodium lactate stress and calcium lactate stress conditions. Gene expression profiling identified 712 and 1213 significantly regulated genes in response to calcium lactate stress and sodium lactate stress, respectively. Gene ontology assignments of the differentially expressed genes were performed. KEGG pathway enrichment analysis revealed that ‘ATP-binding cassette transporters’ were significantly affected by calcium lactate stress, and ‘amino sugar and nucleotide sugar metabolism’ was significantly affected by sodium lactate stress. It was also found that lactate fermentation was less affected by calcium lactate stress than by sodium lactate stress. Sodium lactate stress had negative effect on the expression of ‘glycolysis/gluconeogenesis’ genes but positive effect on the expression of ‘citrate cycle (TCA cycle)’ genes. However, calcium lactate stress had positive influence on the expression of ‘glycolysis/gluconeogenesis’ genes and had minor influence on ‘citrate cycle (TCA cycle)’ genes. Thus, our findings offer new insights into the responses of B. coagulans to different lactate stresses. Notably, our RNA-seq dataset constitute a robust database for investigating the functions of genes induced by lactate stress in the future and identify potential targets for genetic engineering to further improve L-lactic acid production by B. coagulans. PMID:25875592

The BMI1 inhibitor PTC-209 is a potential compound to halt cellular growth in biliary tract cancer cells

PubMed Central

Mayr, Christian; Wagner, Andrej; Loeffelberger, Magdalena; Bruckner, Daniela; Jakab, Martin; Berr, Frieder; Di Fazio, Pietro; Ocker, Matthias; Neureiter, Daniel; Pichler, Martin; Kiesslich, Tobias

2016-01-01

BMI1 is a core component of the polycomb repressive complex 1 (PRC1) and is up-regulated in biliary tract cancer (BTC), contributing to aggressive clinical features. In this study we investigated the cytotoxic effects of PTC-209, a recently developed inhibitor of BMI1, in BTC cells. PTC-209 reduced overall viability in BTC cell lines in a dose-dependent fashion (0.04 - 20 μM). Treatment with PTC-209 led to slightly enhanced caspase activity and stop of cell proliferation. Cell cycle analysis revealed that PTC-209 caused cell cycle arrest at the G1/S checkpoint. A comprehensive investigation of expression changes of cell cycle-related genes showed that PTC-209 caused significant down-regulation of cell cycle-promoting genes as well as of genes that contribute to DNA synthesis initiation and DNA repair, respectively. This was accompanied by significantly elevated mRNA levels of cell cycle inhibitors. In addition, PTC-209 reduced sphere formation and, in a cell line-dependent manner, aldehyde dehydrogease-1 positive cells. We conclude that PTC-209 might be a promising drug for future in vitro and in vivo studies in BTC. PMID:26623561

Sunspot Time Series - Relations Inferred from the Location of the Longest Spotless Segments

NASA Astrophysics Data System (ADS)

Zięba, Stanisław; Nieckarz, Zenon

2012-06-01

Spotless days ( i.e., days when no sunspots are observed on the Sun) occur during the interval between the declining phase of the old sunspot cycle and the rising phase of the new sunspot cycle, being greatest in number and of longest continuous length near a new cycle minimum. In this paper, we introduce the concept of the longest spotless segment (LSS) and examine its statistical relation to selected characteristic points in the sunspot time series (STS), such as the occurrences of first spotless day and sunspot maximum. The analysis has revealed statistically significant relations that appear to be of predictive value. For example, for Cycle 24 the last spotless day during its rising phase should be about August 2012 (± 9.1 months), the daily maximum sunspot number should be about 227 (± 50; occurring about January 2014±9.5 months), and the maximum Gaussian smoothed sunspot number should be about 87 (± 25; occurring about July 2014). Using the Gaussian-filtered values, slightly earlier dates of August 2011 and March 2013 are indicated for the last spotless day and sunspot maximum for Cycle 24, respectively.

Mig-6 regulates endometrial genes involved in cell cycle and progesterone signaling

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

Yoo, Jung-Yoon; Kim, Tae Hoon; Lee, Jae Hee

2015-07-10

Mitogen inducible gene 6 (Mig-6) is an important mediator of progesterone (P4) signaling to inhibit estrogen (E2) signaling in the uterus. Ablation of Mig-6 in the murine uterus leads to the development of endometrial hyperplasia and E2-induced endometrial cancer. To identify the molecular pathways regulated by Mig-6, we performed microarray analysis on the uterus of ovariectomized Mig-6{sup f/f} and PGR{sup cre/+}Mig-6{sup f/f} (Mig-6{sup d/d}) mice treated with vehicle or P4 for 6 h. The results revealed that 772 transcripts were significantly regulated in the Mig-6{sup d/d} uterus treated with vehicle as compared with Mig-6{sup f/f} mice. The pathway analysis showed thatmore » Mig-6 suppressed the expression of gene-related cell cycle regulation in the absence of ovarian steroid hormone. The epithelium of Mig-6{sup d/d} mice showed a significant increase in the number of proliferative cells compared to Mig-6{sup f/f} mice. This microarray analysis also revealed that 324 genes are regulated by P4 as well as Mig-6. Cited2, the developmentally important transcription factor, was identified as being regulated by the P4-Mig-6 axis. To determine the role of Cited2 in the uterus, we used the mice with Cited2 that were conditionally ablated in progesterone receptor-positive cells (PGR{sup cre/+}Cited2{sup f/f}; Cited2{sup d/d}). Ablation of Cited2 in the uterus resulted in a significant reduction in the ability of the uterus to undergo a hormonally induced decidual reaction. Identification and analysis of these responsive genes will help define the role of P4 as well as Mig-6 in regulating uterine biology. - Highlights: • We identify Mig-6- and P4-regulated uterine genes by microarray analysis. • Mig-6 suppresses cell cycle progression and epithelial cell proliferation in uterus. • We identify the Mig-6 dependent induced genes by P4. • Cited2 plays an important role for decidualization as a P4 and Mig-6 target gene.« less

Cycles, scaling and crossover phenomenon in length of the day (LOD) time series

NASA Astrophysics Data System (ADS)

Telesca, Luciano

2007-06-01

The dynamics of the temporal fluctuations of the length of the day (LOD) time series from January 1, 1962 to November 2, 2006 were investigated. The power spectrum of the whole time series has revealed annual, semi-annual, decadal and daily oscillatory behaviors, correlated with oceanic-atmospheric processes and interactions. The scaling behavior was analyzed by using the detrended fluctuation analysis (DFA), which has revealed two different scaling regimes, separated by a crossover timescale at approximately 23 days. Flicker-noise process can describe the dynamics of the LOD time regime involving intermediate and long timescales, while Brownian dynamics characterizes the LOD time series for small timescales.

Presence of the acute phase protein, bikunin, in the endometrium of gilts during estrous cycle and early pregnancy.

PubMed

Hettinger, A M; Allen, M R; Zhang, B R; Goad, D W; Malayer, J R; Geisert, R D

2001-08-01

Noninvasive, epitheliochorial placental attachment in the pig is regulated through endometrial production of protease inhibitors. The objective of the present study was to determine if the light-chain serine protease inhibitor of the inter-alpha-trypsin inhibitor family, bikunin, is produced by the porcine endometrium during the estrous cycle and early pregnancy. Western blot analysis revealed the presence of bikunin in uterine flushings of gilts collected during the luteal phase of the estrous cycle and early pregnancy (Days 12-18). However, bikunin unbound to the inter-alpha-trypsin heavy chains was detected only in endometrial explant culture medium obtained from estrus and pregnant (Days 12, 15, and 18) gilts. Endometrial bikunin gene expression was lowest on Day 10 of the estrous cycle and pregnancy, followed by a 30- to 77-fold increase on Day 15 of the estrous cycle and pregnancy. Bikunin gene expression decreased on Day 18 of the estrous cycle, whereas endometrial bikunin gene expression continued to increase in pregnant gilts. Bikunin mRNA was localized to the uterine glands between Days 15 and 18 of the estrous cycle and pregnancy. In addition to its role as a protease inhibitor, bikunin functions in stabilization of the extracellular matrix, which suggests that bikunin could be involved with facilitating placental attachment to the uterine epithelial surface in the pig.

Microbial iron redox cycling in a circumneutral-pH groundwater seep.

PubMed

Blöthe, Marco; Roden, Eric E

2009-01-01

The potential for microbially mediated redox cycling of iron (Fe) in a circumneutral-pH groundwater seep in north central Alabama was studied. Incubation of freshly collected seep material under anoxic conditions with acetate-lactate or H(2) as an electron donor revealed the potential for rapid Fe(III) oxide reduction (ca. 700 to 2,000 micromol liter(-1) day(-1)). Fe(III) reduction at lower but significant rates took place in unamended controls (ca. 300 micromol liter(-1) day(-1)). Culture-based enumerations (most probable numbers [MPNs]) revealed significant numbers (10(2) to 10(6) cells ml(-1)) of organic carbon- and H(2)-oxidizing dissimilatory Fe(III)-reducing microorganisms. Three isolates with the ability to reduce Fe(III) oxides by dissimilatory or fermentative metabolism were obtained (Geobacter sp. strain IST-3, Shewanella sp. strain IST-21, and Bacillus sp. strain IST-38). MPN analysis also revealed the presence of microaerophilic Fe(II)-oxidizing microorganisms (10(3) to 10(5) cells ml(-1)). A 16S rRNA gene library from the iron seep was dominated by representatives of the Betaproteobacteria including Gallionella, Leptothrix, and Comamonas species. Aerobic Fe(II)-oxidizing Comamonas sp. strain IST-3 was isolated. The 16S rRNA gene sequence of this organism is 100% similar to the type strain of the betaproteobacterium Comamonas testosteroni (M11224). Testing of the type strain showed no Fe(II) oxidation. Collectively our results suggest that active microbial Fe redox cycling occurred within this habitat and support previous conceptual models for how microbial Fe oxidation and reduction can be coupled in surface and subsurface sedimentary environments.

Candidate genes and pathogenesis investigation for sepsis-related acute respiratory distress syndrome based on gene expression profile.

PubMed

Wang, Min; Yan, Jingjun; He, Xingxing; Zhong, Qiang; Zhan, Chengye; Li, Shusheng

2016-04-18

Acute respiratory distress syndrome (ARDS) is a potentially devastating form of acute inflammatory lung injury as well as a major cause of acute respiratory failure. Although researchers have made significant progresses in elucidating the pathophysiology of this complex syndrome over the years, the absence of a universal detail disease mechanism up until now has led to a series of practical problems for a definitive treatment. This study aimed to predict some genes or pathways associated with sepsis-related ARDS based on a public microarray dataset and to further explore the molecular mechanism of ARDS. A total of 122 up-regulated DEGs and 91 down-regulated differentially expressed genes (DEGs) were obtained. The up- and down-regulated DEGs were mainly involved in functions like mitotic cell cycle and pathway like cell cycle. Protein-protein interaction network of ARDS analysis revealed 20 hub genes including cyclin B1 (CCNB1), cyclin B2 (CCNB2) and topoisomerase II alpha (TOP2A). A total of seven transcription factors including forkhead box protein M1 (FOXM1) and 30 target genes were revealed in the transcription factor-target gene regulation network. Furthermore, co-cited genes including CCNB2-CCNB1 were revealed in literature mining for the relations ARDS related genes. Pathways like mitotic cell cycle were closed related with the development of ARDS. Genes including CCNB1, CCNB2 and TOP2A, as well as transcription factors like FOXM1 might be used as the novel gene therapy targets for sepsis related ARDS.

Environmental controls on microbial abundance and activity on the greenland ice sheet: a multivariate analysis approach.

PubMed

Stibal, Marek; Telling, Jon; Cook, Joe; Mak, Ka Man; Hodson, Andy; Anesio, Alexandre M

2012-01-01

Microbes in supraglacial ecosystems have been proposed to be significant contributors to regional and possibly global carbon cycling, and quantifying the biogeochemical cycling of carbon in glacial ecosystems is of great significance for global carbon flow estimations. Here we present data on microbial abundance and productivity, collected along a transect across the ablation zone of the Greenland ice sheet (GrIS) in summer 2010. We analyse the relationships between the physical, chemical and biological variables using multivariate statistical analysis. Concentrations of debris-bound nutrients increased with distance from the ice sheet margin, as did both cell numbers and activity rates before reaching a peak (photosynthesis) or a plateau (respiration, abundance) between 10 and 20 km from the margin. The results of productivity measurements suggest an overall net autotrophy on the GrIS and support the proposed role of ice sheet ecosystems in carbon cycling as regional sinks of CO(2) and places of production of organic matter that can be a potential source of nutrients for downstream ecosystems. Principal component analysis based on chemical and biological data revealed three clusters of sites, corresponding to three 'glacier ecological zones', confirmed by a redundancy analysis (RDA) using physical data as predictors. RDA using data from the largest 'bare ice zone' showed that glacier surface slope, a proxy for melt water flow, accounted for most of the variation in the data. Variation in the chemical data was fully explainable by the determined physical variables. Abundance of phototrophic microbes and their proportion in the community were identified as significant controls of the carbon cycling-related microbial processes.

Physiological and Proteomics Analyses Reveal Low-Phosphorus Stress Affected the Regulation of Photosynthesis in Soybean.

PubMed

Chu, Shanshan; Li, Hongyan; Zhang, Xiangqian; Yu, Kaiye; Chao, Maoni; Han, Suoyi; Zhang, Dan

2018-06-06

Previous studies have revealed a significant genetic relationship between phosphorus (P)-efficiency and photosynthesis-related traits in soybean. In this study, we used proteome profiling in combination with expression analysis, biochemical investigations, and leaf ultrastructural analysis to identify the underlying physiological and molecular responses. The expression analysis and ultrastructural analysis showed that the photosynthesis key genes were decreased at transcript levels and the leaf mesophyll and chloroplast were severely damaged after low-P stress. Approximately 55 protein spots showed changes under low-P condition by mass spectrometry, of which 17 were involved in various photosynthetic processes. Further analysis revealed the depression of photosynthesis caused by low-P stress mainly involves the regulation of leaf structure, adenosine triphosphate (ATP) synthesis, absorption and transportation of CO₂, photosynthetic electron transport, production of assimilatory power, and levels of enzymes related to the Calvin cycle. In summary, our findings indicated that the existence of a stringent relationship between P supply and the genomic control of photosynthesis in soybean. As an important strategy to protect soybean photosynthesis, P could maintain the stability of cell structure, up-regulate the enzymes’ activities, recover the process of photosystem II (PSII), and induce the expression of low-P responsive genes and proteins.

Widespread occurrence of lysine methylation in Plasmodium falciparum proteins at asexual blood stages.

PubMed

Kaur, Inderjeet; Zeeshan, Mohammad; Saini, Ekta; Kaushik, Abhinav; Mohmmed, Asif; Gupta, Dinesh; Malhotra, Pawan

2016-10-20

Post-transcriptional and post-translational modifications play a major role in Plasmodium life cycle regulation. Lysine methylation of histone proteins is well documented in several organisms, however in recent years lysine methylation of proteins outside histone code is emerging out as an important post-translational modification (PTM). In the present study we have performed global analysis of lysine methylation of proteins in asexual blood stages of Plasmodium falciparum development. We immunoprecipitated stage specific Plasmodium lysates using anti-methyl lysine specific antibodies that immunostained the asexual blood stage parasites. Using liquid chromatography and tandem mass spectrometry analysis, 570 lysine methylated proteins at three different blood stages were identified. Analysis of the peptide sequences identified 605 methylated sites within 422 proteins. Functional classification of the methylated proteins revealed that the proteins are mainly involved in nucleotide metabolic processes, chromatin organization, transport, homeostatic processes and protein folding. The motif analysis of the methylated lysine peptides reveals novel motifs. Many of the identified lysine methylated proteins are also interacting partners/substrates of PfSET domain proteins as revealed by STRING database analysis. Our findings suggest that the protein methylation at lysine residues is widespread in Plasmodium and plays an important regulatory role in diverse set of the parasite pathways.

Transcriptome-wide analysis of the Trypanosoma cruzi proliferative cycle identifies the periodically expressed mRNAs and their multiple levels of control

PubMed Central

Chávez, Santiago; Eastman, Guillermo; Smircich, Pablo; Becco, Lorena Lourdes; Oliveira-Rizzo, Carolina; Fort, Rafael; Potenza, Mariana; Garat, Beatriz; Sotelo-Silveira, José Roberto

2017-01-01

Trypanosoma cruzi is the protozoan parasite causing American trypanosomiasis or Chagas disease, a neglected parasitosis with important human health impact in Latin America. The efficacy of current therapy is limited, and its toxicity is high. Since parasite proliferation is a fundamental target for rational drug design, we sought to progress into its understanding by applying a genome-wide approach. Treating a TcI linage strain with hydroxyurea, we isolated epimastigotes in late G1, S and G2/M cell cycle stages at 70% purity. The sequencing of each phase identified 305 stage-specific transcripts (1.5-fold change, p≤0.01), coding for conserved cell cycle regulated proteins and numerous proteins whose cell cycle dependence has not been recognized before. Comparisons with the parasite T. brucei and the human host reveal important differences. The meta-analysis of T. cruzi transcriptomic and ribonomic data indicates that cell cycle regulated mRNAs are subject to sub-cellular compartmentalization. Compositional and structural biases of these genes- including CAI, GC content, UTR length, and polycistron position- may contribute to their regulation. To discover nucleotide motifs responsible for the co-regulation of cell cycle regulated genes, we looked for overrepresented motifs at their UTRs and found a variant of the cell cycle sequence motif at the 3' UTR of most of the S and G2 stage genes. We additionally identified hairpin structures at the 5' UTRs of a high proportion of the transcripts, suggesting that periodic gene expression might also rely on translation initiation in T. cruzi. In summary, we report a comprehensive list of T. cruzi cell cycle regulated genes, including many previously unstudied proteins, we show evidence favoring a multi-step control of their expression, and we identify mRNA motifs that may mediate their regulation. Our results provide novel information of the T. cruzi proliferative proteins and the integrated levels of their gene expression control. PMID:29182646

Characterization of Sinorhizobium sp. LM21 Prophages and Virus-Encoded DNA Methyltransferases in the Light of Comparative Genomic Analyses of the Sinorhizobial Virome

PubMed Central

Decewicz, Przemyslaw; Radlinska, Monika; Dziewit, Lukasz

2017-01-01

The genus Sinorhizobium/Ensifer mostly groups nitrogen-fixing bacteria that create root or stem nodules on leguminous plants and transform atmospheric nitrogen into ammonia, which improves the productivity of the plants. Although these biotechnologically-important bacteria are commonly found in various soil environments, little is known about their phages. In this study, the genome of Sinorhizobium sp. LM21 isolated from a heavy-metal-contaminated copper mine in Poland was investigated for the presence of prophages and DNA methyltransferase-encoding genes. In addition to the previously identified temperate phage, ΦLM21, and the phage-plasmid, pLM21S1, the analysis revealed the presence of three prophage regions. Moreover, four novel phage-encoded DNA methyltransferase (MTase) genes were identified and the enzymes were characterized. It was shown that two of the identified viral MTases methylated the same target sequence (GANTC) as cell cycle-regulated methyltransferase (CcrM) of the bacterial host strain, LM21. This discovery was recognized as an example of the evolutionary convergence between enzymes of sinorhizobial viruses and their host, which may play an important role in virus cycle. In the last part of the study, thorough comparative analyses of 31 sinorhizobial (pro)phages (including active sinorhizobial phages and novel putative prophages retrieved and manually re-annotated from Sinorhizobium spp. genomes) were performed. The networking analysis revealed the presence of highly conserved proteins (e.g., holins and endolysins) and a high diversity of viral integrases. The analysis also revealed a large number of viral DNA MTases, whose genes were frequently located within the predicted replication modules of analyzed prophages, which may suggest their important regulatory role. Summarizing, complex analysis of the phage protein similarity network enabled a new insight into overall sinorhizobial virome diversity. PMID:28672885

Cyclicity of Suicides May Be Modulated by Internal or External - 11-Year Cycles: An Example of Suicide Rates in Finland

NASA Astrophysics Data System (ADS)

Dimitrov, B. D.; Atanassova, P. A.; Rachkova, M. I.

2009-12-01

Multicomponent cyclicity in monthly suicides (periods T = 18, 46 and 198 months) was found and close similarity with heliogeophysical activity (HGA) suggested by Dimitrov in 1999. The current report aimed at scrutinizing the results on suicide annual cyclicity (seasonality) in Slovenia as reported by Oravecz et al in 2007 as well as at analyzing suicide data from Finland in this regard. We postulated that: (i) trans-year (12-24 months) or far-trans-year long-term cycles of suicides might interfere with their seasonality; and (ii) associations to environmental factors with alike cyclicity (e.g. HGA, temperature) could exist. Annual suicide incidence from Oulu, Finland over years 1987-1999 was analyzed. Annual data on solar activity (sunspot index Rz or Wolf number), planetary geomagnetic activity (aa-index) and local daily mean temperatures were used. The exploration of underlying chronomes (time structures) was done by periodogram regression analysis with trigonometric approximation. We analyzed temporal dynamics, revealed cyclicity, decomposed and reconstructed significant cycles and correlated the time series data. Suicide seasonality in Slovenia during the years 1971-2002 (n=384 months, peak May-June) was considered and, although some discrepancies and methodological weaknesses were suspected, we further hypothesized about trans-year and/or longer (far-transyear) cyclic components. Suicide incidence data from Finland indicated that the 12.5-year cyclic component (or trend) was almost parallel (coherent) to the cyclic heliogeophysical parameters and similar to local decreasing temperature dynamics. Also, 8-year and 24.5-year cycles were revealed. A correlation between the 12.5-year suicide cycle and 11-year solar cycle was found (R=0.919, p=0.000009). Above findings on cyclicity and temporal correlations of suicides with cyclic environmental factors, even being still preliminary, might not only allow for further more specific analyses. They might also corroborate to improved forecasting and prevention and confer a better understanding of suicide dynamics and aetiology.

Influence of deep frying on the unsaponifiable fraction of vegetable edible oils enriched with natural antioxidants.

PubMed

Orozco, Mara I; Priego-Capote, Feliciano; Luque de Castro, Maria D

2011-07-13

The influence of deep frying, mimicked by 20 heating cycles at 180 °C (each cycle from ambient temperature to 180 °C maintained for 5 min), on the unsaponifiable fraction of vegetable edible oils represented by three characteristic families of compounds (namely, phytosterols, aliphatic alcohols, and triterpenic compounds) has been studied. The target oils were extra virgin olive oil (with intrinsic content of phenolic antioxidants), refined sunflower oil enriched with antioxidant phenolic compounds isolated from olive pomace, refined sunflower oil enriched with an autoxidation inhibitor (dimethylpolysiloxane), and refined sunflower oil without enrichment. Monitoring of the target analytes as a function of both heating cycle and the presence of natural antioxidants was also evaluated by comparison of the profiles after each heating cycle. Identification and quantitation of the target compounds were performed by gas cromatography-mass spectrometry in single ion monitoring mode. Analysis of the heated oils revealed that the addition of natural antioxidants could be an excellent strategy to decrease degradation of lipidic components of the unsaponifiable fraction with the consequent improvement of stability.

The Comparative Effects of Prediction/Discussion-Based Learning Cycle, Conceptual Change Text, and Traditional Instructions on Student Understanding of Genetics

NASA Astrophysics Data System (ADS)

Yilmaz, Diba; Tekkaya, Ceren; Sungur, Semra

2011-03-01

The present study examined the comparative effects of a prediction/discussion-based learning cycle, conceptual change text (CCT), and traditional instructions on students' understanding of genetics concepts. A quasi-experimental research design of the pre-test-post-test non-equivalent control group was adopted. The three intact classes, taught by the same science teacher, were randomly assigned as prediction/discussion-based learning cycle class (N = 30), CCT class (N = 25), and traditional class (N = 26). Participants completed the genetics concept test as pre-test, post-test, and delayed post-test to examine the effects of instructional strategies on their genetics understanding and retention. While the dependent variable of this study was students' understanding of genetics, the independent variables were time (Time 1, Time 2, and Time 3) and mode of instruction. The mixed between-within subjects analysis of variance revealed that students in both prediction/discussion-based learning cycle and CCT groups understood the genetics concepts and retained their knowledge significantly better than students in the traditional instruction group.

[Morphological changes in the thyroid gland of rats during various phases of the estral cycle].

PubMed

Pliner, L I; Ledovskaia, S M

1975-08-01

The functional state of the thyroid gland and the concentration of thyroid hormones in the peripheral blood were studied in 20 mature female albino rats during their estral cycle. Evaluation of the thyroid functional state was made according to data of histological, morphological (the diameter of folliculi, the height of the thyroid epithelium) and histochemical analysis (determination of NAD and NADP-dehydrogenase, succinatedehydrogenase, lactate dehydrogenase, peroxydase, acid and alkaline phosphatase) as well as biochemical determination of iodine bound with protein (IBP) in the blood plasma and investigation of the ratio of the parameters in question under conditions of the sex cycle. The cyclic changes of the morphological state of the thyroid gland attended by the phases of the estral cycle were revealed. The activation of the organ was observed in proestrus and estrus which was evidenced by high levels of activity of the enzymes under study, high concentration of IBP in the blood and increased height of thyreocytes. A decreased function of the thyroid parenchyma was observed at the period of metaestrus-diestrus.

Productive HIV-1 Infection of Human Cervical Tissue Ex Vivo is Associated with the Secretory Phase of the Menstrual Cycle

PubMed Central

Saba, Elisa; Origoni, Massimo; Taccagni, Gianluca; Ferrari, Davide; Doglioni, Claudio; Nava, Alice; Lisco, Andrea; Grivel, Jean-Charles; Margolis, Leonid; Poli, Guido

2013-01-01

Cervical tissue explants (CTE) from 22 HIV-1 seronegative women were exposed to R5 HIV-1 ex vivo. Eight CTE were productively infected in terms of HIV-1 p24Gag release in culture supernatants whereas 14 were not. Nonetheless, both accumulation of HIV-1gag DNA and of p24Gag+ CD4+ T cells and macrophages occurred in both productive and, at lower levels, in nonproductive CTE. Nonproductive CTE differed from productive CTE for higher secretion of CCL3 and CCL5. A post-hoc analysis revealed that all productive CTE were established from women in their secretory phase of the menstrual cycle, whereas nonproductive CTE derived from women either in their secretory (28%) or proliferative (36%) menstrual cycle phases or with an atrophic endometrium (36%). Thus, our results support the epidemiological observation that sexual HIV-1 transmission from males to women as well as from women to men is more efficient during their secretory phase of the menstrual cycle. PMID:23385427

Generic Synthesis of Carbon Nanotube Branches on Metal Oxide Arrays Exhibiting Stable High-Rate and Long-Cycle Sodium-Ion Storage.

PubMed

Xia, Xinhui; Chao, Dongliang; Zhang, Yongqi; Zhan, Jiye; Zhong, Yu; Wang, Xiuli; Wang, Yadong; Shen, Ze Xiang; Tu, Jiangping; Fan, Hong Jin

2016-06-01

A new and generic strategy to construct interwoven carbon nanotube (CNT) branches on various metal oxide nanostructure arrays (exemplified by V2 O3 nanoflakes, Co3 O4 nanowires, Co3 O4 -CoTiO3 composite nanotubes, and ZnO microrods), in order to enhance their electrochemical performance, is demonstrated for the first time. In the second part, the V2 O3 /CNTs core/branch composite arrays as the host for Na(+) storage are investigated in detail. This V2 O3 /CNTs hybrid electrode achieves a reversible charge storage capacity of 612 mAh g(-1) at 0.1 A g(-1) and outstanding high-rate cycling stability (a capacity retention of 100% after 6000 cycles at 2 A g(-1) , and 70% after 10 000 cycles at 10 A g(-1) ). Kinetics analysis reveals that the Na(+) storage is a pseudocapacitive dominating process and the CNTs improve the levels of pseudocapacitive energy by providing a conductive network. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dominance of Epsilonproteobacteria associated with a whale fall at a 4204 m depth - South Atlantic Ocean

NASA Astrophysics Data System (ADS)

Cavalett, Angélica; Silva, Marcus Adonai Castro da; Toyofuku, Takashi; Mendes, Rodrigo; Taketani, Rodrigo Gouvêa; Pedrini, Jéssica; Freitas, Robert Cardoso de; Sumida, Paulo Yukio Gomes; Yamanaka, Toshiro; Nagano, Yuriko; Pellizari, Vivian Helena; Perez, José Angel Alvarez; Kitazato, Hiroshi; Lima, André Oliveira de Souza

2017-12-01

The deep ocean is the largest marine environment on Earth and is home to a large reservoir of biodiversity. Within the deep ocean, large organic falls attract a suite of metazoans and microorganisms, which form an important community that, in part, relies on reduced chemical compounds. Here, we describe a deep-sea (4204 m) microbial community associated with sediments collected underneath a whale fall skeleton in the South Atlantic Ocean. Metagenomic analysis of 1 Gb of Illumina HiSeq. 2000 reads, including taxonomic and functional genes, was performed by using the MG-RAST pipeline, SEED, COG and the KEGG database. The results showed that Proteobacteria (79%) was the main phylum represented. The most dominant bacterial class in this phylum was Epsilonproteobacteria (69%), and Sulfurovum sp. NBC37-1 (97%) was the dominant species. Different species of Epsilonproteobacteria have been described in marine and terrestrial environments as important organisms for nutrient cycling. Functional analysis revealed key genes for nitrogen and sulfur cycles, including protein sequences for Sox system (sulfur oxidation) enzymes. These enzymes were mainly those of the Epsilonproteobacteria, indicating their importance for nitrogen and sulfur cycles and the balance of nutrients in this environment.

The MAPK Signaling Cascade is a Central Hub in the Regulation of Cell Cycle, Apoptosis and Cytoskeleton Remodeling by Tripeptidyl-Peptidase II

PubMed Central

Sompallae, Ramakrishna; Stavropoulou, Vaia; Houde, Mathieu; Masucci, Maria G.

2008-01-01

Tripeptidyl-peptidase II (TPPII) is a serine peptidase highly expressed in malignant Burkitt’s lymphoma cells (BL). We have previously shown that overexpression of TPPII correlates with chromosomal instability, centrosomal and mitotic spindle abnormalities and resistance to apoptosis induced by spindle poisons. Furthermore, TPPII knockdown by RNAi was associated with endoreplication and the accumulation of polynucleated cells that failed to complete cell division, indicating a role of TPPII in the cell cycle. Here we have applied a global approach of gene expression analysis to gain insights on the mechanism by which TPPII regulates this phenotype. mRNA profiling of control and TPPII knockdown BL cells identified one hundred and eighty five differentially expressed genes. Functional categorization of these genes highlighted major physiological functions such as apoptosis, cell cycle progression, cytoskeleton remodeling, proteolysis, and signal transduction. Pathways and protein interactome analysis revealed a significant enrichment in components of MAP kinases signaling. These findings suggest that TPPII influences a wide network of signaling pathways that are regulated by MAPKs and exerts thereby a pleiotropic effect on biological processes associated with cell survival, proliferation and genomic instability. PMID:19787088

Flow field analysis of high-speed helium turboexpander for cryogenic refrigeration and liquefaction cycles

NASA Astrophysics Data System (ADS)

Sam, Ashish Alex; Ghosh, Parthasarathi

2017-03-01

Turboexpander constitutes one of the vital components of Claude cycle based helium refrigerators and liquefiers that are gaining increasing technological importance. These turboexpanders which are of radial inflow in configuration are generally high-speed micro turbines, due to the low molecular weight and density of helium. Any improvement in efficiency of these machines requires a detailed understanding of the flow field. Computational Fluid Dynamics analysis (CFD) has emerged as a necessary tool for the determination of the flow fields in cryogenic turboexpanders, which is often not possible through experiments. In the present work three-dimensional transient flow analysis of a cryogenic turboexpander for helium refrigeration and liquefaction cycles were performed using Ansys CFX®, to understand the flow field of a high-speed helium turboexpander, which in turn will help in taking appropriate decisions regarding modifications of established design methodology for improved efficiency of these machines. The turboexpander is designed based on Balje's nsds diagram and the inverse design blade profile generation formalism prescribed by Hasselgruber and Balje. The analyses include the study of several losses, their origins, the increase in entropy due to these losses, quantification of losses and the effects of various geometrical parameters on these losses. Through the flow field analysis it was observed that in the nozzle, flow separation at the nozzle blade suction side and trailing edge vortices resulted in loss generation, which calls for better nozzle blade profile. The turbine wheel flow field analysis revealed that the significant geometrical parameters of the turbine wheel blade like blade inlet angle, blade profile, tip clearance height and trailing edge thickness need to be optimised for improved performance of the turboexpander. The detailed flow field analysis in this paper can be used to improve the mean line design methodology for turboexpanders used in helium refrigeration and liquefaction cycles.

A Pilot Exploration of Symptom Trajectories in Adolescents with Cancer during Chemotherapy

PubMed Central

Ameringer, Suzanne; Elswick, R. K.; Shockey, Debra P.; Dillon, Robyn

2012-01-01

Background Chemotherapy is frequently administered in repetitive cycles. Adolescents with cancer suffer from multiple symptoms related to chemotherapy but knowledge of symptom trajectories across a cycle is limited. Examining trajectories over a cycle may reveal key periods to manage symptoms. Objectives The aims of this pilot were to describe the trajectory of symptoms (pain, sleep, fatigue, appetite, nausea, fatigue) and biological and behavioral variables (anxiety, stress, hematologic function) across one cycle; and examine relationships between variables. Interventions/Methods Nine adolescents with cancer within six months of diagnosis participated. Data were collected by surveys, chart review, and biologic measures on days 1 and 2 of the cycle, one week later (nadir), and day 1 of the following cycle. To evaluate the trajectory, a simple random effects repeated measures analysis was computed. Results The significant trajectories were fatigue (P = 0.003), difficulty sleeping (P = 0.032), and nausea (P = 0.04). Most of the adolescents reported some anticipatory anxiety about receiving chemotherapy. Significant correlations between symptoms and biobehavioral variables included anticipatory anxiety and nausea (P = 0.86, P = 0.003), trait anxiety and fatigue (r = −0.82, P < 0.001), and stress and pain (r = 0.78, P = 0.039). Conclusions Multiple symptoms were experienced across the cycle. Three symptoms displayed significant trajectories indicating that patterns of symptoms may be anticipated. Implications for Practice Pilot findings suggest monitoring symptoms, stress and anxiety across a cycle is important, not only during chemotherapy administration, but also prior to being admitted for chemotherapy. PMID:22561919

Elevated serum estradiol levels in artificial autologous frozen embryo transfer cycles negatively impact ongoing pregnancy and live birth rates.

PubMed

Fritz, Rani; Jindal, Sangita; Feil, Heather; Buyuk, Erkan

2017-12-01

The aim of this study is to evaluate the correlation between serum estradiol (E 2 ) levels during artificial autologous frozen embryo transfer (FET) cycles and ongoing pregnancy/live birth rates (OP/LB). A historical cohort study was conducted in an academic setting in order to correlate peak and average estradiol levels with ongoing pregnancy/live birth rates for all autologous artificial frozen embryo transfer cycles performed from 1/2011 to 12/2014. Average and peak E 2 levels from 110 autologous artificial FET cycles from 95 patients were analyzed. Average E 2 levels were significantly lower in cycles resulting in OP/LB compared to those that did not (234.1 ± 16.6 pg/ml vs. 315 ± 24.8 pg/ml, respectively, p = 0.04). Although peak E 2 levels were not significantly different between cycles resulting in OP/LB compared with those that did not (366.9 ± 27.7 pg/ml vs. 459.1 ± 32.3 pg/ml, respectively, p = 0.19), correlation analysis revealed a statistically significant (p = 0.02) downward trend in OP/LB rates with increasing peak E 2 levels. This study suggests that elevated E 2 levels in artificial autologous FET cycles are associated with lower OP/LB rates. Estradiol levels should be monitored during artificial FET cycles.

Estradiol modulates functional brain organization during the menstrual cycle: an analysis of interhemispheric inhibition.

PubMed

Weis, Susanne; Hausmann, Markus; Stoffers, Barbara; Vohn, René; Kellermann, Thilo; Sturm, Walter

2008-12-10

According to the hypothesis of progesterone-mediated interhemispheric decoupling (Hausmann and Güntürkün, 2000), functional cerebral asymmetries (FCAs), which are stable in men and change during the menstrual cycle in women, are generated by interhemispheric inhibition of the dominant on the nondominant hemisphere. The change of lateralization during the menstrual cycle in women might indicate that sex hormones play an important role in modulating FCAs. We used functional magnetic resonance imaging to examine the role of estradiol in determining cyclic changes of interhemispheric inhibition. Women performed a word-matching task, while they were scanned twice during the cycle, once during the menstrual and once during the follicular phase. By use of a connectivity analysis we found that the inhibitory influence of left-hemispheric language areas on homotopic areas of the right hemisphere is strongest during the menses, resulting in a pronounced lateralization. During the follicular phase, due to rising estradiol levels, inhibition and thus functional cerebral asymmetries are reduced. These results reveal a powerful neuromodulatory action of estradiol on the dynamics of functional brain organization in the female brain. They may further contribute to the ongoing discussion of sex differences in brain function in that they help explain the dynamic part of functional brain organization in which the female differs from the male brain.

The pleiotropic effects of fisetin and hesperetin on human acute promyelocytic leukemia cells are mediated through apoptosis, cell cycle arrest, and alterations in signaling networks.

PubMed

Adan, Aysun; Baran, Yusuf

2015-11-01

Fisetin and hesperetin, flavonoids from various plants, have several pharmaceutical activities including antioxidative, anti-inflammatory, and anticancer effects. However, studies elucidating the role and the mechanism(s) of action of fisetin and hesperetin in acute promyelocytic leukemia are absent. In this study, we investigated the mechanism of the antiproliferative and apoptotic actions exerted by fisetin and hesperetin on human HL60 acute promyelocytic leukemia cells. The viability of HL60 cells was evaluated using the MTT assay, apoptosis by annexin V/propidium iodide (PI) staining and cell cycle distribution using flow cytometry, and changes in caspase-3 enzyme activity and mitochondrial transmembrane potential. Moreover, we performed whole-genome microarray gene expression analysis to reveal genes affected by fisetin and hesperetin that can be important for developing of future targeted therapy. Based on data obtained from microarray analysis, we also described biological networks modulated after fisetin and hesperetin treatment by KEGG and IPA analysis. Fisetin and hesperetin treatment showed a concentration- and time-dependent inhibition of proliferation and induced G2/M arrest for both agents and G0/G1 arrest for hesperetin at only the highest concentrations. There was a disruption of mitochondrial membrane potential together with increased caspase-3 activity. Furthermore, fisetin- and hesperetin-triggered apoptosis was confirmed by annexin V/PI analysis. The microarray gene profiling analysis revealed some important biological pathways including mitogen-activated protein kinases (MAPK) and inhibitor of DNA binding (ID) signaling pathways altered by fisetin and hesperetin treatment as well as gave a list of genes modulated ≥2-fold involved in cell proliferation, cell division, and apoptosis. Altogether, data suggested that fisetin and hesperetin have anticancer properties and deserve further investigation.

Nuclear orphan receptor TLX affects gene expression, proliferation and cell apoptosis in beta cells

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

Shi, Xiaoli; Xiong, Xiaokan; Dai, Zhe

2015-12-04

Nuclear orphan receptor TLX is an essential regulator of the growth of neural stem cells. However, its exact function in pancreatic islet cells is still unknown. In the present study, gene expression profiling analysis revealed that overexpression of TLX in beta cell line MIN6 causes suppression of 176 genes and upregulation of 49 genes, including a cadre of cell cycle, cell proliferation and cell death control genes, such as Btg2, Ddit3 and Gadd45a. We next examined the effects of TLX overexpression on proliferation, apoptosis and insulin secretion in MIN6 cells. Proliferation analysis using EdU assay showed that overexpression of TLXmore » increased percentage of EdU-positive cells. Cell cycle and apoptosis analysis revealed that overexpression of TLX in MIN6 cells resulted in higher percentage of cells exiting G1 into S-phase, and a 58.8% decrease of cell apoptosis induced by 0.5 mM palmitate. Moreover, TLX overexpression did not cause impairment of insulin secretion. Together, we conclude that TLX is among factors capable of controlling beta cell proliferation and survival, which may serve as a target for the development of novel therapies for diabetes. - Highlights: • TLX overexpression in MIN6 cell causes significant expression changes of 225 genes. • TLX overexpression promotes MIN6 cell proliferation and decreases cell apoptosis. • TLX overexpression does not cause impairment of insulin secretion.« less

Visual gene-network analysis reveals the cancer gene co-expression in human endometrial cancer

PubMed Central

2014-01-01

Background Endometrial cancers (ECs) are the most common form of gynecologic malignancy. Recent studies have reported that ECs reveal distinct markers for molecular pathogenesis, which in turn is linked to the various histological types of ECs. To understand further the molecular events contributing to ECs and endometrial tumorigenesis in general, a more precise identification of cancer-associated molecules and signaling networks would be useful for the detection and monitoring of malignancy, improving clinical cancer therapy, and personalization of treatments. Results ECs-specific gene co-expression networks were constructed by differential expression analysis and weighted gene co-expression network analysis (WGCNA). Important pathways and putative cancer hub genes contribution to tumorigenesis of ECs were identified. An elastic-net regularized classification model was built using the cancer hub gene signatures to predict the phenotypic characteristics of ECs. The 19 cancer hub gene signatures had high predictive power to distinguish among three key principal features of ECs: grade, type, and stage. Intriguingly, these hub gene networks seem to contribute to ECs progression and malignancy via cell-cycle regulation, antigen processing and the citric acid (TCA) cycle. Conclusions The results of this study provide a powerful biomarker discovery platform to better understand the progression of ECs and to uncover potential therapeutic targets in the treatment of ECs. This information might lead to improved monitoring of ECs and resulting improvement of treatment of ECs, the 4th most common of cancer in women. PMID:24758163

Environmental impacts in the life cycle of olive oil: a literature review.

PubMed

Banias, Georgios; Achillas, Charisios; Vlachokostas, Christos; Moussiopoulos, Nicolas; Stefanou, Maria

2017-04-01

The production of olive oil is considered to be one of the largest agricultural business sectors in the Mediterranean area. Apart from its significant impact on the economies of countries in Southern Europe, Northern Africa and Middle East, olive oil production also involves considerable social and environmental considerations. However, despite such importance, the environmental effects of olive oil production have not been studied as much other agricultural productions and farming systems, which are more characteristic of central and northern Europe. We present a thorough and systematic literature review of scientific publications with respect to the use of environmental tools in the life cycle of olive oil. The analysis takes into consideration the farming of olive trees, the manufacture of olive oil, packaging, transportation and reverse logistics. To that end, journal publications up to 2015 in this specific field are recorded and, at the same time, the most important environmental impacts are revealed and a gap analysis is carried out. The analysis conducted reveals that farming of olive trees (with pesticide use and waste/by-product production being the 'hottest' topics) and the manufacturing of olive oil (concentrating mostly on waste/by-product production and management) are the phases with the highest environmental focus from the scientific community. Moreover, gaps in the literature are detected mostly with respect to fuel consumption and the use and promotion of renewable energy sources in olive oil production. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Thermal Non-equilibrium Revealed by Periodic Pulses of Random Amplitudes in Solar Coronal Loops

NASA Astrophysics Data System (ADS)

Auchère, F.; Froment, C.; Bocchialini, K.; Buchlin, E.; Solomon, J.

2016-08-01

We recently detected variations in extreme ultraviolet intensity in coronal loops repeating with periods of several hours. Models of loops including stratified and quasi-steady heating predict the development of a state of thermal non-equilibrium (TNE): cycles of evaporative upflows at the footpoints followed by falling condensations at the apex. Based on Fourier and wavelet analysis, we demonstrate that the observed periodic signals are indeed not signatures of vibrational modes. Instead, superimposed on the power law expected from the stochastic background emission, the power spectra of the time series exhibit the discrete harmonics and continua expected from periodic trains of pulses of random amplitudes. These characteristics reinforce our earlier interpretation of these pulsations as being aborted TNE cycles.

Thermal Non-Equilibrium Revealed by Periodic Pulses of Random Amplitudes in Solar Coronal Loops

NASA Astrophysics Data System (ADS)

Auchère, F.; Froment, C.; Bocchialini, K.; Buchlin, E.; Solomon, J.

2016-10-01

We recently detected variations in extreme ultraviolet intensity in coronal loops repeating with periods of several hours. Models of loops including stratified and quasi-steady heating predict the development of a state of thermal non-equilibrium (TNE): cycles of evaporative upflows at the footpoints followed by falling condensations at the apex. Based on Fourier and wavelet analysis, we demonstrate that the observed periodic signals are indeed not signatures of vibrational modes. Instead, superimposed on the power law expected from the stochastic background emission, the power spectra of the time series exhibit the discrete harmonics and continua expected from periodic trains of pulses of random amplitudes. These characteristics reinforce our earlier interpretation of these pulsations as being aborted TNE cycles.

Metagenomic analyses of the late Pleistocene permafrost - additional tools for reconstruction of environmental conditions

NASA Astrophysics Data System (ADS)

Rivkina, Elizaveta; Petrovskaya, Lada; Vishnivetskaya, Tatiana; Krivushin, Kirill; Shmakova, Lyubov; Tutukina, Maria; Meyers, Arthur; Kondrashov, Fyodor

2016-04-01

A comparative analysis of the metagenomes from two 30 000-year-old permafrost samples, one of lake-alluvial origin and the other from late Pleistocene Ice Complex sediments, revealed significant differences within microbial communities. The late Pleistocene Ice Complex sediments (which have been characterized by the absence of methane with lower values of redox potential and Fe2+ content) showed a low abundance of methanogenic archaea and enzymes from both the carbon and nitrogen cycles, but a higher abundance of enzymes associated with the sulfur cycle. The metagenomic and geochemical analyses described in the paper provide evidence that the formation of the sampled late Pleistocene Ice Complex sediments likely took place under much more aerobic conditions than lake-alluvial sediments.

Quantum and semiclassical physics behind ultrafast optical nonlinearity in the midinfrared: the role of ionization dynamics within the field half cycle.

PubMed

Serebryannikov, E E; Zheltikov, A M

2014-07-25

Ultrafast ionization dynamics within the field half cycle is shown to be the key physical factor that controls the properties of optical nonlinearity as a function of the carrier wavelength and intensity of a driving laser field. The Schrödinger-equation analysis of a generic hydrogen quantum system reveals universal tendencies in the wavelength dependence of optical nonlinearity, shedding light on unusual properties of optical nonlinearities in the midinfrared. For high-intensity low-frequency fields, free-state electrons are shown to dominate over bound electrons in the overall nonlinear response of a quantum system. In this regime, semiclassical models are shown to offer useful insights into the physics behind optical nonlinearity.

Radiation of a resonant medium excited by few-cycle optical pulses at superluminal velocity

NASA Astrophysics Data System (ADS)

Arkhipov, R. M.; Pakhomov, A. V.; Arkhipov, M. V.; Babushkin, I.; Tolmachev, Yu A.; Rosanov, N. N.

2017-05-01

Recent progress in generation of optical pulses of durations comparable to one optical cycle has presented great opportunities for studies of the fundamental processes in matter as well as time-resolved spectroscopy of ultrafast processes in nonlinear media. It opened up a new area of research in modern ultrafast nonlinear optics and led to appearance of the attosecond science. In parallel, a new research area related to emission from resonant media excited by superluminally propagating ultrashort bursts of electromagnetic radiation has been actively developed over the last few years. In this paper, we review our recent results on theoretical analysis of the Cherenkov-type radiation of a resonant medium excited by few-cycle optical pulses propagating at superluminal velocity. This situation can be realized when an electromagnetic pulse with a plane wavefront incidents on a straight string of resonant atoms or a spot of light rotates at very large angular frequency and excites a distant circular string of resonant dipoles. Theoretical analysis revealed some unusual and remarkable features of the Cherenkov radiation generated in this case. This radiation arises in a transient regime which leads to the occurrence of new frequencies in the radiation spectrum. Analysis of the characteristics of this radiation can be used for the study of the resonant structure properties. In addition, a nonlinear resonant medium excited at superluminal velocity can emit unipolar optical pulses, which can be important in ultrafast control of wave-packet dynamics of matter. Specifics of the few-cycle pulse-driven optical response of a resonant medium composed of linear and nonlinear oscillators is discussed.

The Plio-Pleistocene Evolution of the Indian Ocean Monsoonal System: Evidence from the Arabian Sea and East Africa

NASA Astrophysics Data System (ADS)

Wilson, K. E.; Maslin, M. A.; Mackay, A. W.; Leng, M. J.; Kingston, J.; Deino, A.

2011-12-01

It is important to identify the teleconnections between high latitude forcing and tropical monsoonal circulation in order to understand climate change in East Africa during the Plio-Pleistocene. Here we present a record of aeolian dust transport to the Arabian Sea between approximately 2.9 and 2.3 million years ago (Ma), constructed from the high-resolution XRF scanning of sediment cores from ODP Sites 721 and 722. Variations in the delivery of aeolian dust to the Arabian Sea, reflected in normalised flux of titanium, show that monsoonal circulation prior to 2.6 Ma, and after 2.5 Ma, was highly variable and primarily driven by orbitally-forced changes in tropical summer insolation, strongly modulated by the 400,000 year cycle of orbital eccentricity. This is confirmed by the presence of lakes in the East African Rift Valley during key eccentricity maxima. The dust record is coupled with the analysis of a well-dated series of diatomite units from the Baringo-Bogoria Basin which document the rhythmic cycling of large, precessionally-driven freshwater lakes which periodically occupied the Central Kenyan Rift Valley between 2.7 and 2.58 Ma. Analysis of one of these lake sequences using stable oxygen isotope measurements of diatom silica, combined with the XRF analysis of whole-sample geochemistry, reveals that the deep lake phase was characterised by fluctuations in rainfall and lake depth over cycles lasting, on average, 1,400 years. The presence of these millennial-scale fluctuations is confirmed by evidence of abrupt climate cycles in the oceanic dust record from the Arabian Sea.

Electrochemical performance studies of MnO{sub 2} nanoflowers recovered from spent battery

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

Ali, Gomaa A.M.; Chemistry Department, Faculty of Science, Al-Azhar University, Assiut 71524; Tan, Ling Ling

2014-12-15

Highlights: • MnO{sub 2} is recovered from spent zinc–carbon batteries as nanoflowers structure. • Recovered MnO{sub 2} nanoflowers show high specific capacitance. • Recovered MnO{sub 2} nanoflowers show stable electrochemical cycling up to 900 cycles. • Recovered MnO{sub 2} nanoflowers show low resistance in EIS data. - Abstract: The electrochemical performance of MnO{sub 2} nanoflowers recovered from spent household zinc–carbon battery is studied by cyclic voltammetry, galvanostatic charge/discharge cycling and electrochemical impedance spectroscopy. MnO{sub 2} nanoflowers are recovered from spent zinc–carbon battery by combination of solution leaching and electrowinning techniques. In an effort to utilize recovered MnO{sub 2} nanoflowers asmore » energy storage supercapacitor, it is crucial to understand their structure and electrochemical performance. X-ray diffraction analysis confirms the recovery of MnO{sub 2} in birnessite phase, while electron microscopy analysis shows the MnO{sub 2} is recovered as 3D nanostructure with nanoflower morphology. The recovered MnO{sub 2} nanoflowers exhibit high specific capacitance (294 F g{sup −1} at 10 mV s{sup −1}; 208.5 F g{sup −1} at 0.1 A g{sup −1}) in 1 M Na{sub 2}SO{sub 4} electrolyte, with stable electrochemical cycling. Electrochemical data analysis reveal the great potential of MnO{sub 2} nanoflowers recovered from spent zinc–carbon battery in the development of high performance energy storage supercapacitor system.« less

Gene disruption reveals a dispensable role for plasmepsin VII in the Plasmodium berghei life cycle.

PubMed

Mastan, Babu S; Kumari, Anchala; Gupta, Dinesh; Mishra, Satish; Kumar, Kota Arun

2014-06-01

Plasmepsins (PM), aspartic proteases of Plasmodium, comprises a family of ten proteins that perform critical functions in Plasmodium life cycle. Except VII and VIII, functions of the remaining plasmepsin members have been well characterized. Here, we have generated a mutant parasite lacking PM VII in Plasmodium berghei using reverse genetics approach. Systematic comparison of growth kinetics and infection in both mosquito and vertebrate host revealed that PM VII depleted mutants exhibited no defects in development and progressed normally throughout the parasite life cycle. These studies suggest a dispensable role for PM VII in Plasmodium berghei life cycle. Copyright © 2014 Elsevier B.V. All rights reserved.

Does It Have a Life Cycle?

ERIC Educational Resources Information Center

Keeley, Page

2010-01-01

If life continues from generation to generation, then all plants and animals must go through a life cycle, even though it may be different from organism to organism. Is this what students have "learned," or do they have their own private conceptions about life cycles? The formative assessment probe "Does It Have a Life Cycle?" reveals some…

Advancing biopharmaceutical process development by system-level data analysis and integration of omics data.

PubMed

Schaub, Jochen; Clemens, Christoph; Kaufmann, Hitto; Schulz, Torsten W

2012-01-01

Development of efficient bioprocesses is essential for cost-effective manufacturing of recombinant therapeutic proteins. To achieve further process improvement and process rationalization comprehensive data analysis of both process data and phenotypic cell-level data is essential. Here, we present a framework for advanced bioprocess data analysis consisting of multivariate data analysis (MVDA), metabolic flux analysis (MFA), and pathway analysis for mapping of large-scale gene expression data sets. This data analysis platform was applied in a process development project with an IgG-producing Chinese hamster ovary (CHO) cell line in which the maximal product titer could be increased from about 5 to 8 g/L.Principal component analysis (PCA), k-means clustering, and partial least-squares (PLS) models were applied to analyze the macroscopic bioprocess data. MFA and gene expression analysis revealed intracellular information on the characteristics of high-performance cell cultivations. By MVDA, for example, correlations between several essential amino acids and the product concentration were observed. Also, a grouping into rather cell specific productivity-driven and process control-driven processes could be unraveled. By MFA, phenotypic characteristics in glycolysis, glutaminolysis, pentose phosphate pathway, citrate cycle, coupling of amino acid metabolism to citrate cycle, and in the energy yield could be identified. By gene expression analysis 247 deregulated metabolic genes were identified which are involved, inter alia, in amino acid metabolism, transport, and protein synthesis.

Lithium Vanadium Oxide (Li 1.1V 3O 8) Coated with Amorphous Lithium Phosphorous Oxynitride (LiPON): Role of Material Morphology and Interfacial Structure on Resulting Electrochemistry

DOE PAGES

Zhang, Qing; Kercher, Andrew K.; Veith, Gabriel M.; ...

2017-05-16

In the present work, lithium vanadium oxide (Li 1.1V 3O 8) particles synthesized at two different temperatures were coated with an amorphous lithium phosphorous oxynitride (LiPON) film for the first time, and the effects of the LiPON coating on the electrochemistry of the Li 1.1V 3O 8 materials with different morphologies were systematically investigated by comparing uncoated Li 1.1V 3O 8 and Li 1.1V 3O 8 coated with LiPON of various thicknesses. Galvanostatic discharge-charge cycling revealed increased functional capacity for the LiPON-coated materials. Post-cycling electrochemical impedance spectroscopy showed that LiPON-coated Li 1.1V 3O 8 materials developed less interfacial resistance withmore » extended cycling, rationalized by vanadium migration into the LiPON coating seen by electron energy loss spectra. Post-mortem quantitative analysis of the anodes revealed more severe vanadium dissolution for the more irregularly shaped Li 1.1V 3O 8 materials with less LiPON coverage. Thus, this study highlights the specific benefits and limitations of LiPON coatings for stabilizing a moderate voltage Li 1.1V 3O 8 cathode material under extended cycling in liquid electrolyte, and describes a generally applicable approach for comprehensive characterization of a composite electroactive material which can be used to understand interfacial transport properties in other functional systems.« less

Lithium Vanadium Oxide (Li 1.1V 3O 8) Coated with Amorphous Lithium Phosphorous Oxynitride (LiPON): Role of Material Morphology and Interfacial Structure on Resulting Electrochemistry

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

Zhang, Qing; Kercher, Andrew K.; Veith, Gabriel M.

In the present work, lithium vanadium oxide (Li 1.1V 3O 8) particles synthesized at two different temperatures were coated with an amorphous lithium phosphorous oxynitride (LiPON) film for the first time, and the effects of the LiPON coating on the electrochemistry of the Li 1.1V 3O 8 materials with different morphologies were systematically investigated by comparing uncoated Li 1.1V 3O 8 and Li 1.1V 3O 8 coated with LiPON of various thicknesses. Galvanostatic discharge-charge cycling revealed increased functional capacity for the LiPON-coated materials. Post-cycling electrochemical impedance spectroscopy showed that LiPON-coated Li 1.1V 3O 8 materials developed less interfacial resistance withmore » extended cycling, rationalized by vanadium migration into the LiPON coating seen by electron energy loss spectra. Post-mortem quantitative analysis of the anodes revealed more severe vanadium dissolution for the more irregularly shaped Li 1.1V 3O 8 materials with less LiPON coverage. Thus, this study highlights the specific benefits and limitations of LiPON coatings for stabilizing a moderate voltage Li 1.1V 3O 8 cathode material under extended cycling in liquid electrolyte, and describes a generally applicable approach for comprehensive characterization of a composite electroactive material which can be used to understand interfacial transport properties in other functional systems.« less

Activation of pyruvate dehydrogenase by dichloroacetate has the potential to induce epigenetic remodeling in the heart.

PubMed

Matsuhashi, Tomohiro; Hishiki, Takako; Zhou, Heping; Ono, Tomohiko; Kaneda, Ruri; Iso, Tatsuya; Yamaguchi, Aiko; Endo, Jin; Katsumata, Yoshinori; Atsushi, Anzai; Yamamoto, Tsunehisa; Shirakawa, Kohsuke; Yan, Xiaoxiang; Shinmura, Ken; Suematsu, Makoto; Fukuda, Keiichi; Sano, Motoaki

2015-05-01

Dichloroacetate (DCA) promotes pyruvate entry into the Krebs cycle by inhibiting pyruvate dehydrogenase (PDH) kinase and thereby maintaining PDH in the active dephosphorylated state. DCA has recently gained attention as a potential metabolic-targeting therapy for heart failure but the molecular basis of the therapeutic effect of DCA in the heart remains a mystery. Once-daily oral administration of DCA alleviates pressure overload-induced left ventricular remodeling. We examined changes in the metabolic fate of pyruvate carbon (derived from glucose) entering the Krebs cycle by metabolic interventions of DCA. (13)C6-glucose pathway tracing analysis revealed that instead of being completely oxidized in the mitochondria for ATP production, DCA-mediated PDH dephosphorylation results in an increased acetyl-CoA pool both in control and pressure-overloaded hearts. DCA induces hyperacetylation of histone H3K9 and H4 in a dose-dependent manner in parallel to the dephosphorylation of PDH in cultured cardiomyocytes. DCA administration increases histone H3K9 acetylation in in vivo mouse heart. Interestingly, DCA-dependent histone acetylation was associated with an up-regulation of 2.3% of genes (545 out of 23,474 examined). Gene ontology analysis revealed that these genes are highly enriched in transcription-related categories. This evidence suggests that sustained activation of PDH by DCA results in an overproduction of acetyl-CoA, which exceeds oxidation in the Krebs cycle and results in histone acetylation. We propose that DCA-mediated PDH activation has the potential to induce epigenetic remodeling in the heart, which, at least in part, forms the molecular basis for the therapeutic effect of DCA in the heart. Copyright © 2015 Elsevier Ltd. All rights reserved.

Revealing cell cycle control by combining model-based detection of periodic expression with novel cis-regulatory descriptors

PubMed Central

Andersson, Claes R; Hvidsten, Torgeir R; Isaksson, Anders; Gustafsson, Mats G; Komorowski, Jan

2007-01-01

Background We address the issue of explaining the presence or absence of phase-specific transcription in budding yeast cultures under different conditions. To this end we use a model-based detector of gene expression periodicity to divide genes into classes depending on their behavior in experiments using different synchronization methods. While computational inference of gene regulatory circuits typically relies on expression similarity (clustering) in order to find classes of potentially co-regulated genes, this method instead takes advantage of known time profile signatures related to the studied process. Results We explain the regulatory mechanisms of the inferred periodic classes with cis-regulatory descriptors that combine upstream sequence motifs with experimentally determined binding of transcription factors. By systematic statistical analysis we show that periodic classes are best explained by combinations of descriptors rather than single descriptors, and that different combinations correspond to periodic expression in different classes. We also find evidence for additive regulation in that the combinations of cis-regulatory descriptors associated with genes periodically expressed in fewer conditions are frequently subsets of combinations associated with genes periodically expression in more conditions. Finally, we demonstrate that our approach retrieves combinations that are more specific towards known cell-cycle related regulators than the frequently used clustering approach. Conclusion The results illustrate how a model-based approach to expression analysis may be particularly well suited to detect biologically relevant mechanisms. Our new approach makes it possible to provide more refined hypotheses about regulatory mechanisms of the cell cycle and it can easily be adjusted to reveal regulation of other, non-periodic, cellular processes. PMID:17939860

Environmental life cycle assessment of methanol and electricity co-production system based on coal gasification technology.

PubMed

Śliwińska, Anna; Burchart-Korol, Dorota; Smoliński, Adam

2017-01-01

This paper presents a life cycle assessment (LCA) of greenhouse gas emissions generated through methanol and electricity co-production system based on coal gasification technology. The analysis focuses on polygeneration technologies from which two products are produced, and thus, issues related to an allocation procedure for LCA are addressed in this paper. In the LCA, two methods were used: a 'system expansion' method based on two approaches, the 'avoided burdens approach' and 'direct system enlargement' methods and an 'allocation' method involving proportional partitioning based on physical relationships in a technological process. Cause-effect relationships in the analysed production process were identified, allowing for the identification of allocation factors. The 'system expansion' method involved expanding the analysis to include five additional variants of electricity production technologies in Poland (alternative technologies). This method revealed environmental consequences of implementation for the analysed technologies. It was found that the LCA of polygeneration technologies based on the 'system expansion' method generated a more complete source of information on environmental consequences than the 'allocation' method. The analysis shows that alternative technologies chosen for generating LCA results are crucial. Life cycle assessment was performed for the analysed, reference and variant alternative technologies. Comparative analysis was performed between the analysed technologies of methanol and electricity co-production from coal gasification as well as a reference technology of methanol production from the natural gas reforming process. Copyright © 2016 Elsevier B.V. All rights reserved.

Grand Minima and Equatorward Propagation in a Cycling Stellar Convective Dynamo

NASA Astrophysics Data System (ADS)

Augustson, Kyle C.; Brun, Allan Sacha; Miesch, Mark; Toomre, Juri

2015-08-01

The 3-D magnetohydrodynamic (MHD) Anelastic Spherical Harmonic (ASH) code, using slope-limited diffusion, is employed to capture convective and dynamo processes achieved in a global-scale stellar convection simulation for a model solar-mass star rotating at three times the solar rate. The dynamo generated magnetic fields possesses many time scales, with a prominent polarity cycle occurring roughly every 6.2 years. The magnetic field forms large-scale toroidal wreaths, whose formation is tied to the low Rossby number of the convection in this simulation. The polarity reversals are linked to the weakened differential rotation and a resistive collapse of the large-scale magnetic field. An equatorial migration of the magnetic field is seen, which is due to the strong modulation of the differential rotation rather than a dynamo wave. A poleward migration of magnetic flux from the equator eventually leads to the reversal of the polarity of the high-latitude magnetic field. This simulation also enters an interval with reduced magnetic energy at low latitudes lasting roughly 16 years (about 2.5 polarity cycles), during which the polarity cycles are disrupted and after which the dynamo recovers its regular polarity cycles. An analysis of this grand minimum reveals that it likely arises through the interplay of symmetric and antisymmetric dynamo families. This intermittent dynamo state potentially results from the simulations relatively low magnetic Prandtl number. A mean-field-based analysis of this dynamo simulation demonstrates that it is of the α-Ω type. The time scales that appear to be relevant to the magnetic polarity reversal are also identified.

Grand Minima and Equatorward Propagation in a Cycling Stellar Convective Dynamo

NASA Astrophysics Data System (ADS)

Augustson, Kyle; Brun, Allan Sacha; Miesch, Mark; Toomre, Juri

2015-08-01

The 3D MHD Anelastic Spherical Harmonic code, using slope-limited diffusion, is employed to capture convective and dynamo processes achieved in a global-scale stellar convection simulation for a model solar-mass star rotating at three times the solar rate. The dynamo-generated magnetic fields possesses many timescales, with a prominent polarity cycle occurring roughly every 6.2 years. The magnetic field forms large-scale toroidal wreaths, whose formation is tied to the low Rossby number of the convection in this simulation. The polarity reversals are linked to the weakened differential rotation and a resistive collapse of the large-scale magnetic field. An equatorial migration of the magnetic field is seen, which is due to the strong modulation of the differential rotation rather than a dynamo wave. A poleward migration of magnetic flux from the equator eventually leads to the reversal of the polarity of the high-latitude magnetic field. This simulation also enters an interval with reduced magnetic energy at low latitudes lasting roughly 16 years (about 2.5 polarity cycles), during which the polarity cycles are disrupted and after which the dynamo recovers its regular polarity cycles. An analysis of this grand minimum reveals that it likely arises through the interplay of symmetric and antisymmetric dynamo families. This intermittent dynamo state potentially results from the simulation’s relatively low magnetic Prandtl number. A mean-field-based analysis of this dynamo simulation demonstrates that it is of the α-Ω type. The timescales that appear to be relevant to the magnetic polarity reversal are also identified.

GRAND MINIMA AND EQUATORWARD PROPAGATION IN A CYCLING STELLAR CONVECTIVE DYNAMO

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

Augustson, Kyle; Miesch, Mark; Brun, Allan Sacha

2015-08-20

The 3D MHD Anelastic Spherical Harmonic code, using slope-limited diffusion, is employed to capture convective and dynamo processes achieved in a global-scale stellar convection simulation for a model solar-mass star rotating at three times the solar rate. The dynamo-generated magnetic fields possesses many timescales, with a prominent polarity cycle occurring roughly every 6.2 years. The magnetic field forms large-scale toroidal wreaths, whose formation is tied to the low Rossby number of the convection in this simulation. The polarity reversals are linked to the weakened differential rotation and a resistive collapse of the large-scale magnetic field. An equatorial migration of themore » magnetic field is seen, which is due to the strong modulation of the differential rotation rather than a dynamo wave. A poleward migration of magnetic flux from the equator eventually leads to the reversal of the polarity of the high-latitude magnetic field. This simulation also enters an interval with reduced magnetic energy at low latitudes lasting roughly 16 years (about 2.5 polarity cycles), during which the polarity cycles are disrupted and after which the dynamo recovers its regular polarity cycles. An analysis of this grand minimum reveals that it likely arises through the interplay of symmetric and antisymmetric dynamo families. This intermittent dynamo state potentially results from the simulation’s relatively low magnetic Prandtl number. A mean-field-based analysis of this dynamo simulation demonstrates that it is of the α-Ω type. The timescales that appear to be relevant to the magnetic polarity reversal are also identified.« less

Genome-wide Analysis of the H3K4 Histone Demethylase RBP2 Reveals a Transcriptional Program Controlling Differentiation

PubMed Central

Lopez-Bigas, Nuria; Kisiel, Tomasz A.; DeWaal, Dannielle C.; Holmes, Katie B.; Volkert, Tom L.; Gupta, Sumeet; Love, Jennifer; Murray, Heather L.; Young, Richard A.; Benevolenskaya, Elizaveta V.

2010-01-01

SUMMARY Retinoblastoma protein (pRB) mediates cell-cycle withdrawal and differentiation by interacting with a variety of proteins. RB-Binding Protein 2 (RBP2) has been shown to be a key effector. We sought to determine transcriptional regulation by RBP2 genome-wide by using location analysis and gene expression profiling experiments. We describe that RBP2 shows high correlation with the presence of H3K4me3 and its target genes are separated into two functionally distinct classes: differentiation-independent and differentiation-dependent genes. The former class is enriched by genes that encode mitochondrial proteins, while the latter is represented by cell-cycle genes. We demonstrate the role of RBP2 in mitochondrial biogenesis, which involves regulation of H3K4me3-modified nucleosomes. Analysis of expression changes upon RBP2 depletion depicted genes with a signature of differentiation control, analogous to the changes seen upon reintroduction of pRB. We conclude that, during differentiation, RBP2 exerts inhibitory effects on multiple genes through direct interaction with their promoters. PMID:18722178

A study for systematic errors of the GLA forecast model in tropical regions

NASA Technical Reports Server (NTRS)

Chen, Tsing-Chang; Baker, Wayman E.; Pfaendtner, James; Corrigan, Martin

1988-01-01

From the sensitivity studies performed with the Goddard Laboratory for Atmospheres (GLA) analysis/forecast system, it was revealed that the forecast errors in the tropics affect the ability to forecast midlatitude weather in some cases. Apparently, the forecast errors occurring in the tropics can propagate to midlatitudes. Therefore, the systematic error analysis of the GLA forecast system becomes a necessary step in improving the model's forecast performance. The major effort of this study is to examine the possible impact of the hydrological-cycle forecast error on dynamical fields in the GLA forecast system.

Resolvent analysis of suboptimal control for turbulent skin friction drag reduction

NASA Astrophysics Data System (ADS)

Nakashima, Satoshi; Fukagata, Koji; Luhar, Mitul

2017-11-01

We study the drag reduction mechanisms of suboptimal control (Lee et al. 1998) via the resolvent formulation developed by McKeon and Sharma (2010). Under this formulation, the nonlinear term in the Navier-Stokes equations is regarded as a forcing which acts upon the linear dynamics to output a velocity response across Fourier space. This analysis enables targeted analyses of the effects of the control on modes resembling dynamically important coherent structures such as the near-wall (NW) cycle. Suboptimal control generates blowing and suction at the wall that is proportional to the streamwise (Case ST) or spanwise (Case SP) wall shear-stress, with the magnitude of blowing and suction being a design parameter. Both Case ST and SP can suppress resolvent modes resembling the NW cycle. However, for Case ST, the analysis reveals that the control leads to substantial increase in amplification for structures that are long in the spanwise direction. High actuation of such energetic spanwise structures was confirmed by conducting limited direct numerical simulations. In addition to the study of modes resembling the NW cycle, we will discuss modes of varying propagating speed and wavelength to provide insight into the effects of suboptimal control across spectral space. This work was supported through Grant-in-Aid for Scientific Research (C) (No. 25420129) by Japan Society for the Promotion of Science (JSPS).

Five years (2004-2009) of a restrictive law-regulating ART in Italy significantly reduced delivery rate: analysis of 10,706 cycles.

PubMed

Levi Setti, P E; Albani, E; Matteo, M; Morenghi, E; Zannoni, E; Baggiani, A M; Arfuso, V; Patrizio, P

2013-02-01

Was the delivery rate of ART cycles negatively affected by the enactment of the Law 40/2004 by the Italian Parliament which imposed a long list of restrictions for ART procedures? This large and extensive comparative analysis of ART outcomes prior to and after the introduction of the Law 40 revealed a significant reduction in pregnancy and delivery rates per cycle, independent of age or other clinical variables, once the law went into effect. Several studies have been published on the effect of Law 40/2004 on ART outcomes, some authors demonstrating a negative impact of the Law in relation to specific etiologies of infertility, other authors showing opposite conclusions. Retrospective clinical study of 3808 patients treated prior to the enactment of the Law, September 1996-March 2004 (Group I) and 6898 treated during the Law, March 2004-May 2009 (Group II). A total of 10 706 ART cycles were analysed, 3808 performed before and 6898 after the application of the Law. An intention-to-treat statistical analysis was performed to detect pregnancy and delivery rates (pregnancies ≥ 24 weeks) per started cycle. A P value of <0.05 was considered statistically significant. We analysed different outcomes: differences in fertilization, pregnancy and delivery rate, multiple pregnancies and miscarriage rates between the two time periods. The delivery rate for started cycle was 20% before and 16.0% after the introduction of the Law representing a 25% reduction (P < 0.001). The multivariate analysis, corrected by female age of >38 years, duration of infertility, basal FSH level and number of retrieved oocytes, showed a 16% lower delivery rate (odds ratio: 0.84; confidence interval: 0.75-0.94). This statistical approach removed the risk that the observed effects were due to chance and confirmed unequivocally that the Law was an independent factor responsible for the reduced likelihood of a successful outcome. This is a retrospective study. A prospective randomized study, with patients treated in the same time period and randomized to restrictions or not, would have minimized potential limitations due to differences in years of treatments. Our findings based on the analysis of such a large number of cycles proved clearly and unequivocally that imposing restrictions on the practice of ART penalized patients. These data represent a relevant clinical contribution for countries still debating the enactment of restrictive limitations of ART.

High cycle fatigue in the transmission electron microscope

DOE PAGES

Bufford, Daniel C.; Stauffer, Douglas; Mook, William M.; ...

2016-06-28

One of the most common causes of structural failure in metals is fatigue induced by cyclic loading. Historically, microstructure-level analysis of fatigue cracks has primarily been performed post mortem. However, such investigations do not directly reveal the internal structural processes at work near micro- and nanoscale fatigue cracks and thus do not provide direct evidence of active microstructural mechanisms. In this paper, the tension–tension fatigue behavior of nanocrystalline Cu was monitored in real time at the nanoscale by utilizing a new capability for quantitative cyclic mechanical loading performed in situ in a transmission electron microscope (TEM). Controllable loads were appliedmore » at frequencies from one to several hundred hertz, enabling accumulations of 10 6 cycles within 1 h. The nanometer-scale spatial resolution of the TEM allows quantitative fatigue crack growth studies at very slow crack growth rates, measured here at ~10 –12 m·cycle –1. This represents an incipient threshold regime that is well below the tensile yield stress and near the minimum conditions for fatigue crack growth. Evidence of localized deformation and grain growth within 150 nm of the crack tip was observed by both standard imaging and precession electron diffraction orientation mapping. Finally, these observations begin to reveal with unprecedented detail the local microstructural processes that govern damage accumulation, crack nucleation, and crack propagation during fatigue loading in nanocrystalline Cu.« less

Ecotoxicological assessment of cobalt using Hydra model: ROS, oxidative stress, DNA damage, cell cycle arrest, and apoptosis as mechanisms of toxicity.

PubMed

Zeeshan, Mohammed; Murugadas, Anbazhagan; Ghaskadbi, Surendra; Ramaswamy, Babu Rajendran; Akbarsha, Mohammad Abdulkader

2017-05-01

The mechanisms underlying cobalt toxicity in aquatic species in general and cnidarians in particular remain poorly understood. Herein we investigated cobalt toxicity in a Hydra model from morphological, histological, developmental, and molecular biological perspectives. Hydra, exposed to cobalt (0-60 mg/L), were altered in morphology, histology, and regeneration. Exposure to standardized sublethal doses of cobalt impaired feeding by affecting nematocytes, which in turn affected reproduction. At the cellular level, excessive ROS generation, as the principal mechanism of action, primarily occurred in the lysosomes, which was accompanied by the upregulation of expression of the antioxidant genes SOD, GST, GPx, and G6PD. The number of Hsp70 and FoxO transcripts also increased. Interestingly, the upregulations were higher in the 24-h than in the 48-h time-point group, indicating that ROS overwhelmed the cellular defense mechanisms at the latter time-point. Comet assay revealed DNA damage. Cell cycle analysis indicated the induction of apoptosis accompanied or not by cell cycle arrest. Immunoblot analyses revealed that cobalt treatment triggered mitochondria-mediated apoptosis as inferred from the modulation of the key proteins Bax, Bcl-2, and caspase-3. From this data, we suggest the use of Hydra as a model organism for the risk assessment of heavy metal pollution in aquatic ecosystems. Copyright © 2016 Elsevier Ltd. All rights reserved.

High cycle fatigue in the transmission electron microscope

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

Bufford, Daniel C.; Stauffer, Douglas; Mook, William M.

One of the most common causes of structural failure in metals is fatigue induced by cyclic loading. Historically, microstructure-level analysis of fatigue cracks has primarily been performed post mortem. However, such investigations do not directly reveal the internal structural processes at work near micro- and nanoscale fatigue cracks and thus do not provide direct evidence of active microstructural mechanisms. In this paper, the tension–tension fatigue behavior of nanocrystalline Cu was monitored in real time at the nanoscale by utilizing a new capability for quantitative cyclic mechanical loading performed in situ in a transmission electron microscope (TEM). Controllable loads were appliedmore » at frequencies from one to several hundred hertz, enabling accumulations of 10 6 cycles within 1 h. The nanometer-scale spatial resolution of the TEM allows quantitative fatigue crack growth studies at very slow crack growth rates, measured here at ~10 –12 m·cycle –1. This represents an incipient threshold regime that is well below the tensile yield stress and near the minimum conditions for fatigue crack growth. Evidence of localized deformation and grain growth within 150 nm of the crack tip was observed by both standard imaging and precession electron diffraction orientation mapping. Finally, these observations begin to reveal with unprecedented detail the local microstructural processes that govern damage accumulation, crack nucleation, and crack propagation during fatigue loading in nanocrystalline Cu.« less

Functional Differentiation of SWI/SNF Remodelers in Transcription and Cell Cycle Control▿ †

PubMed Central

Moshkin, Yuri M.; Mohrmann, Lisette; van Ijcken, Wilfred F. J.; Verrijzer, C. Peter

2007-01-01

Drosophila BAP and PBAP represent two evolutionarily conserved subclasses of SWI/SNF chromatin remodelers. The two complexes share the same core subunits, including the BRM ATPase, but differ in a few signature subunits: OSA defines BAP, whereas Polybromo (PB) and BAP170 specify PBAP. Here, we present a comprehensive structure-function analysis of BAP and PBAP. An RNA interference knockdown survey revealed that the core subunits BRM and MOR are critical for the structural integrity of both complexes. Whole-genome expression profiling suggested that the SWI/SNF core complex is largely dysfunctional in cells. Regulation of the majority of target genes required the signature subunit OSA, PB, or BAP170, suggesting that SWI/SNF remodelers function mostly as holoenzymes. BAP and PBAP execute similar, independent, or antagonistic functions in transcription control and appear to direct mostly distinct biological processes. BAP, but not PBAP, is required for cell cycle progression through mitosis. Because in yeast the PBAP-homologous complex, RSC, controls cell cycle progression, our finding reveals a functional switch during evolution. BAP mediates G2/M transition through direct regulation of string/cdc25. Its signature subunit, OSA, is required for directing BAP to the string/cdc25 promoter. Our results suggest that the core subunits play architectural and enzymatic roles but that the signature subunits determine most of the functional specificity of SWI/SNF holoenzymes in general gene control. PMID:17101803

Histological analysis on adhesive molecules of renal intravascular large B cell lymphoma treated with CHOP chemotherapy and rituximab.

PubMed

Kusaba, T; Hatta, T; Tanda, S; Kameyama, H; Tamagaki, K; Okigaki, M; Inaba, T; Shimazaki, C; Sasaki, S

2006-03-01

A 48-year-old man was admitted to our hospital for investigation of mild renal dysfunction. A blood examination revealed mild elevation of creatinine level (1.77 mg/dl). Urinary examination revealed mild protein excretion (0.54 g/day) and microhematuria; renal biopsy revealed the focal proliferation of large mononuclear cells with mitosis in glomerular capillaries. According to immunohistochemical analysis, the intravascular lymphomatous cells stained positively with anti-leukocyte common antigen (LCA: CD45) and CD20, indicating a B lymphocyte lineage. In electron microscopy, the glomerular capillary was filled with lymphoma cells and epithelial foot process fusion was noted. Immunohistochemical analysis on adhesive molecules revealed a lack of CD11a expression on lymphoma cells, but positive CD54 expression on endothelial cells. Systemic 18F-fluorodeoxyglucose positron emission tomography (FDG-PET) revealed no abnormal uptake of isotopes. On the basis of these findings, we diagnosed intravascular diffuse large B cell lymphoma localized in the kidney. Despite treatment with rituximab and CHOP (prednisolone, doxorubicin, vincristine, cyclophosphamide) for 3 cycles at 1-month intervals, the renal dysfunction did not change. In histopathological analysis of the second biopsy, lymphoma cells disappeared, but focal segmental glomerulosclerosis and moderate interstitial fibrosis were noted. Electron microscopic findings revealed severe subendothelial edema with mesangial interposition, indicating severe endothelial damage. Epithelial foot process fusion was improved. These pathological analyses let us conclude that a lack of CD11a could be a candidate factor for prevention of the extravasation of lymphoma cells from blood vessels in our patient. We also presumed that the intraglomerular endothelial damage occurred due to chemotherapy-associated cell injury.

Comparative proteomic analysis provides insight into the biological role of protein phosphatase inhibitor-2 from Arabidopsis.

PubMed

Ahsan, Nagib; Chen, Mingjie; Salvato, Fernanda; Wilson, Rashaun S; Shyama Prasad Rao, R; Thelen, Jay J

2017-08-08

Protein phosphatase inhibitor-2 (PPI-2) is a conserved eukaryotic effector protein that inhibits type one protein phosphatases (TOPP). A transfer-DNA knockdown of AtPPI-2 resulted in stunted growth in both vegetative and reproductive phases of Arabidopsis development. At the cellular level, AtPPI-2 knockdown had 35 to 40% smaller cells in developing roots and leaves. This developmental phenotype was rescued by transgenic expression of the AtPPI-2 cDNA behind a constitutive promoter. Comparative proteomics of developing leaves of wild type (WT) and AtPPI-2 mutant revealed reduced levels of proteins associated with chloroplast development, ribosome biogenesis, transport, and cell cycle regulation processes. Decreased abundance of several ribosomal proteins, a DEAD box RNA helicase family protein (AtRH3), Clp protease (ClpP3) and proteins associated with cell division suggests a bottleneck in chloroplast ribosomal biogenesis and cell cycle regulation in AtPPI-2 mutant plants. In contrast, eight out of nine Arabidopsis TOPP isoforms were increased at the transcript level in AtPPI-2 leaves compared to WT. A protein-protein interaction network revealed that >75% of the differentially accumulated proteins have at least secondary and/or tertiary connections with AtPPI-2. Collectively, these data reveal a potential basis for the growth defects of AtPPI-2 and support the presumed role of AtPPI-2 as a master regulator for TOPPs, which regulate diverse growth and developmental processes. Comparative label-free proteomics was used to characterize an AtPPI-2T-DNA knockdown mutant. The complex, reduced growth phenotype supports the notion that AtPPI-2 is a global regulator of TOPPs, and possibly other proteins. Comparative proteomics revealed a range of differences in protein abundance from various cellular processes such as chloroplast development, ribosome biogenesis, and transporter activity in the AtPPI-2 mutant relative to WT Arabidopsis. Collectively the results of proteomic analysis and the protein-protein network suggest that AtPPI-2 is involved in a wide range of biological processes either directly or indirectly including plastid biogenesis, translational mechanisms, and cell cycle regulation. The proposed protein interaction network comprises a testable model underlying changes in protein abundance in the AtPPI-2 mutant, and provides a better framework for future studies. Copyright © 2017 Elsevier B.V. All rights reserved.

Biological Redox Cycling Of Iron In Nontronite And Its Potential Application In Nitrate Removal

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

Zhao, Linduo; Dong, Hailiang; Kukkadapu, Ravi K.

2015-05-05

Redox cycling of structural Fe in phyllosilicates provides a potential method to remediate nitrate contamination in natural environment. Past research has only studied chemical redox cycles or a single biologically mediated redox cycle of Fe in phyllosilicates. The objective of this research was to study three microbially driven redox cycles of Fe in one phyllosilicate, nontronite (NAu-2). During the reduction phase structural Fe(III) in NAu-2 served as electron acceptor, lactate as electron donor, AQDS as electron shuttle, and dissimilatory Fe(III)-reducing bacteria Shewanella putrefaciens CN32 as mediator in bicarbonate-buffered and PIPES-buffered media. During the oxidation phase, biogenic Fe(II) served an electronmore » donor, nitrate as electron acceptor, and nitrate-dependent Fe(II)-oxidizing bacteria Pseudogulbenkiania sp. strain 2002 as mediator in the same media. For all three cycles, structural Fe in NAu-2 was able to reversibly undergo 3 redox cycles without significant reductive or oxidative dissolution. X-ray diffraction and scanning and transmission electron microscopy revealed that NAu-2 was the dominant residual mineral throughout the 3 redox cycles with some dissolution textures but no significant secondary mineralization. Mössbauer spectroscopy revealed that Fe(II) in bio-reduced samples likely occurred in two distinct environments, at edges and the interior of the NAu-2 structure. Nitrate was completely reduced to nitrogen gas under both buffer conditions and this extent and rate did not change with Fe redox cycles. Mössbauer spectroscopy further revealed that nitrate reduction was coupled to predominant/preferred oxidation of edge Fe(II). These results suggest that structural Fe in phyllosilicates may represent a renewable source to continuously remove nitrate in natural environments.« less

Idealized Numerical Modeling Experiments of the Diurnal Cycle of Tropical Cyclones

NASA Astrophysics Data System (ADS)

Navarro, Erika L.

Numerical experiments are performed to evaluate the role of the daily cycle of radiation on axisymmetric hurricane structure. Although a diurnal response in the high cloudiness of tropical cyclones (TCs) has been well documented in the past, the impact to storm structure and intensity remains unknown. Previous modeling work attributes differences in results to experimental setup (e.g., initial and boundary conditions) as well as to radiative parameterization schemes. Here, a numerically-simulated TC in a statistical steady-state is examined to quantify the TC response to the daily cycle of radiation, and a modified, Sawyer-Eliassen approach is applied to evaluate the dynamical mechanism. Fourier analysis in time reveals a spatially coherent pattern in the temperature, wind, and latent heating tendency fields that is statistically significant at the 95% level. This signal accounts for up to 62% of the variance in the temperature field of the upper troposphere, and is mainly concentrated in the TC outflow layer. Composite analysis reveals a cycle in the storm intensity in the low-levels, which lags a periodic response in the latent heating tendency by 6 h. Average magnitudes of the azimuthal wind anomalies near the radius of maximum wind (RMW) are 1 m/s and account for 21% of the overall variance. A hypothesis is drawn from these results that the TC diurnal cycle is comprised of two distinct, periodic circulations: (1) a radiatively-driven circulation in the TC outflow layer due to absorption of solar radiation, and (2) a convectively-driven circulation in the lower and middle troposphere due to anomalous latent heating from convection. These responses are coupled and are periodic with respect to the diurnal cycle. Using a modified, Sawyer-Eliassen approach for time-varying heating, these hypotheses are evaluated to determine the impact of periodic diurnal heating on a balanced vortex. Periodic heating near the top of the vortex produces a local overturning circulation in the region of heating that manifests as inertia-buoyancy waves in the storm environment. Periodic heating in the lower troposphere drives an overturning circulation that resembles the Sawyer-Eliassen solution. This low-level heating induces a positive perturbation azimuthal wind response of 4 m/s near the RMW, which lags the maximum in streamfunction by 6 h. Comparison of these solutions to the numerically-simulated TC reveals a close correspondence of results, suggesting that the axisymmetric TC diurnal cycle is a balanced response driven by periodic heating. The sensitivity of these results to the length of the diurnal period and the vortex intensity are evaluated using the modified, Sawyer-Eliassen approach. Although the true diurnal period is fixed in nature, these experiments allow for the relationship between the magnitude and structure of the TC diurnal signal to the length of the diurnal period to be explored. Results demonstrate that the TC diurnal cycle exhibits large variance, even for the same heating distributions. High-frequency forcing projects mainly onto inertia-buoyancy waves, while low-frequency produces a balanced response resembling the Sawyer-Eliassen solution. Comparison to two, numerically simulated TCs with modified diurnal periods show similar results. In addition, stronger diurnal signals are observed for stronger vortices, suggesting a dependence of the TC diurnal signal on the underlying state of the vortex. These results imply that the magnitude and structure of the TC diurnal signal in nature varies throughout the storm lifetime, and is a function of the structure and intensity of the vortex.

Proteomic analysis of pancreatic cancer stem cells: Functional role of fatty acid synthesis and mevalonate pathways.

PubMed

Brandi, Jessica; Dando, Ilaria; Pozza, Elisa Dalla; Biondani, Giulia; Jenkins, Rosalind; Elliott, Victoria; Park, Kevin; Fanelli, Giuseppina; Zolla, Lello; Costello, Eithne; Scarpa, Aldo; Cecconi, Daniela; Palmieri, Marta

2017-01-06

Recently, we have shown that the secretome of pancreatic cancer stem cells (CSCs) is characterized by proteins that participate in cancer differentiation, invasion, and metastasis. However, the differentially expressed intracellular proteins that lead to the specific characteristics of pancreatic CSCs have not yet been identified, and as a consequence the deranged metabolic pathways are yet to be elucidated. To identify the modulated proteins of pancreatic CSCs, iTRAQ-based proteomic analysis was performed to compare the proteome of Panc1 CSCs and Panc1 parental cells, identifying 230 modulated proteins. Pathway analysis revealed activation of glycolysis, the pentose phosphate pathway, the pyruvate-malate cycle, and lipid metabolism as well as downregulation of the Krebs cycle, the splicesome and non-homologous end joining. These findings were supported by metabolomics and immunoblotting analysis. It was also found that inhibition of fatty acid synthase by cerulenin and of mevalonate pathways by atorvastatin have a greater anti-proliferative effect on cancer stem cells than parental cells. Taken together, these results clarify some important aspects of the metabolic network signature of pancreatic cancer stem cells, shedding light on key and novel therapeutic targets and suggesting that fatty acid synthesis and mevalonate pathways play a key role in ensuring their viability. To better understand the altered metabolic pathways of pancreatic cancer stem cells (CSCs), a comprehensive proteomic analysis and metabolite profiling investigation of Panc1 and Panc1 CSCs were carried out. The findings obtained indicate that Panc1 CSCs are characterized by upregulation of glycolysis, pentose phosphate pathway, pyruvate-malate cycle, and lipid metabolism and by downregulation of Krebs cycle, spliceosome and non-homologous end joining. Moreover, fatty acid synthesis and mevalonate pathways are shown to play a critical contribution to the survival of pancreatic cancer stem cells. This study is helpful for broadening the knowledge of pancreatic cancer stem cells and could accelerate the development of novel therapeutic strategies. Copyright © 2016 Elsevier B.V. All rights reserved.

Mechanisms of G1 cell cycle arrest and apoptosis in myeloma cells induced by hybrid-compound histone deacetylase inhibitor

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

Fujii, Seiko; Division of Maxillofacial Surgery, Kyushu Dental University; Okinaga, Toshinori

2013-05-10

Highlights: •Novel histone deacetylase inhibitor Ky-2, remarkably inhibits myeloma cell growth. •Ky-2 demonstrates no cytotoxicity against normal lymphocytic cells. •Ky-2 induces cell cycle arrest through the cell cycle-associated proteins. •Ky-2 induces Bcl-2-inhibitable apoptosis through a caspase-dependent cascade. -- Abstract: Objectives: Histone deacetylase (HDAC) inhibitors are new therapeutic agents, used to treat various types of malignant cancers. In the present study, we investigated the effects of Ky-2, a hybrid-compound HDAC inhibitor, on the growth of mouse myeloma cells. Materials and methods: Myeloma cells, HS-72, P3U1, and mouse normal cells were used in this study. Effect of HDAC inhibitors on cell viabilitymore » was determined by WST-assay and trypan blue assay. Cell cycle was analyzed using flow cytometer. The expression of cell cycle regulatory and the apoptosis associated proteins were examined by Western blot analysis. Hoechst’s staining was used to detect apoptotic cells. Results: Our findings showed that Ky-2 decreased the levels of HDACs, while it enhanced acetylation of histone H3. Myeloma cell proliferation was inhibited by Ky-2 treatment. Interestingly, Ky-2 had no cytotoxic effects on mouse normal cells. Ky-2 treatment induced G1-phase cell cycle arrest and accumulation of a sub-G1 phase population, while Western blotting analysis revealed that expressions of the cell cycle-associated proteins were up-regulated. Also, Ky-2 enhanced the cleavage of caspase-9 and -3 in myeloma cells, followed by DNA fragmentation. In addition, Ky-2 was not found to induce apoptosis in bcl-2 overexpressing myeloma cells. Conclusion: These findings suggest that Ky-2 induces apoptosis via a caspase-dependent cascade and Bcl-2-inhibitable mechanism in myeloma cells.« less

The tRNA-modifying function of MnmE is controlled by post-hydrolysis steps of its GTPase cycle

PubMed Central

Prado, Silvia; Villarroya, Magda; Medina, Milagros; Armengod, M.-Eugenia

2013-01-01

MnmE is a homodimeric multi-domain GTPase involved in tRNA modification. This protein differs from Ras-like GTPases in its low affinity for guanine nucleotides and mechanism of activation, which occurs by a cis, nucleotide- and potassium-dependent dimerization of its G-domains. Moreover, MnmE requires GTP hydrolysis to be functionally active. However, how GTP hydrolysis drives tRNA modification and how the MnmE GTPase cycle is regulated remains unresolved. Here, the kinetics of the MnmE GTPase cycle was studied under single-turnover conditions using stopped- and quench-flow techniques. We found that the G-domain dissociation is the rate-limiting step of the overall reaction. Mutational analysis and fast kinetics assays revealed that GTP hydrolysis, G-domain dissociation and Pi release can be uncoupled and that G-domain dissociation is directly responsible for the ‘ON’ state of MnmE. Thus, MnmE provides a new paradigm of how the ON/OFF cycling of GTPases may regulate a cellular process. We also demonstrate that the MnmE GTPase cycle is negatively controlled by the reaction products GDP and Pi. This feedback mechanism may prevent inefficacious GTP hydrolysis in vivo. We propose a biological model whereby a conformational change triggered by tRNA binding is required to remove product inhibition and initiate a new GTPase/tRNA-modification cycle. PMID:23630314

Electrochemical performance evaluations and safety investigations of pentafluoro(phenoxy)cyclotriphosphazene as a flame retardant electrolyte additive for application in lithium ion battery systems using a newly designed apparatus for improved self-extinguishing time measurements

NASA Astrophysics Data System (ADS)

Dagger, Tim; Lürenbaum, Constantin; Schappacher, Falko M.; Winter, Martin

2017-02-01

A modified self-extinguishing time (SET) device which enhances the reproducibility of the results is presented. Pentafluoro(phenoxy)cyclotriphosphazene (FPPN) is investigated as flame retardant electrolyte additive for lithium ion batteries (LIBs) in terms of thermal stability and electrochemical performance. SET measurements and adiabatic reaction calorimetry are applied to determine the flammability and the reactivity of a standard LIB electrolyte containing 5% FPPN. The results reveal that the additive-containing electrolyte is nonflammable for 10 s whereas the commercially available reference electrolyte inflames instantaneously after 1 s of ignition. The onset temperature of the safety enhanced electrolyte is delayed by ≈ 21 °C. Compatibility tests in half cells show that the electrolyte is reductively stable while the cyclic voltammogram indicates oxidative decomposition during the first cycle. Cycling experiments in full cells show improved cycling performance and rate capability, which can be attributed to cathode passivation during the first cycle. Post-mortem analysis of the electrolyte by gas chromatography-mass spectrometry confirms the presence of the additive in high amounts after 501 cycles which ensures enhanced safety of the electrolyte. The investigations present FPPN as stable electrolyte additive that improves the intrinsic safety of the electrolyte and its cycling performance at the same time.

Nanoplankton and picoplankton in the Western English Channel: abundance and seasonality from 2007-2013

NASA Astrophysics Data System (ADS)

Tarran, Glen A.; Bruun, John T.

2015-09-01

The nano- and picoplankton community at Station L4 in the Western English Channel was studied between 2007 and 2013 by flow cytometry to quantify abundance and investigate seasonal cycles within these communities. Nanoplankton included both photosynthetic and heterotrophic eukaryotic single-celled organisms while the picoplankton included picoeukaryote phytoplankton, Synechococcus sp. cyanobacteria and heterotrophic bacteria. A Box-Jenkins Transfer Function climatology analysis of surface data revealed that Synechococcus sp., cryptophytes, and heterotrophic flagellates had bimodal annual cycles. Nanoeukaryotes and both high and low nucleic acid-containing bacteria (HNA and LNA, respectively) groups exhibited unimodal annual cycles. Phaeocystis sp., whilst having clearly defined abundance maxima in spring was not detectable the rest of the year. Coccolithophores exhibited a weak seasonal cycle, with abundance peaks in spring and autumn. Picoeukaryotes did not exhibit a discernable seasonal cycle at the surface. Timings of maximum group abundance varied through the year. Phaeocystis sp. and heterotrophic flagellates peaked in April/May. Nanoeukaryotes and HNA bacteria peaked in June/July and had relatively high abundance throughout the summer. Synechococcus sp., cryptophytes and LNA bacteria all peaked from mid to late September. The transfer function model techniques used represent a useful means of identifying repeating annual cycles in time series data with the added ability to detect trends and harmonic terms at different time scales from months to decades.

The water-water cycle is essential for chloroplast protection in the absence of stress.

PubMed

Rizhsky, Ludmila; Liang, Hongjian; Mittler, Ron

2003-10-03

Maintaining electron flow through the photosynthetic apparatus, even in the absence of a sufficient amount of NADP+ as an electron acceptor, is essential for chloroplast protection from photooxidative stress. At least two different pathways are thought to participate in this process, i.e. cyclic electron flow and the water-water cycle. Although the function of the water-water cycle was inferred from a number of biochemical and physiological studies, genetic evidence for the function of this cycle is very limited. Here we show that knockdown Arabidopsis plants with suppressed expression of the key water-water cycle enzyme, thylakoid-attached copper/zinc superoxide dismutase (KD-SOD), are suppressed in their growth and development. Chloroplast size, chlorophyll content, and photosynthetic activity were also reduced in KD-SOD plants. Microarray analysis of KD-SOD plants, grown under controlled conditions, revealed changes in transcript expression consistent with an acclimation response to light stress. Although a number of transcripts involved in the defense of plants from oxidative stress were induced in KD-SOD plants, and seedlings of KD-SOD plants were more tolerant to oxidative stress, these mechanisms were unable to compensate for the suppression of the water-water cycle in mature leaves. Thus, the localization of copper/zinc superoxide dismutase at the vicinity of photosystem I may be essential for its function. Our studies provide genetic evidence for the importance of the water-water cycle in protecting the photosynthetic apparatus of higher plants from photooxidative damage.

Modeling of kinetic, ionospheric and auroral contributions to the 557.7-nm nightglow

NASA Astrophysics Data System (ADS)

Campbell, L.; Brunger, M. J.

2010-11-01

Emission of 557.7-nm radiation from the Earth's upper atmosphere is produced by kinetic, ionospheric and auroral excitation of oxygen atoms. The mechanisms and hence the relative contributions of these three sources are not fully understood. A ground-based mid-latitude recording of the 557.7-nm emissions over the previous solar cycle facilitates a comparison of measurements with theoretical predictions. In this paper the predicted kinetic and ionospheric contributions are simulated and compared with the observations. Semi-quantitative agreement is found between the kinetic contribution and the observations, particularly in the presence of annual, semi-annual and solar cycle variations. An observed enhancement in the emissions in the years following solar maximum is not predicted by the kinetic model. However, correlation analysis reveals a component in the observed values that is related to the auroral hemispheric power. When this extra component is included, a better fit to the pre-midnight observations over the full solar cycle is found.

Designable ultra-smooth ultra-thin solid-electrolyte interphases of three alkali metal anodes.

PubMed

Gu, Yu; Wang, Wei-Wei; Li, Yi-Juan; Wu, Qi-Hui; Tang, Shuai; Yan, Jia-Wei; Zheng, Ming-Sen; Wu, De-Yin; Fan, Chun-Hai; Hu, Wei-Qiang; Chen, Zhao-Bin; Fang, Yuan; Zhang, Qing-Hong; Dong, Quan-Feng; Mao, Bing-Wei

2018-04-09

Dendrite growth of alkali metal anodes limited their lifetime for charge/discharge cycling. Here, we report near-perfect anodes of lithium, sodium, and potassium metals achieved by electrochemical polishing, which removes microscopic defects and creates ultra-smooth ultra-thin solid-electrolyte interphase layers at metal surfaces for providing a homogeneous environment. Precise characterizations by AFM force probing with corroborative in-depth XPS profile analysis reveal that the ultra-smooth ultra-thin solid-electrolyte interphase can be designed to have alternating inorganic-rich and organic-rich/mixed multi-layered structure, which offers mechanical property of coupled rigidity and elasticity. The polished metal anodes exhibit significantly enhanced cycling stability, specifically the lithium anodes can cycle for over 200 times at a real current density of 2 mA cm -2 with 100% depth of discharge. Our work illustrates that an ultra-smooth ultra-thin solid-electrolyte interphase may be robust enough to suppress dendrite growth and thus serve as an initial layer for further improved protection of alkali metal anodes.

New 1982-1990 photometry of Lambda Andromedae and its 11-year cycle

NASA Technical Reports Server (NTRS)

Hall, Douglas S.; Henry, Gregory W.; Boehme, Dietmar; Brooks, Peter A.; Chang, Sandy; Dolzan, Ales; Fortier, George L.; Fried, Robert E.; Genet, Russell M.; Grim, Bruce S.

1991-01-01

The paper presents photoelectric photometry of Lambda And never before published, obtained between February 1982 and December 1990 at 29 different observatories. Then it is combined with all other photometry available (previously published, contained in the I.A.U. Commission 27 Archives, and obtained with the Vanderbilt 16-inch automatic telescope but not yet published), to yield a 14.8-year data base. Analysis reveals a long-term cycle in mean brightness, with a full range of 0.15 m and a period of 11.4 +/- 0.4 years. Because most of the new photometry was concentrated in the 1983-1984 observing season, this one well-defined light curve is analyzed with a two-spot model. Spot A keeps a 0.04 m amplitude throughout four rotation cycles whereas the amplitude of spot B diminishes from 0.09 m down almost to 0.03 m. The spot rotation periods were 55.9 d +/- 0.6 d and 52.8 d +/- 1.0 d, respectively.

Closure of fatigue cracks at high strains

NASA Technical Reports Server (NTRS)

Iyyer, N. S.; Dowling, N. E.

1985-01-01

Experiments were conducted on smooth specimens to study the closure behavior of short cracks at high cyclic strains under completely reversed cycling. Testing procedures and methodology, and closure measurement techniques, are described in detail. The strain levels chosen for the study cover from predominantly elastic to grossly plastic strains. Crack closure measurements are made at different crack lengths. The study reveals that, at high strains, cracks close only as the lowest stress level in the cycle is approached. The crack opening is observed to occur in the compressive part of the loading cycle. The applied stress needed to open a short crack under high strain is found to be less than for cracks under small scale yielding. For increased plastic deformations, the value of sigma sub op/sigma sub max is observed to decrease and approaches the value of R. Comparison of the experimental results with existing analysis is made and indicates the limitations of the small scale yielding approach where gross plastic deformation behavior occurs.

A sex-inducing pheromone triggers cell cycle arrest and mate attraction in the diatom Seminavis robusta

PubMed Central

Moeys, Sara; Frenkel, Johannes; Lembke, Christine; Gillard, Jeroen T. F.; Devos, Valerie; Van den Berge, Koen; Bouillon, Barbara; Huysman, Marie J. J.; De Decker, Sam; Scharf, Julia; Bones, Atle; Brembu, Tore; Winge, Per; Sabbe, Koen; Vuylsteke, Marnik; Clement, Lieven; De Veylder, Lieven; Pohnert, Georg; Vyverman, Wim

2016-01-01

Although sexual reproduction is believed to play a major role in the high diversification rates and species richness of diatoms, a mechanistic understanding of diatom life cycle control is virtually lacking. Diatom sexual signalling is controlled by a complex, yet largely unknown, pheromone system. Here, a sex-inducing pheromone (SIP+) of the benthic pennate diatom Seminavis robusta was identified by comparative metabolomics, subsequently purified, and physicochemically characterized. Transcriptome analysis revealed that SIP+ triggers the switch from mitosis-to-meiosis in the opposing mating type, coupled with the transcriptional induction of proline biosynthesis genes, and the release of the proline-derived attraction pheromone. The induction of cell cycle arrest by a pheromone, chemically distinct from the one used to attract the opposite mating type, highlights the existence of a sophisticated mechanism to increase chances of mate finding, while keeping the metabolic losses associated with the release of an attraction pheromone to a minimum. PMID:26786712

Identification of a Golgi apparatus protein complex important for the asexual erythrocytic cycle of the malaria parasite Plasmodium falciparum.

PubMed

Hallée, Stéphanie; Thériault, Catherine; Gagnon, Dominic; Kehrer, Jessica; Frischknecht, Friedrich; Mair, Gunnar R; Richard, Dave

2018-03-26

Compared with other eukaryotic cell types, malaria parasites appear to possess a more rudimentary Golgi apparatus being composed of dispersed, unstacked cis and trans-cisternae. Despite playing a central role in the secretory pathway of the parasite, few Plasmodium Golgi resident proteins have been characterised. We had previously identified a new Golgi resident protein of unknown function, which we had named Golgi Protein 1, and now show that it forms a complex with a previously uncharacterised transmembrane protein (Golgi Protein 2, GP2). The Golgi Protein complex localises to the cis-Golgi throughout the erythrocytic cycle and potentially also during the mosquito stages. Analysis of parasite strains where GP1 expression is conditionally repressed and/or the GP2 gene is inactivated reveals that though the Golgi protein complex is not essential at any stage of the parasite life cycle, it is important for optimal asexual development in the blood stages. © 2018 John Wiley & Sons Ltd.

Resident challenges with daily life in Chinese long-term care facilities: A qualitative pilot study.

PubMed

Song, Yuting; Scales, Kezia; Anderson, Ruth A; Wu, Bei; Corazzini, Kirsten N

As traditional family-based care in China declines, the demand for residential care increases. Knowledge of residents' experiences with long-term care (LTC) facilities is essential to improving quality of care. This pilot study aimed to describe residents' experiences in LTC facilities, particularly as it related to physical function. Semi-structured open-ended interviews were conducted in two facilities with residents stratified by three functional levels (n = 5). Directed content analysis was guided by the Adaptive Leadership Framework. A two-cycle coding approach was used with a first-cycle descriptive coding and second-cycle dramaturgical coding. Interviews provided examples of challenges faced by residents in meeting their daily care needs. Five themes emerged: staff care, care from family members, physical environment, other residents in the facility, and personal strategies. Findings demonstrate the significance of organizational context for care quality and reveal foci for future research. Copyright © 2017 Elsevier Inc. All rights reserved.

Greatly Suppressed Shuttle Effect for Improved Lithium Sulfur Battery Performance through Short Chain Intermediates.

PubMed

Xu, Na; Qian, Tao; Liu, Xuejun; Liu, Jie; Chen, Yu; Yan, Chenglin

2017-01-11

The high solubility of long-chain lithium polysulfides and their infamous shuttle effect in lithium sulfur battery lead to rapid capacity fading along with low Coulombic efficiency. To address above issues, we propose a new strategy to suppress the shuttle effect for greatly enhanced lithium sulfur battery performance mainly through the formation of short-chain intermediates during discharging, which allows significant improvements including high capacity retention of 1022 mAh/g with 87% retention for 450 cycles. Without LiNO 3 -containing electrolytes, the excellent Coulombic efficiency of ∼99.5% for more than 500 cycles is obtained, suggesting the greatly suppressed shuttle effect. In situ UV/vis analysis of electrolyte during cycling reveals that the short-chain Li 2 S 2 and Li 2 S 3 polysulfides are detected as main intermediates, which are theoretically verified by density functional theory (DFT) calculations. Our strategy may open up a new avenue for practical application of lithium sulfur battery.

Effects of cathode electrolyte interfacial (CEI) layer on long term cycling of all-solid-state thin-film batteries

DOE PAGES

Wang, Ziying; Lee, Jungwoo Z.; Xin, Huolin L.; ...

2016-05-30

All-solid-state lithium-ion batteries have the potential to not only push the current limits of energy density by utilizing Li metal, but also improve safety by avoiding flammable organic electrolyte. However, understanding the role of solid electrolyte – electrode interfaces will be critical to improve performance. In this paper, we conducted long term cycling on commercially available lithium cobalt oxide (LCO)/lithium phosphorus oxynitride (LiPON)/lithium (Li) cells at elevated temperature to investigate the interfacial phenomena that lead to capacity decay. STEM-EELS analysis of samples revealed a previously unreported disordered layer between the LCO cathode and LiPON electrolyte. This electrochemically inactive layer grewmore » in thickness leading to loss of capacity and increase of interfacial resistance when cycled at 80 °C. Finally, the stabilization of this layer through interfacial engineering is crucial to improve the long term performance of thin-film batteries especially under thermal stress.« less

The impact of resource limitation and the phenology of parasitoid attack on the duration of insect herbivore outbreaks.

PubMed

Umbanhowar, James; Hastings, Alan

2002-11-01

Fluctuations in resource quality and quantity, and changes in mortality due to predators and parasites are thought to be of prime importance in the regular fluctuations of forest insects. We examine how food limitation and parasitoids with different phenologies of attack regulate the population cycles of insect hosts. Our analysis of the limit cycle of a model with a biologically realistic form of density dependence in the host yields two novel predictions. First, outbreaks will typically last for only 2 generations after parasitoids begin to reduce the host population below the maximum density. Second, host growth rate is important in determining cycle length only when parasitoids attack before the impacts of resource limitation affect the host. The robustness of these predictions are tested using a more general form of density dependence in the host, revealing that our predictions are valid as long as density dependence in the host is not too overcompensatory.

The Rice B-Box Zinc Finger Gene Family: Genomic Identification, Characterization, Expression Profiling and Diurnal Analysis

PubMed Central

Huang, Jianyan; Zhao, Xiaobo; Weng, Xiaoyu; Wang, Lei; Xie, Weibo

2012-01-01

Background The B-box (BBX) -containing proteins are a class of zinc finger proteins that contain one or two B-box domains and play important roles in plant growth and development. The Arabidopsis BBX gene family has recently been re-identified and renamed. However, there has not been a genome-wide survey of the rice BBX (OsBBX) gene family until now. Methodology/Principal Findings In this study, we identified 30 rice BBX genes through a comprehensive bioinformatics analysis. Each gene was assigned a uniform nomenclature. We described the chromosome localizations, gene structures, protein domains, phylogenetic relationship, whole life-cycle expression profile and diurnal expression patterns of the OsBBX family members. Based on the phylogeny and domain constitution, the OsBBX gene family was classified into five subfamilies. The gene duplication analysis revealed that only chromosomal segmental duplication contributed to the expansion of the OsBBX gene family. The expression profile of the OsBBX genes was analyzed by Affymetrix GeneChip microarrays throughout the entire life-cycle of rice cultivar Zhenshan 97 (ZS97). In addition, microarray analysis was performed to obtain the expression patterns of these genes under light/dark conditions and after three phytohormone treatments. This analysis revealed that the expression patterns of the OsBBX genes could be classified into eight groups. Eight genes were regulated under the light/dark treatments, and eleven genes showed differential expression under at least one phytohormone treatment. Moreover, we verified the diurnal expression of the OsBBX genes using the data obtained from the Diurnal Project and qPCR analysis, and the results indicated that many of these genes had a diurnal expression pattern. Conclusions/Significance The combination of the genome-wide identification and the expression and diurnal analysis of the OsBBX gene family should facilitate additional functional studies of the OsBBX genes. PMID:23118960

Analysis of monthly, winter, and annual temperatures in Zagreb, Croatia, from 1864 to 2010: the 7.7-year cycle and the North Atlantic Oscillation

NASA Astrophysics Data System (ADS)

Sen, Asok K.; Ogrin, Darko

2016-02-01

Long instrumental records of meteorological variables such as temperature and precipitation are very useful for studying regional climate in the past, present, and future. They can also be useful for understanding the influence of large-scale atmospheric circulation processes on the regional climate. This paper investigates the monthly, winter, and annual temperature time series obtained from the instrumental records in Zagreb, Croatia, for the period 1864-2010. Using wavelet analysis, the dominant modes of variability in these temperature series are identified, and the time intervals over which these modes may persist are delineated. The results reveal that all three temperature records exhibit low-frequency variability with a dominant periodicity at around 7.7 years. The 7.7-year cycle has also been observed in the temperature data recorded at several other stations in Europe, especially in Northern and Western Europe, and may be linked to the North Atlantic Oscillation (NAO) and/or solar/geomagnetic activity.

High-Resolution Melting (HRM) of the Cytochrome B Gene: A Powerful Approach to Identify Blood-Meal Sources in Chagas Disease Vectors

PubMed Central

Peña, Victor H.; Fernández, Geysson J.; Gómez-Palacio, Andrés M.; Mejía-Jaramillo, Ana M.; Cantillo, Omar; Triana-Chávez, Omar

2012-01-01

Methods to determine blood-meal sources of hematophagous Triatominae bugs (Chagas disease vectors) are serological or based on PCR employing species-specific primers or heteroduplex analysis, but these are expensive, inaccurate, or problematic when the insect has fed on more than one species. To solve those problems, we developed a technique based on HRM analysis of the mitochondrial gene cytochrome B (Cyt b). This technique recognized 14 species involved in several ecoepidemiological cycles of the transmission of Trypanosoma cruzi and it was suitable with DNA extracted from intestinal content and feces 30 days after feeding, revealing a resolution power that can display mixed feedings. Field samples were analyzed showing blood meal sources corresponding to domestic, peridomiciliary and sylvatic cycles. The technique only requires a single pair of primers that amplify the Cyt b gene in vertebrates and no other standardization, making it quick, easy, relatively inexpensive, and highly accurate. PMID:22389739

Low cycle fatigue behavior of a ferritic reactor pressure vessel steel

NASA Astrophysics Data System (ADS)

Sarkar, Apu; Kumawat, Bhupendra K.; Chakravartty, J. K.

2015-07-01

The cyclic stress-strain response and the low cycle fatigue (LCF) behavior of 20MnMoNi55 pressure vessel steel were studied. Tensile strength and LCF properties were examined at room temperature (RT) using specimens cut from rolling direction of a rolled block. The fully reversed strain-controlled LCF tests were conducted at a constant total strain rate with different axial strain amplitude levels. The cyclic strain-stress relationships and the strain-life relationships were obtained through the test results, and related LCF parameters of the steel were calculated. The studied steel exhibits cyclic softening behavior. Furthermore, analysis of stabilized hysteresis loops showed that the steel exhibits non-Masing behavior. Complementary scanning electron microscopy examinations were also carried out on fracture surfaces to reveal dominant damage mechanisms during crack initiation, propagation and fracture. Multiple crack initiation sites were observed on the fracture surface. The investigated LCF behavior can provide reference for pressure vessel life assessment and fracture mechanisms analysis.

Transcriptome and Metabolite Profiling of the Infection Cycle of Zymoseptoria tritici on Wheat Reveals a Biphasic Interaction with Plant Immunity Involving Differential Pathogen Chromosomal Contributions and a Variation on the Hemibiotrophic Lifestyle Definition1[OPEN

PubMed Central

Rudd, Jason J.; Kanyuka, Kostya; Hassani-Pak, Keywan; Derbyshire, Mark; Andongabo, Ambrose; Devonshire, Jean; Lysenko, Artem; Saqi, Mansoor; Desai, Nalini M.; Powers, Stephen J.; Hooper, Juliet; Ambroso, Linda; Bharti, Arvind; Farmer, Andrew; Hammond-Kosack, Kim E.; Dietrich, Robert A.; Courbot, Mikael

2015-01-01

The hemibiotrophic fungus Zymoseptoria tritici causes Septoria tritici blotch disease of wheat (Triticum aestivum). Pathogen reproduction on wheat occurs without cell penetration, suggesting that dynamic and intimate intercellular communication occurs between fungus and plant throughout the disease cycle. We used deep RNA sequencing and metabolomics to investigate the physiology of plant and pathogen throughout an asexual reproductive cycle of Z. tritici on wheat leaves. Over 3,000 pathogen genes, more than 7,000 wheat genes, and more than 300 metabolites were differentially regulated. Intriguingly, individual fungal chromosomes contributed unequally to the overall gene expression changes. Early transcriptional down-regulation of putative host defense genes was detected in inoculated leaves. There was little evidence for fungal nutrient acquisition from the plant throughout symptomless colonization by Z. tritici, which may instead be utilizing lipid and fatty acid stores for growth. However, the fungus then subsequently manipulated specific plant carbohydrates, including fructan metabolites, during the switch to necrotrophic growth and reproduction. This switch coincided with increased expression of jasmonic acid biosynthesis genes and large-scale activation of other plant defense responses. Fungal genes encoding putative secondary metabolite clusters and secreted effector proteins were identified with distinct infection phase-specific expression patterns, although functional analysis suggested that many have overlapping/redundant functions in virulence. The pathogenic lifestyle of Z. tritici on wheat revealed through this study, involving initial defense suppression by a slow-growing extracellular and nutritionally limited pathogen followed by defense (hyper) activation during reproduction, reveals a subtle modification of the conceptual definition of hemibiotrophic plant infection. PMID:25596183

Oligonucleotide microarray analysis of apoptosis induced by 15-methoxypinusolidic acid in microglial BV2 cells

PubMed Central

Choi, Y; Lim, SY; Jeong, HS; Koo, KA; Sung, SH; Kim, YC

2009-01-01

Background and purpose: We conducted a genome wide gene expression analysis to explore the biological aspects of 15-methoxypinusolidic acid (15-MPA) isolated from Biota orientalis and tried to confirm the suitability of 15-MPA as a therapeutic candidate for CNS injuries focusing on microglia. Experimental approach: Murine microglial BV2 cells were treated with 15-MPA, and their transcriptome was analysed by using oligonucleotide microarrays. Genes differentially expressed upon 15-MPA treatment were selected for RT-PCR (reverse transcription-polymerase chain reaction) analysis to confirm the gene expression. Inhibition of cell proliferation and induction of apoptosis by 15-MPA were examined by bromodeoxyuridine assay, Western blot analysis of poly-ADP-ribose polymerase and flow cytometry. Key results: A total of 514 genes were differentially expressed by 15-MPA treatment. Biological pathway analysis revealed that 15-MPA induced significant changes in expression of genes in the cell cycle pathway. Genes involved in growth arrest and DNA damage [gadd45α, gadd45γ and ddit3 (DNA damage-inducible transcript 3)] and cyclin-dependent kinase inhibitor (cdkn2b) were up-regulated, whereas genes involved in cell cycle progression (ccnd1, ccnd3 and ccne1), DNA replication (mcm4, orc1l and cdc6) and cell proliferation (fos and jun) were down-regulated. RT-PCR analysis for representative genes confirmed the expression levels. 15-MPA significantly reduced bromodeoxyuridine incorporation, increased poly-ADP-ribose polymerase cleavage and the number of apoptotic cells, indicating that 15-MPA induces apoptosis in BV2 cells. Conclusion and implications: 15-MPA induced apoptosis in murine microglial cells, presumably via inhibition of the cell cycle progression. As microglial activation is detrimental in CNS injuries, these data suggest a strong therapeutic potential of 15-MPA. PMID:19466985

The energy cycle and structural evolution of cyclones over southeastern South America in three case studies

NASA Astrophysics Data System (ADS)

Dias Pinto, JoãO. Rafael; Da Rocha, Rosmeri PorfíRio

2011-07-01

In this paper, the Lorenz energy cycle over a limited area was applied for three cyclones with different origins and evolutions, where each of them was formed in an important cyclogenetic region near southeastern South America. The synoptic conditions and energetics were analyzed during each system's life cycle and showed important relationships between their energy cycle and the evolution of their vertical structure. In the case of the weak baroclinic cyclone which formed on Brazil's south-southeastern coast, the analysis showed that it originated through a midlevel cutoff low with contribution from barotropic instability. Its evolution would indicate potential transition to a hybrid system if the convective activity were stronger. The system that occurred in the La Plata River mouth had features of an oceanic bomb-type cyclogenesis and showed an important contribution from the available potential energy generation term through the latent heat release by the convection. Meanwhile, the system of the southern Argentina coast presented a classical baroclinic development of extratropical cyclogenesis in the energy cycle, from the wave amplification up to the final occlusion of the associated frontal system. These analyses revealed that the development of some cyclones that occur in eastern South America can present different mechanisms that are not related to the classical extratropical cyclogenesis.

The Impact of Amazonian Deforestation on Dry-Season Rainfall

NASA Technical Reports Server (NTRS)

Negri, Andrew J.; Adler, Robert F.; Xu, Li-Ming; Surratt, Jason; Starr, David OC. (Technical Monitor)

2002-01-01

Many modeling studies have concluded that widespread deforestation of Amazonia would lead to decreased rainfall. We analyze geosynchronous infrared satellite data with respect percent cloudiness, and analyze rain estimates from microwave sensors aboard the Tropical Rainfall Measuring Mission satellite. We conclude that in the dry-season, when the effects of the surface are not overwhelmed by synoptic-scale weather disturbances, deep convective cloudiness, as well as rainfall occurrence, all increase over the deforested and non-forested (savanna) regions. This is in response to a local circulation initiated by the differential heating of the region's varying forestation. Analysis of the diurnal cycle of cloudiness reveals a shift toward afternoon hours in the deforested and savanna regions, compared to the forested regions. Analysis of 14 years of data from the Special Sensor Microwave/Imager data revealed that only in August did rainfall amounts increase over the deforested region.

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer

NASA Astrophysics Data System (ADS)

Tully, B. J.; Wheat, C. G.; Glazer, B. T.; Huber, J. A.

2017-12-01

The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized genomic reconstruction of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement. Twenty-one samples were collected during a two-year period at three different depths and two locations with the basaltic aquifer to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the two years, yet a dynamic microbial community was present in the crustal fluids that underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the dataset and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in a diverse group of microorganisms. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes and alternative electron acceptors. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles.

Exploring the Underlying Mechanisms of the Xenopus laevis Embryonic Cell Cycle.

PubMed

Zhang, Kun; Wang, Jin

2018-05-31

The cell cycle is an indispensable process in proliferation and development. Despite significant efforts, global quantification and physical understanding are still challenging. In this study, we explored the mechanisms of the Xenopus laevis embryonic cell cycle by quantifying the underlying landscape and flux. We uncovered the Mexican hat landscape of the Xenopus laevis embryonic cell cycle with several local basins and barriers on the oscillation path. The local basins characterize the different phases of the Xenopus laevis embryonic cell cycle, and the local barriers represent the checkpoints. The checkpoint mechanism of the cell cycle is revealed by the landscape basins and barriers. While landscape shape determines the stabilities of the states on the oscillation path, the curl flux force determines the stability of the cell cycle flow. Replication is fundamental for biology of living cells. We quantify the input energy (through the entropy production) as the thermodynamic requirement for initiation and sustainability of single cell life (cell cycle). Furthermore, we also quantify curl flux originated from the input energy as the dynamical requirement for the emergence of a new stable phase (cell cycle). This can provide a new quantitative insight for the origin of single cell life. In fact, the curl flux originated from the energy input or nutrition supply determines the speed and guarantees the progression of the cell cycle. The speed of the cell cycle is a hallmark of cancer. We characterized the quality of the cell cycle by the coherence time and found it is supported by the flux and energy cost. We are also able to quantify the degree of time irreversibility by the cross correlation function forward and backward in time from the stochastic traces in the simulation or experiments, providing a way for the quantification of the time irreversibility and the flux. Through global sensitivity analysis upon landscape and flux, we can identify the key elements for controlling the cell cycle speed. This can help to design an effective strategy for drug discovery against cancer.

Master and novice secondary science teachers' understandings and use of the learning cycle

NASA Astrophysics Data System (ADS)

Reap, Melanie Ann

2000-09-01

The learning cycle paradigm had been used in science classrooms for nearly four decades. This investigation seeks to reveal how the 1earning cycle, as originally designed, is currently understood and implemented by teachers in authentic classroom settings. The specific purposes of this study were: (1) to describe teachers who use the learning cycle and compare their understandings and perceptions of the learning cycle procedure in instruction; (2) to elicit novice and master teacher perspectives on their instruction and determine their perception of the process by which learning cycles are implemented in the science classroom; (3) to describe the context of science instruction in the novice and master teacher's classroom to ascertain how the teacher facilitates implementation of the learning cycle paradigm in their authentic classroom setting. The study used a learning cycle survey, interviews and classroom observations using the Learning Cycle Teacher Behavior Instruments and the Verbal Interaction Category System to explore these features of learning cycle instruction. The learning cycle survey was administered to a sample of teachers who use the learning cycle, including master and novice learning cycle teachers. One master and one novice learning cycle teacher were selected from this sample for further study. Analysis of the surveys showed no significant differences in master and novice teacher understandings of the learning cycle as assessed by the instrument. However, interviews and observations of the selected master and novice learning cycle teachers showed several differences in how the paradigm is understood and implemented in the classroom. The master learning cycle teacher showed a more developed teaching philosophy and had more engaged, extensive interactions with students. The novice learning cycle teacher held a more naive teaching philosophy and had fewer, less developed interactions with students. The most significant difference was seen in the use of questioning and discussion. The master teacher used diverse questioning techniques and guided students in discussion of their findings while the novice teachers used more rote response questions and controlled the discussion. The findings of this study have implications for science teacher education, especially in the preparation of teachers in science methods courses and student teaching, and in in-service education programs.

Effects of the menstrual cycle phases on the tilt testing results in vasovagal patients.

PubMed

Zyśko, Dorota; Gajek, Jacek; Terpiłowski, Lukasz; Agrawal, Anil Kumar; Wróblewski, Paweł; Rudnicki, Jerzy

2012-08-01

The aim of the study was to assess the distribution of positive tilt testing (TT) throughout the menstrual cycle and to determine if the phase of menstrual cycle contributes to the duration of the loss of consciousness. TT results of 183 premenopausal women, aged 29.5 ± 9.8 years, were studied. The menstrual cycle was divided into four phases based on the first day of the last menstrual bleeding: perimenstrual (M), preovulatory (F), periovulatory (O) and postovulatory (L). Positive TT results were equally distributed. In patients with TT in O phase, the highest percentage of NTG provocation was needed. Patients in L phase had significantly lower incidence of cardioinhibitory reaction. The longest duration of loss of consciousness was in the M phase. Multiple regression analysis revealed that the duration of loss of consciousness during positive TT was significantly associated with higher number of syncopal events, TT performed in M phase and lower heart rate at TT termination. Cardiodepressive type of neurocardiogenic reaction was more frequent during M and O phase than during L phase. The distribution of positive TT results as well as syncope and presyncope does not differ throughout the menstrual cycle. Diagnostic TT in premenopausal women with unexplained syncope could be performed irrespective of the phase of menstrual cycle. TT has similar sensitivity throughout the menstrual cycle. During the postovulatory phase, cardioinhibitory reaction is less frequent than in M and O phases. The duration of loss of consciousness is longer during the M phase of the menstrual cycle independently of the higher syncope number and lower heart rate at TT termination.

Revealing the cellular localization of STAT1 during the cell cycle by super-resolution imaging

PubMed Central

Gao, Jing; Wang, Feng; Liu, Yanhou; Cai, Mingjun; Xu, Haijiao; Jiang, Junguang; Wang, Hongda

2015-01-01

Signal transducers and activators of transcription (STATs) can transduce cytokine signals and regulate gene expression. The cellular localization and nuclear trafficking of STAT1, a representative of the STAT family with multiple transcriptional functions, is tightly related with transcription process, which usually happens in the interphase of the cell cycle. However, these priority questions regarding STAT1 distribution and localization at the different cell-cycle stages remain unclear. By using direct stochastic optical reconstruction microscopy (dSTORM), we found that the nuclear expression level of STAT1 increased gradually as the cell cycle carried out, especially after EGF stimulation. Furthermore, STAT1 formed clusters in the whole cell during the cell cycle, with the size and the number of clusters also increasing significantly from G1 to G2 phase, suggesting that transcription and other cell-cycle related activities can promote STAT1 to form more and larger clusters for fast response to signals. Our work reveals that the cellular localization and clustering distribution of STAT1 are associated with the cell cycle, and further provides an insight into the mechanism of cell-cycle regulated STAT1 signal transduction. PMID:25762114

Members of the Dof transcription factor family in Triticum aestivum are associated with light-mediated gene regulation.

PubMed

Shaw, Lindsay M; McIntyre, C Lynne; Gresshoff, Peter M; Xue, Gang-Ping

2009-11-01

DNA binding with One Finger (Dof) protein is a plant-specific transcription factor implicated in the regulation of many important plant-specific processes, including photosynthesis and carbohydrate metabolism. This study has identified 31 Dof genes (TaDof) in bread wheat through extensive analysis of current nucleotide databases. Phylogenetic analysis suggests that the TaDof family can be divided into four clades. Expression analysis of the TaDof family across all major organs using quantitative RT-PCR and searches of the wheat genome array database revealed that the majority of TaDof members were predominately expressed in vegetative organs. A large number of TaDof members were down-regulated by drought and/or were responsive to the light and dark cycle. Further expression analysis revealed that light up-regulated TaDof members were highly correlated in expression with a number of genes that are involved in photosynthesis or sucrose transport. These data suggest that the TaDof family may have an important role in light-mediated gene regulation, including involvement in the photosynthetic process.

A Method of Accounting for Enzyme Costs in Flux Balance Analysis Reveals Alternative Pathways and Metabolite Stores in an Illuminated Arabidopsis Leaf.

PubMed

Cheung, C Y Maurice; Ratcliffe, R George; Sweetlove, Lee J

2015-11-01

Flux balance analysis of plant metabolism is an established method for predicting metabolic flux phenotypes and for exploring the way in which the plant metabolic network delivers specific outcomes in different cell types, tissues, and temporal phases. A recurring theme is the need to explore the flexibility of the network in meeting its objectives and, in particular, to establish the extent to which alternative pathways can contribute to achieving specific outcomes. Unfortunately, predictions from conventional flux balance analysis minimize the simultaneous operation of alternative pathways, but by introducing flux-weighting factors to allow for the variable intrinsic cost of supporting each flux, it is possible to activate different pathways in individual simulations and, thus, to explore alternative pathways by averaging thousands of simulations. This new method has been applied to a diel genome-scale model of Arabidopsis (Arabidopsis thaliana) leaf metabolism to explore the flexibility of the network in meeting the metabolic requirements of the leaf in the light. This identified alternative flux modes in the Calvin-Benson cycle revealed the potential for alternative transitory carbon stores in leaves and led to predictions about the light-dependent contribution of alternative electron flow pathways and futile cycles in energy rebalancing. Notable features of the analysis include the light-dependent tradeoff between the use of carbohydrates and four-carbon organic acids as transitory storage forms and the way in which multiple pathways for the consumption of ATP and NADPH can contribute to the balancing of the requirements of photosynthetic metabolism with the energy available from photon capture. © 2015 American Society of Plant Biologists. All Rights Reserved.

THERMAL NON-EQUILIBRIUM REVEALED BY PERIODIC PULSES OF RANDOM AMPLITUDES IN SOLAR CORONAL LOOPS

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

Auchère, F.; Froment, C.; Bocchialini, K.

2016-08-20

We recently detected variations in extreme ultraviolet intensity in coronal loops repeating with periods of several hours. Models of loops including stratified and quasi-steady heating predict the development of a state of thermal non-equilibrium (TNE): cycles of evaporative upflows at the footpoints followed by falling condensations at the apex. Based on Fourier and wavelet analysis, we demonstrate that the observed periodic signals are indeed not signatures of vibrational modes. Instead, superimposed on the power law expected from the stochastic background emission, the power spectra of the time series exhibit the discrete harmonics and continua expected from periodic trains of pulsesmore » of random amplitudes. These characteristics reinforce our earlier interpretation of these pulsations as being aborted TNE cycles.« less

Channel width dependence of electrical characteristics of a-Si:H TFTs under bending stresses

NASA Astrophysics Data System (ADS)

Oh, Hyungon; Cho, Kyoungah; Kim, Sangsig

2017-04-01

In this study, we investigate the electrical characteristics of bendable a-Si:H thin-film transistors (TFTs) with various channel widths as a function of bending stress. Compared with a narrower channel TFT, a wider channel TFT exhibits a stable performance even at a bending strain of 1.3%. Our stress and strain distribution analysis reveals an inverse relationship between the channel width and the channel stress. As the channel width widens from 8 to 50 μm, the stress experienced by the middle channel region decreases from 545 to 277 MPa. Moreover, a 50 μm-channel-width TFT operates stably even after a 15 000 bending cycle while the 8 μm-channel-width TFT fails to operate after a 2000 bending cycle.

Seasonal water storage, stress modulation, and California seismicity.

PubMed

Johnson, Christopher W; Fu, Yuning; Bürgmann, Roland

2017-06-16

Establishing what controls the timing of earthquakes is fundamental to understanding the nature of the earthquake cycle and critical to determining time-dependent earthquake hazard. Seasonal loading provides a natural laboratory to explore the crustal response to a quantifiable transient force. In California, water storage deforms the crust as snow and water accumulates during the wet winter months. We used 9 years of global positioning system (GPS) vertical deformation time series to constrain models of monthly hydrospheric loading and the resulting stress changes on fault planes of small earthquakes. The seasonal loading analysis reveals earthquakes occurring more frequently during stress conditions that favor earthquake rupture. We infer that California seismicity rates are modestly modulated by natural hydrological loading cycles. Copyright © 2017, American Association for the Advancement of Science.

Synthesis and anticancer activity of novel curcumin-quinolone hybrids.

PubMed

Raghavan, Saiharish; Manogaran, Prasath; Gadepalli Narasimha, Krishna Kumari; Kalpattu Kuppusami, Balasubramanian; Mariyappan, Palanivelu; Gopalakrishnan, Anjana; Venkatraman, Ganesh

2015-09-01

A number of new curcumin-quinolone hybrids were synthesised from differently substituted 3-formyl-2-quinolones and vanillin and their in vitro cytotoxicity was determined on a panel of representative cell lines (A549, MCF7, SKOV3 and H460) using MTT assay. The most potent compound 14, was analysed for its mode of action using various cell biology experiments. SKOV3 cells treated with compound 14 showed distorted cell morphology under phase contrast imaging and induction of apoptosis was confirmed by Annexin V/PE assay. Further experiments on generation of reactive oxygen species (ROS) and cell cycle analysis revealed that these hybrids induce apoptosis by ROS generation and arrest cell cycle progression in S and G2/M phase. Copyright © 2015 Elsevier Ltd. All rights reserved.

Purine analogue ENERGI-F706 induces apoptosis of 786-O renal carcinoma cells via 5'-adenosine monophosphate-activated protein kinase activation.

PubMed

Hsu, Chao-Yu; Lin, Chun-Hsiang; Lin, Jiun-Tsai; Cheng, Yi-Fang; Chen, Han-Min; Kao, Shao-Hsuan

2015-09-01

Purine compounds are known to activate 5'-adenosine monophosphate-activated protein kinase (AMPK), which has important roles in treatments for renal cell carcinoma. The present study was aimed to investigate the effects of the purine analogue ENERGI‑F706 on the human renal carcinoma cell line 786‑O and the underlying mechanisms. The results revealed that ENERGI‑F706 (0.2‑0.6 mg/ml) significantly decreased the cell viability to up to 36.4±2.4% of that of the control. Compared to 786‑O cells, ENERGI‑F706 exerted less suppressive effects on the viability of the human non‑tumorigenic renal cell line HK‑2. Flow cytometric analysis showed that ENERGI‑F706 contributed to cell cycle arrest at S‑phase and triggered apoptosis of 786‑O cells. Immunoblot analysis revealed that anti‑apoptotic B‑cell lymphoma 2 (Bcl‑2) levels were reduced and pro‑apoptotic Bcl‑2‑associated X protein levels were diminished. In addition, activation of caspase‑9, caspase‑3 and poly(adenosine diphosphate ribose) polymerase (PARP) was promoted in 786‑O cells in response to ENERGI‑F706. Effects of ENERGI‑F706 on AMPK cascades were investigated and the results showed that ENERGI‑F706 enhanced phosphorylation of AMPKα (T172) and p53 (S15), a downstream target of AMPK. In addition, the AMPK activation, p53 (S15) phosphorylation, reduction of Bcl‑2, cleavage of caspase‑3 and PARP as well as suppressed cell viability induced by ENERGI‑F706 were reversed in the presence of AMPK inhibitor compound C (dorsomorphin). In conclusion, the findings of the present study revealed that ENERGI‑F706 significantly suppressed the viability of 786‑O cells via induction of cell cycle arrest and apoptosis, attributing to AMPK and p53 activation and subsequent cell cycle regulatory and apoptotic signaling. It was therefore indicated that ENERGI‑F706 may be suitable for the treatment of renal cell carcinoma.

Analysis of the weekly cycle of aerosol optical depth using AERONET and MODIS data

NASA Astrophysics Data System (ADS)

Xia, Xiangao; Eck, Tom F.; Holben, Brent N.; Phillippe, Goloub; Chen, Hongbin

2008-07-01

Multi-year Aerosol Robotic Network (AERONET) and Moderate Resolution Imaging Spectroradiometer (MODIS) aerosol optical depth (AOD) data are used to study AOD weekly variations at the global scale. A clear weekly cycle of AOD is observed in the United States (U.S.) and Central Europe. AOD during the weekday is larger than that during the weekend in 36 out of 43 AERONET sites in the U.S. The average U.S. weekend effect (the percent difference in AOD during the weekday and the weekend) is 3.8%. A weekly periodicity with lower AODs on Sunday and Monday and higher AODs from Wednesday until Saturday is revealed over Central Europe and the average weekend effect there is 4.0%. The weekly cycle in urban sites is greater than that in rural sites. AOD during the weekday is also significantly larger than that during the weekend in urban AERONET sites in South America and South Korea. However, a reversed AOD weekly cycle is observed in the Middle East and India. AODs on Thursday and Friday, the "weekend" for Middle East cultures, are relatively lower than AODs on other days. There is no clear weekly variation of AOD over eastern China. The striking feature in this region is the occurrence of much higher AOD on Sunday and this phenomenon is independent of season. The analysis of MODIS aerosol data is in good agreement with that of AERONET data.

Fisetin and hesperetin induced apoptosis and cell cycle arrest in chronic myeloid leukemia cells accompanied by modulation of cellular signaling.

PubMed

Adan, Aysun; Baran, Yusuf

2016-05-01

Fisetin and hesperetin, naturally occurring flavonoids, have been reported as novel antioxidants with chemopreventive/chemotherapeutic potential against various types of cancer. However, their mechanism of action in CML is still unknown. This particular study aims to evaluate the therapeutic potentials of fisetin and hesperetin and their effects on cell proliferation, apoptosis, and cell cycle progression in human K562 CML cells. The results indicated that fisetin and hesperetin inhibited cell proliferation and triggered programmed cell death in these cells. The latter was confırmed by mitochondrial membrane depolarization and an increase in caspase-3 activation. In addition to that, we have detected S and G2/M cell cycle arrests and G0/G1 arrest upon fisetin and hesperetin treatment, respectively. To identify the altered genes and genetic networks in response to fisetin and hesperetin, whole-genome microarray analysis was performed. The microarray gene profiling analysis revealed some important signaling pathways including JAK/STAT pathway, KIT receptor signaling, and growth hormone receptor signaling that were altered upon fisetin and hesperetin treatment. Moreover, microarray data suggested potential candidate genes for targeted CML therapy. Fisetin and hesperetin significantly modulated the expression of genes involved in cell proliferation and division, apoptosis, cell cycle regulation, and other significant cellular processes such as replication, transcription, and translation. In conclusion, our results suggest that fisetin and hesperetin as potential natural agents for CML therapy.

Evidence of solar activity and El Niño signals in tree rings of Araucaria araucana and A. angustifolia in South America

NASA Astrophysics Data System (ADS)

Perone, A.; Lombardi, F.; Marchetti, M.; Tognetti, R.; Lasserre, B.

2016-10-01

Tree rings reveal climatic variations through years, but also the effect of solar activity in influencing the climate on a large scale. In order to investigate the role of solar cycles on climatic variability and to analyse their influences on tree growth, we focused on tree-ring chronologies of Araucaria angustifolia and Araucaria araucana in four study areas: Irati and Curitiba in Brazil, Caviahue in Chile, and Tolhuaca in Argentina. We obtained an average tree-ring chronology of 218, 117, 439, and 849 years for these areas, respectively. Particularly, the older chronologies also included the period of the Maunder and Dalton minima. To identify periodicities and trends observable in tree growth, the time series were analysed using spectral, wavelet and cross-wavelet techniques. Analysis based on the Multitaper method of annual growth rates identified 2 cycles with periodicities of 11 (Schwebe cycle) and 5.5 years (second harmonic of Schwebe cycle). In the Chilean and Argentinian sites, significant agreement between the time series of tree rings and the 11-year solar cycle was found during the periods of maximum solar activity. Results also showed oscillation with periods of 2-7 years, probably induced by local environmental variations, and possibly also related to the El-Niño events. Moreover, the Morlet complex wavelet analysis was applied to study the most relevant variability factors affecting tree-ring time series. Finally, we applied the cross-wavelet spectral analysis to evaluate the time lags between tree-ring and sunspot-number time series, as well as for the interaction between tree rings, the Southern Oscillation Index (SOI) and temperature and precipitation. Trees sampled in Chile and Argentina showed more evident responses of fluctuations in tree-ring time series to the variations of short and long periodicities in comparison with the Brazilian ones. These results provided new evidence on the solar activity-climate pattern-tree ring connections over centuries.

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

Gurgenashvili, Eka; Zaqarashvili, Teimuraz V.; Kukhianidze, Vasil

Rieger-type periodicity has been detected in different activity indices over many solar cycles. It was recently shown that the periodicity correlates with solar activity having a shorter period during stronger cycles. Solar activity level is generally asymmetric between northern and southern hemispheres, which could suggest the presence of a similar behavior in the Rieger-type periodicity. We analyze the sunspot area/number and the total magnetic flux data for northern and southern hemispheres during solar cycles 19–23, which had remarkable north–south asymmetry. Using wavelet analysis of sunspot area and number during the north-dominated cycles (19–20), we obtained the periodicity of 160–165 daysmore » in the stronger northern hemisphere and 180–190 days in the weaker southern hemisphere. On the other hand, south-dominated cycles (21–23) display the periodicity of 155–160 days in the stronger southern hemisphere and 175–188 days in the weaker northern hemisphere. Therefore, the Rieger-type periodicity has the north–south asymmetry in sunspot area/number data during solar cycles with strong hemispheric asymmetry. We suggest that the periodicity is caused by magnetic Rossby waves in the internal dynamo layer. Using the dispersion relation of magnetic Rossby waves and observed Rieger periodicity, we estimated the magnetic field strength in the layer as 45–49 kG in more active hemispheres (north during cycles 19–20 and south during cycles 21–23) and 33–40 kG in weaker hemispheres. The estimated difference in the hemispheric field strength is around 10 kG, which provides a challenge for dynamo models. Total magnetic flux data during cycles 20–23 reveals no clear north–south asymmetry, which needs to be explained in the future.« less

How well do we know the global water cycle? - Intercomparison and Performance Analysis of the Hydrological Cycle in Three State-of-the-Art Reanalyses

NASA Astrophysics Data System (ADS)

Kunstmann, H.; Lorenz, C.

2012-12-01

The three state-of-the-art global atmospheric reanalysis models—namely, ECMWF Interim Re-Analysis (ERA-Interim), Modern-Era Retrospective Analysis for Research and Applications (MERRA; NASA), and Climate Forecast System Reanalysis (CFSR; NCEP)—are analyzed and compared with independent observations (GPCC; GPCP; CRU; CPC; DEL; HOAPS) in the period between 1989 and 2006. Comparison of precipitation and temperature estimates from the three models with gridded observations reveals large differences between the reanalyses and also of the observation datasets. A major source of uncertainty in the observations is the spatial distribution and change of the number of gauges over time. In South America for example, active measuring stations were reduced from 4267 to 390. The quality of precipitation estimates from the reanalyses strongly depends on the geographic location, as there are significant differences especially in tropical regions. The closure of the water cycle in the three reanalyses is analyzed by estimating long-term mean values for precipitation, evapotranspiration, surface runoff, and moisture flux divergence. Major shortcomings in the moisture budgets of the datasets are mainly due to inconsistencies of the net precipitation minus evaporation and evapotranspiration, respectively, (P-E) estimates over the oceans and landmasses. This imbalance largely originates from the assimilation of radiance sounding data from the NOAA-15 satellite, which results in an unrealistic increase of oceanic P-E in the MERRA and CFSR budgets. Overall, ERA-Interim shows both a comparatively reasonable closure of the terrestrial and atmospheric water balance and a reasonable agreement with the observation datasets. The limited performance of the three state-of-the-art reanalyses in reproducing the hydrological cycle, however, puts the use of these models for climate trend analyses and long-term water budget studies into question.

Molecular characterization and phylogenetic relationships among microsporidian isolates infecting silkworm, Bombyx mori using small subunit rRNA (SSU-rRNA) gene sequence analysis.

PubMed

Nath, B Surendra; Gupta, S K; Bajpai, A K

2012-12-01

The life cycle, spore morphology, pathogenicity, tissue specificity, mode of transmission and small subunit rRNA (SSU-rRNA) gene sequence analysis of the five new microsporidian isolates viz., NIWB-11bp, NIWB-12n, NIWB-13md, NIWB-14b and NIWB-15mb identified from the silkworm, Bombyx mori have been studied along with type species, NIK-1s_mys. The life cycle of the microsporidians identified exhibited the sequential developmental cycles that are similar to the general developmental cycle of the genus, Nosema. The spores showed considerable variations in their shape, length and width. The pathogenicity observed was dose-dependent and differed from each of the microsporidian isolates; the NIWB-15mb was found to be more virulent than other isolates. All of the microsporidians were found to infect most of the tissues examined and showed gonadal infection and transovarial transmission in the infected silkworms. SSU-rRNA sequence based phylogenetic tree placed NIWB-14b, NIWB-12n and NIWB-11bp in a separate branch along with other Nosema species and Nosema bombycis; while NIWB-15mb and NIWB-13md together formed another cluster along with other Nosema species. NIK-1s_mys revealed a signature sequence similar to standard type species, N. bombycis, indicating that NIK-1s_mys is similar to N. bombycis. Based on phylogenetic relationships, branch length information based on genetic distance and nucleotide differences, we conclude that the microsporidian isolates identified are distinctly different from the other known species and belonging to the genus, Nosema. This SSU-rRNA gene sequence analysis method is found to be more useful approach in detecting different and closely related microsporidians of this economically important domestic insect.

Micropollutants in urban watersheds : substance flow analysis as management tool

NASA Astrophysics Data System (ADS)

Rossi, L.; Copin, P. J.; Barry, A. D.; Bader, H.-P.; Scheidegger, R.; Chèvre, N.

2009-04-01

Micropollutants released by cities into water are of increasing concern as they are suspected of inducing long-term effects on both aquatic organisms and humans (eg., hormonally active substances). Substances found in the urban water cycle have different sources in the urban area and different fates in this cycle. For example, the pollutants emitted from traffic, like copper or PAHs get to surface water during rain events often without any treatment. Pharmaceuticals resulting from human medical treatments get to surface water mainly through wastewater treatment plants, where they are only partly treated and eliminated. One other source of contamination in urban areas for these compounds are combined sewer overflows (CSOs). Once in the receiving waters (lakes, rivers, groundwater), these substances may re-enter the cycle through drinking water. It is therefore crucial to study the behaviour of micropollutants in the urban water cycle and to get flexible tools for urban water management. Substance flow analysis (SFA) has recently been proposed as instrument for water pollution management in urban water systems. This kind of analysis is an extension of material flow analysis (MFA) originally developed in the economic sector and later adapted to regional investigations. In this study, we propose to test the application of SFA for a large number of classes of micropollutants to evaluate its use for urban water management. We chose the city of Lausanne as case study since the receiving water of this city (Lake Geneva) is an important source of drinking water for the surrounding population. Moreover a profound system-knowledge and many data were available, both on the sewer system and the water quality. We focus our study on one heavy metal (copper) and four pharmaceuticals (diclofenac, ibuprofen, carbamazepine and naproxen). Results conducted on copper reveals that around 1500 kg of copper enter the aquatic compartment yearly. This amount contributes to sediment enrichment, which may pose a long-term risk for the benthic organisms. The major sources (total of 73%) of copper in receiving surface water are roofs and contact lines of trolleybuses. Thus technical solutions have to be found to manage this specific source of contamination. Application of SFA approach to four pharmaceuticals reveals that CSOs represent an important source of contamination: Between 14% (carbamazepine) and 61% (ibuprofen) of the total annual loads of Lausanne city to the Lake are due to CSOs. These results will help in defining the best management strategy to limit Lake Geneva contamination. SFA is thus a promising tool for integrated urban water management.

LIFE CYCLE BASED STUDIES ON BIOETHANOL FUEL FOR SUSTAINABLE TRANSPORTATION: A LITERATURE REVIEW

EPA Science Inventory

A literature search was conducted and revealed 45 publications (1996-2005) that compare bio-ethanol systems to conventional fuel on a life-cycle basis, or using life cycle assessment. Feedstocks, such as sugar beets, wheat, potato, sugar cane, and corn, have been investigated in...

Changing perceptions of cycling in the African American community to encourage participation in a sport that promotes health in adults.

DOT National Transportation Integrated Search

2015-06-01

This study introduces two interventions designed to influence perceptions of cycling among African : Americans. Results from the 2001 National Household Transportation Survey reveal that African Americans : cycle at two-thirds the rate of White and H...

Functional Study of Genes Essential for Autogamy and Nuclear Reorganization in Paramecium▿§

PubMed Central

Nowak, Jacek K.; Gromadka, Robert; Juszczuk, Marek; Jerka-Dziadosz, Maria; Maliszewska, Kamila; Mucchielli, Marie-Hélène; Gout, Jean-François; Arnaiz, Olivier; Agier, Nicolas; Tang, Thomas; Aggerbeck, Lawrence P.; Cohen, Jean; Delacroix, Hervé; Sperling, Linda; Herbert, Christopher J.; Zagulski, Marek; Bétermier, Mireille

2011-01-01

Like all ciliates, Paramecium tetraurelia is a unicellular eukaryote that harbors two kinds of nuclei within its cytoplasm. At each sexual cycle, a new somatic macronucleus (MAC) develops from the germ line micronucleus (MIC) through a sequence of complex events, which includes meiosis, karyogamy, and assembly of the MAC genome from MIC sequences. The latter process involves developmentally programmed genome rearrangements controlled by noncoding RNAs and a specialized RNA interference machinery. We describe our first attempts to identify genes and biological processes that contribute to the progression of the sexual cycle. Given the high percentage of unknown genes annotated in the P. tetraurelia genome, we applied a global strategy to monitor gene expression profiles during autogamy, a self-fertilization process. We focused this pilot study on the genes carried by the largest somatic chromosome and designed dedicated DNA arrays covering 484 genes from this chromosome (1.2% of all genes annotated in the genome). Transcriptome analysis revealed four major patterns of gene expression, including two successive waves of gene induction. Functional analysis of 15 upregulated genes revealed four that are essential for vegetative growth, one of which is involved in the maintenance of MAC integrity and another in cell division or membrane trafficking. Two additional genes, encoding a MIC-specific protein and a putative RNA helicase localizing to the old and then to the new MAC, are specifically required during sexual processes. Our work provides a proof of principle that genes essential for meiosis and nuclear reorganization can be uncovered following genome-wide transcriptome analysis. PMID:21257794

Multilocus sequence analysis of Anaplasma phagocytophilum reveals three distinct lineages with different host ranges in clinically ill French cattle.

PubMed

Chastagner, Amélie; Dugat, Thibaud; Vourc'h, Gwenaël; Verheyden, Hélène; Legrand, Loïc; Bachy, Véronique; Chabanne, Luc; Joncour, Guy; Maillard, Renaud; Boulouis, Henri-Jean; Haddad, Nadia; Bailly, Xavier; Leblond, Agnès

2014-12-09

Molecular epidemiology represents a powerful approach to elucidate the complex epidemiological cycles of multi-host pathogens, such as Anaplasma phagocytophilum. A. phagocytophilum is a tick-borne bacterium that affects a wide range of wild and domesticated animals. Here, we characterized its genetic diversity in populations of French cattle; we then compared the observed genotypes with those found in horses, dogs, and roe deer to determine whether genotypes of A. phagocytophilum are shared among different hosts. We sampled 120 domesticated animals (104 cattle, 13 horses, and 3 dogs) and 40 wild animals (roe deer) and used multilocus sequence analysis on nine loci (ankA, msp4, groESL, typA, pled, gyrA, recG, polA, and an intergenic region) to characterize the genotypes of A. phagocytophilum present. Phylogenic analysis revealed three genetic clusters of bacterial variants in domesticated animals. The two principal clusters included 98% of the bacterial genotypes found in cattle, which were only distantly related to those in roe deer. One cluster comprised only cattle genotypes, while the second contained genotypes from cattle, horses, and dogs. The third contained all roe deer genotypes and three cattle genotypes. Geographical factors could not explain this clustering pattern. These results suggest that roe deer do not contribute to the spread of A. phagocytophilum in cattle in France. Further studies should explore if these different clusters are associated with differing disease severity in domesticated hosts. Additionally, it remains to be seen if the three clusters of A. phagocytophilum genotypes in cattle correspond to distinct epidemiological cycles, potentially involving different reservoir hosts.

Mechanisms of nuclear lamina growth in interphase.

PubMed

Zhironkina, Oxana A; Kurchashova, Svetlana Yu; Pozharskaia, Vasilisa A; Cherepanynets, Varvara D; Strelkova, Olga S; Hozak, Pavel; Kireev, Igor I

2016-04-01

The nuclear lamina represents a multifunctional platform involved in such diverse yet interconnected processes as spatial organization of the genome, maintenance of mechanical stability of the nucleus, regulation of transcription and replication. Most of lamina activities are exerted through tethering of lamina-associated chromatin domains (LADs) to the nuclear periphery. Yet, the lamina is a dynamic structure demonstrating considerable expansion during the cell cycle to accommodate increased number of LADs formed during DNA replication. We analyzed dynamics of nuclear growth during interphase and changes in lamina structure as a function of cell cycle progression. The nuclear lamina demonstrates steady growth from G1 till G2, while quantitative analysis of lamina meshwork by super-resolution microscopy revealed that microdomain organization of the lamina is maintained, with lamin A and lamin B microdomain periodicity and interdomain gap sizes unchanged. FRAP analysis, in contrast, demonstrated differences in lamin A and B1 exchange rates; the latter showing higher recovery rate in S-phase cells. In order to further analyze the mechanism of lamina growth in interphase, we generated a lamina-free nuclear envelope in living interphase cells by reversible hypotonic shock. The nuclear envelope in nuclear buds formed after such a treatment initially lacked lamins, and analysis of lamina formation revealed striking difference in lamin A and B1 assembly: lamin A reassembled within 30 min post-treatment, whereas lamin B1 did not incorporate into the newly formed lamina at all. We suggest that in somatic cells lamin B1 meshwork growth is coordinated with replication of LADs, and lamin A meshwork assembly seems to be chromatin-independent process.

Endometrial thickness as a predictor of the reproductive outcomes in fresh and frozen embryo transfer cycles: A retrospective cohort study of 1512 IVF cycles with morphologically good-quality blastocyst.

PubMed

Zhang, Tao; Li, Zhou; Ren, Xinling; Huang, Bo; Zhu, Guijin; Yang, Wei; Jin, Lei

2018-01-01

To evaluate the relationship between endometrial thickness during fresh in vitro fertilization (IVF) cycles and the clinical outcomes of subsequent frozen embryo transfer (FET) cycles.FET cycles using at least one morphological good-quality blastocyst conducted between 2012 and 2013 at a university-based reproductive center were reviewed retrospectively. Endometrial ultrasonographic characteristics were recorded both on the oocyte retrieval day and on the day of progesterone supplementation in FET cycles. Clinical pregnancy rate, spontaneous abortion rate, and live birth rate were analyzed.One thousand five hundred twelve FET cycles was included. The results showed that significant difference in endometrial thickness on day of oocyte retrieval (P = .03) was observed between the live birth group (n = 844) and no live birth group (n = 668), while no significant difference in FET endometrial thickness was found (P = .261) between the live birth group and no live birth group. For endometrial thickness on oocyte retrieval day, clinical pregnancy rate ranged from 50.0% among patients with an endometrial thickness of ≤6 mm to 84.2% among patients with an endometrial thickness of >16 mm, with live birth rate from 33.3% to 63.2%. Multiple logistic regression analysis of factors related to live birth indicated endometrial thickness on oocyte retrieval day was associated with improved live birth rate (OR was 1.069, 95% CI: 1.011-1.130, P = .019), while FET endometrial thickness did not contribute significantly to pregnancy outcomes following FET cycles. The ROC curves revealed the cut-off points of endometrial thickness on oocyte retrieval day was 8.75 mm for live birth.Endometrial thickness during fresh IVF cycles was a better predictor of endometrial receptivity in subsequent FET cycles than FET cycle endometrial thickness. For those females with thin endometrium in fresh cycles, additional estradiol stimulation might be helpful for adequate endometrial development.

DNA fragmentation and cell cycle arrest: a hallmark of apoptosis induced by crocin from kashmiri saffron in a human pancreatic cancer cell line.

PubMed

Bakshi, Hamid; Sam, Smitha; Rozati, Roya; Sultan, Phalisteen; Islam, Tajamul; Rathore, Babita; Lone, Zahoor; Sharma, Manik; Triphati, Jagrati; Saxena, Ramesh Chand

2010-01-01

Apoptosis, a widely important mechanism that contributes to cell growth reduction, is reported to be induced by Crocus sativus in different cancer types. The present study was designed to elucidate apoptosis induction by crocin, a main component of Crocus sativus in a human pancreatic cancer cell line (BxPC-3). Cell viability was measured by MTT assay, Hoechest33258 staining was used to detect the chromatin condensation characteristic of apoptosis, and DNA fragmentation was assessed by gel electrophoresis and cell cycle analysis by flow cytometry. Crocin induced apoptosis and G1-phase cell cycle arrest of BxPC-3 cells, while decreasing cell viability in a dose dependent and time dependent manner. Cells treated with 10μg/L crocin exhibited apoptotic morphology (brightly blue-fluorescent condensed nuclei on Hoechst 33258 staining) and reduction of volume. DNA analysis revealed typical ladders as early as 12 hours after treatment indicative of apoptosis. Our preclinical study demonstrated a pancreatic cancer cell line to be highly sensitive to crocin-mediated growth inhibition and apoptotic cell death. Although the molecular mechanisms of crocin action are not yet clearly understood, it appears to have potential as a therapeutic agent.

Characterization of Chemosynthetic Microbial Mats Associated with Intertidal Hydrothermal Sulfur Vents in White Point, San Pedro, CA, USA

PubMed Central

Miranda, Priscilla J.; McLain, Nathan K.; Hatzenpichler, Roland; Orphan, Victoria J.; Dillon, Jesse G.

2016-01-01

The shallow-sea hydrothermal vents at White Point (WP) in Palos Verdes on the southern California coast support microbial mats and provide easily accessed settings in which to study chemolithoautotrophic sulfur cycling. Previous studies have cultured sulfur-oxidizing bacteria from the WP mats; however, almost nothing is known about the in situ diversity and activity of the microorganisms in these habitats. We studied the diversity, micron-scale spatial associations and metabolic activity of the mat community via sequence analysis of 16S rRNA and aprA genes, fluorescence in situ hybridization (FISH) microscopy and sulfate reduction rate (SRR) measurements. Sequence analysis revealed a diverse group of bacteria, dominated by sulfur cycling gamma-, epsilon-, and deltaproteobacterial lineages such as Marithrix, Sulfurovum, and Desulfuromusa. FISH microscopy suggests a close physical association between sulfur-oxidizing and sulfur-reducing genotypes, while radiotracer studies showed low, but detectable, SRR. Comparative 16S rRNA gene sequence analyses indicate the WP sulfur vent microbial mat community is similar, but distinct from other hydrothermal vent communities representing a range of biotopes and lithologic settings. These findings suggest a complete biological sulfur cycle is operating in the WP mat ecosystem mediated by diverse bacterial lineages, with some similarity with deep-sea hydrothermal vent communities. PMID:27512390

Fatigue of LiNi0.8Co0.15Al0.05O2 in commercial Li ion batteries

NASA Astrophysics Data System (ADS)

Kleiner, Karin; Dixon, Ditty; Jakes, Peter; Melke, Julia; Yavuz, Murat; Roth, Christina; Nikolowski, Kristian; Liebau, Verena; Ehrenberg, Helmut

2015-01-01

The degradation of LiNi0.8Co0.15Al0.05O2 (LNCAO), a cathode material in lithium-ion-batteries, was studied using in situ powder diffraction and in situ Ni K edge X-ray absorption spectroscopy (XAS). The fatigued material was taken from a 7 Ah battery which was cycled for 34 weeks under defined durability conditions. Meanwhile, a cell was stored, as reference, under controlled conditions without electrochemical treatment. The fatigued LNCAO used in this study showed a capacity loss of 26% ± 9% compared to the non-cycled material. During charge and discharge the local and the overall structure of LNCAO was investigated by X-ray near edge structure (XANES) analysis, the extended X-ray absorption fine structure (EXAFS) analysis and by using Rietveld refinement of in situ powder diffraction patterns. Both powder diffraction and XAS revealed additional, rhombohedral phases which do not change with electrochemical cycling. Moreover, a phase with the lattice parameters of fully lithiated LNCAO was still present in the fatigued material at high potentials, while it was absent in the non-fatigued reference material. The coexistence of these phases is described by domains within the LNCAO particles, in correlation with the observed fatigue.

Toward pre-conceptual genetic analysis of human spermatozoa.

PubMed

Dozortsev, Dmitri; Serafim, Rui; Cardoso, J Jakson; Abdelmassih, Soraya; Nagy, Peter; Diamond, Michael P; Abdelmassih, Roger

2003-01-01

Nuclei of mature mammalian spermatozoa are extraordinarily resistant to chemical and thermal injury. Additionally, decondensation of spermatozoa DNA can be accompanied by little or no visual changes of the sperm head. This study tested whether human spermatozoa could be recovered following several cycles of primer extension preamplification (PEP) and used to achieve fertilization and subsequent development of human oocytes. An attempt was also made to amplify PEP buffer after spermatozoon removal. The results demonstrate that the sperm head can be successfully recovered following treatment with KOH or proteinase K followed by one to four cycles of PEP. It is also shown that following this treatment, the spermatozoa can be injected into the oocytes and will transform into a pronucleus if the oocyte is activated by sperm cytosolic fraction. In some cases, it was also possible to obtain polymerase chain reaction signals using a buffer after sperm cells were removed following several cycles of PEP. Although sperm participation in development was confirmed by fluorescence in-situ hybridization, light microscopy revealed some degree of damage to spermatozoal chromosomes. It is concluded that pre-conceptual analysis of sperm cells may be possible, but more research is necessary to determine the optimal conditions that would preserve sperm DNA integrity while allowing accurate diagnoses.

Cyclic degassing of Erebus volcano, Antarctica

NASA Astrophysics Data System (ADS)

Ilanko, Tehnuka; Oppenheimer, Clive; Burgisser, Alain; Kyle, Philip

2015-06-01

Field observations have previously identified rapid cyclic changes in the behaviour of the lava lake of Erebus volcano. In order to understand more fully the nature and origins of these cycles, we present here a wavelet-based frequency analysis of time series measurements of gas emissions from the lava lake, obtained by open-path Fourier transform infrared spectroscopy. This reveals (i) a cyclic change in total gas column amount, a likely proxy for gas flux, with a period of about 10 min, and (ii) a similarly phased cyclic change in proportions of volcanic gases, which can be explained in terms of chemical equilibria and pressure-dependent solubilities. Notably, the wavelet analysis shows a persistent periodicity in the CO2/CO ratio and strong periodicity in H2O and SO2 degassing. The `peaks' of the cycles, defined by maxima in H2O and SO2 column amounts, coincide with high CO2/CO ratios and proportionally smaller increases in column amounts of CO2, CO, and OCS. We interpret the cycles to arise from recharge of the lake by intermittent pulses of magma from shallow depths, which degas H2O at low pressure, combined with a background gas flux that is decoupled from this very shallow magma degassing.

The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system.

PubMed

Niu, Jiaojiao; Deng, Jie; Xiao, Yunhua; He, Zhili; Zhang, Xian; Van Nostrand, J D; Liang, Yili; Deng, Ye; Liu, Xueduan; Yin, Huaqun

2016-10-04

Bioleaching has been employed commercially to recover metals from low grade ores, but the production efficiency remains to be improved due to limited understanding of the system. This study examined the shift of microbial communities and S&Fe cycling in three subsystems within a copper ore bioleaching system: leaching heap (LH), leaching solution (LS) and sediment under LS. Results showed that both LH and LS had higher relative abundance of S and Fe oxidizing bacteria, while S and Fe reducing bacteria were more abundant in the Sediment. GeoChip analysis showed a stronger functional potential for S 0 oxidation in LH microbial communities. These findings were consistent with measured oxidation activities to S 0 and Fe 2+ , which were highest by microbial communities from LH, lower by those from LS and lowest form Sediment. Moreover, phylogenetic molecular ecological network analysis indicated that these differences might be related to interactions among microbial taxa. Last but not the least, a conceptual model was proposed, linking the S&Fe cycling with responsible microbial populations in the bioleaching systems. Collectively, this study revealed the microbial community and functional structures in all three subsystems of the copper ore, and advanced a holistic understanding of the whole bioleaching system.

The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system

NASA Astrophysics Data System (ADS)

Niu, Jiaojiao; Deng, Jie; Xiao, Yunhua; He, Zhili; Zhang, Xian; van Nostrand, J. D.; Liang, Yili; Deng, Ye; Liu, Xueduan; Yin, Huaqun

2016-10-01

Bioleaching has been employed commercially to recover metals from low grade ores, but the production efficiency remains to be improved due to limited understanding of the system. This study examined the shift of microbial communities and S&Fe cycling in three subsystems within a copper ore bioleaching system: leaching heap (LH), leaching solution (LS) and sediment under LS. Results showed that both LH and LS had higher relative abundance of S and Fe oxidizing bacteria, while S and Fe reducing bacteria were more abundant in the Sediment. GeoChip analysis showed a stronger functional potential for S0 oxidation in LH microbial communities. These findings were consistent with measured oxidation activities to S0 and Fe2+, which were highest by microbial communities from LH, lower by those from LS and lowest form Sediment. Moreover, phylogenetic molecular ecological network analysis indicated that these differences might be related to interactions among microbial taxa. Last but not the least, a conceptual model was proposed, linking the S&Fe cycling with responsible microbial populations in the bioleaching systems. Collectively, this study revealed the microbial community and functional structures in all three subsystems of the copper ore, and advanced a holistic understanding of the whole bioleaching system.

The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system

PubMed Central

Niu, Jiaojiao; Deng, Jie; Xiao, Yunhua; He, Zhili; Zhang, Xian; Van Nostrand, J. D.; Liang, Yili; Deng, Ye; Liu, Xueduan; Yin, Huaqun

2016-01-01

Bioleaching has been employed commercially to recover metals from low grade ores, but the production efficiency remains to be improved due to limited understanding of the system. This study examined the shift of microbial communities and S&Fe cycling in three subsystems within a copper ore bioleaching system: leaching heap (LH), leaching solution (LS) and sediment under LS. Results showed that both LH and LS had higher relative abundance of S and Fe oxidizing bacteria, while S and Fe reducing bacteria were more abundant in the Sediment. GeoChip analysis showed a stronger functional potential for S0 oxidation in LH microbial communities. These findings were consistent with measured oxidation activities to S0 and Fe2+, which were highest by microbial communities from LH, lower by those from LS and lowest form Sediment. Moreover, phylogenetic molecular ecological network analysis indicated that these differences might be related to interactions among microbial taxa. Last but not the least, a conceptual model was proposed, linking the S&Fe cycling with responsible microbial populations in the bioleaching systems. Collectively, this study revealed the microbial community and functional structures in all three subsystems of the copper ore, and advanced a holistic understanding of the whole bioleaching system. PMID:27698381

An involvement of yeast peroxisomal channels in transmembrane transfer of glyoxylate cycle intermediates.

PubMed

Antonenkov, Vasily D; Mindthoff, Sabrina; Grunau, Silke; Erdmann, Ralf; Hiltunen, J Kalervo

2009-12-01

The separate localization of glyoxylate cycle enzymes in the peroxisomes and the cytosol of the yeast Saccharomyces cerevisiae indicates that the peroxisomal membrane must permit the flow of metabolites between the two compartments. The transfer of these metabolites may require peroxisomal membrane channel(s). We used an electrophysiological approach (reconstitution assay in lipid bilayers) to assess the ability of peroxisomal membrane channels to conduct different solutes including metabolites of the glyoxylate cycle. At least two distinct channel-forming activities were detected in peroxisomal preparations. One of these activities was highly inducible by dithiothreitol and showed large-amplitude current increments when 1M KCl was used as a bath solution. Single-channel analysis revealed that the inducible channel is anion-selective (P(Cl(-)) / P(K(+)) = 2.6; P(citrate)/P(K(+)) = 1.6) and displays flickering at holding potentials over + or - 30mV directed upward or downward relative to the main open state of the channel. The channel inducible by DTT facilitates the transfer of solutes with a molecular mass up to 400Da, sufficient to allow the transmembrane trafficking of glyoxylate cycle intermediates between the peroxisomal lumen and the cytoplasm.

Circadian Disruption Changes Gut Microbiome Taxa and Functional Gene Composition.

PubMed

Deaver, Jessica A; Eum, Sung Y; Toborek, Michal

2018-01-01

Disrupted circadian rhythms and alterations of the gut microbiome composition were proposed to affect host health. Therefore, the aim of this research was to identify whether these events are connected and if circadian rhythm disruption by abnormal light-dark (LD) cycles affects microbial community gene expression and host vulnerability to intestinal dysfunction. Mice were subjected to either a 4-week period of constant 24-h light or of normal 12-h LD cycles. Stool samples were collected at the beginning and after the circadian rhythm disruption. A metatranscriptomic analysis revealed an increase in Ruminococcus torques , a bacterial species known to decrease gut barrier integrity, and a decrease in Lactobacillus johnsonii , a bacterium that helps maintain the intestinal epithelial cell layer, after circadian rhythm disruption. In addition, genes involved in pathways promoting host beneficial immune responses were downregulated, while genes involved in the synthesis and transportation of the endotoxin lipopolysaccharide were upregulated in mice with disrupted circadian cycles. Importantly, these mice were also more prone to dysfunction of the intestinal barrier. These results further elucidate the impact of light-cycle disruption on the gut microbiome and its connection with increased incidence of disease in response to circadian rhythm disturbances.

Circadian Disruption Changes Gut Microbiome Taxa and Functional Gene Composition

PubMed Central

Deaver, Jessica A.; Eum, Sung Y.; Toborek, Michal

2018-01-01

Disrupted circadian rhythms and alterations of the gut microbiome composition were proposed to affect host health. Therefore, the aim of this research was to identify whether these events are connected and if circadian rhythm disruption by abnormal light–dark (LD) cycles affects microbial community gene expression and host vulnerability to intestinal dysfunction. Mice were subjected to either a 4-week period of constant 24-h light or of normal 12-h LD cycles. Stool samples were collected at the beginning and after the circadian rhythm disruption. A metatranscriptomic analysis revealed an increase in Ruminococcus torques, a bacterial species known to decrease gut barrier integrity, and a decrease in Lactobacillus johnsonii, a bacterium that helps maintain the intestinal epithelial cell layer, after circadian rhythm disruption. In addition, genes involved in pathways promoting host beneficial immune responses were downregulated, while genes involved in the synthesis and transportation of the endotoxin lipopolysaccharide were upregulated in mice with disrupted circadian cycles. Importantly, these mice were also more prone to dysfunction of the intestinal barrier. These results further elucidate the impact of light-cycle disruption on the gut microbiome and its connection with increased incidence of disease in response to circadian rhythm disturbances. PMID:29706947

Niche partitioning of marine group I Crenarchaeota in the euphotic and upper mesopelagic zones of the East China Sea.

PubMed

Hu, Anyi; Jiao, Nianzhi; Zhang, Rui; Yang, Zao

2011-11-01

Marine group I Crenarchaeota (MGI) represents a ubiquitous and numerically predominant microbial population in marine environments. An understanding of the spatial dynamics of MGI and its controlling mechanisms is essential for an understanding of the role of MGI in energy and element cycling in the ocean. In the present study, we investigated the diversity and abundance of MGI in the East China Sea (ECS) by analysis of crenarchaeal 16S rRNA gene, the ammonia monooxygenase gene amoA, and the biotin carboxylase gene accA. Quantitative PCR analyses revealed that these genes were higher in abundance in the mesopelagic than in the euphotic zone. In addition, the crenarchaeal amoA gene was positively correlated with the copy number of the MGI 16S rRNA gene, suggesting that most of the MGI in the ECS are nitrifiers. Furthermore, the ratios of crenarchaeal accA to amoA or to MGI 16S rRNA genes increased from the euphotic to the mesopelagic zone, suggesting that the role of MGI in carbon cycling may change from the epipelagic to the mesopelagic zones. Denaturing gradient gel electrophoretic profiling of the 16S rRNA genes revealed depth partitioning in MGI community structures. Clone libraries of the crenarchaeal amoA and accA genes showed both "shallow" and "deep" groups, and their relative abundances varied in the water column. Ecotype simulation analysis revealed that MGI in the upper ocean could diverge into special ecotypes associated with depth to adapt to the light gradient across the water column. Overall, our results showed niche partitioning of the MGI population and suggested a shift in their ecological functions between the euphotic and mesopelagic zones of the ECS.

The impact of ergometer design on hip and trunk muscle activity patterns in elite rowers: an electromyographic assessment.

PubMed

Nowicky, Alex V; Horne, Sara; Burdett, Richard

2005-03-01

THIS STUDY USED SURFACE ELECTROMYOGRAPHY (SEMG) TO EXAMINE WHETHER THERE WERE DIFFERENCES IN HIP AND TRUNK MUSCLE ACTIVATION DURING THE ROWING CYCLE ON TWO OF THE MOST WIDELY USED AIR BRAKED ERGOMETERS: the Concept 2C and the Rowperfect. sEMG methods were used to record the muscle activity patterns from the right: m. Erector spinae (ES), m. Rectus Abdominus (RA), m. Rectus Femoris (RF) and m. Biceps Femoris (BF) for their contributions as agonist-antagonist pairs underlying hip and trunk extension/flexion. The sEMG activity patterns of these muscles were examined in six young male elite rowers completing a 2 minute set at a moderate training intensity (23 stroke·min(-1) and 1:47.500 m(-1) split time, 300W). The rowers closely maintained the required target pace through visual inspection of the standard LCD display of each ergometer. The measurements of duration of each rowing cycle and onset of each stroke during the test were recorded simultaneously with the sEMG activity through the additional instrumentation of a foot-pressure switch and handle accelerometry. There were no significant differences between the two ergometer designs in group means for: work rate (i.e., rowing speed and stroke rate), metabolic load as measured by mean heart rate, rowing cycle duration, or timing of the stroke in the cycle. 2-D motion analysis of hip and knee motion for the rowing cycle from the video footage taken during the test also revealed no significant differences in the joint range of motion between the ergometers. Ensemble average sEMG activity profiles based on 30+ strokes were obtained for each participant and normalised per 10% intervals of the cycle duration as well as for peak mean sEMG amplitude for each muscle. A repeated measures ANOVA on the sEMG activity per 10% interval for the four muscles contributing to hip and trunk motion during the rowing cycle revealed no significant differences between the Concept 2C and Rowperfect (F = 0.070, df = 1,5, p = 0.802). The outcome of this study suggests that the two different ergometer designs are equally useful for dry land training. Key PointsThe effects of endurance training on HR recovery after exercise and cardiac ANS modulation were investigated in female marathon runners by comparing with untrained controls.Time and frequency domain analysis of HRV was used to investigate cardiac ANS modulation.As compared with untrained controls, the female marathon runners showed faster HR recovery after exercise, which should result from their higher levels of HRV, higher aerobic capacity and exaggerated blood pressure response to exercise.

The Impact of Ergometer Design on Hip and Trunk Muscle Activity Patterns in Elite Rowers: An Electromyographic Assessment

PubMed Central

Nowicky, Alex V.; Horne, Sara; Burdett, Richard

2005-01-01

This study used surface electromyography (sEMG) to examine whether there were differences in hip and trunk muscle activation during the rowing cycle on two of the most widely used air braked ergometers: the Concept 2C and the Rowperfect. sEMG methods were used to record the muscle activity patterns from the right: m. Erector spinae (ES), m. Rectus Abdominus (RA), m. Rectus Femoris (RF) and m. Biceps Femoris (BF) for their contributions as agonist-antagonist pairs underlying hip and trunk extension/flexion. The sEMG activity patterns of these muscles were examined in six young male elite rowers completing a 2 minute set at a moderate training intensity (23 stroke·min-1 and 1:47.500 m-1 split time, 300W). The rowers closely maintained the required target pace through visual inspection of the standard LCD display of each ergometer. The measurements of duration of each rowing cycle and onset of each stroke during the test were recorded simultaneously with the sEMG activity through the additional instrumentation of a foot-pressure switch and handle accelerometry. There were no significant differences between the two ergometer designs in group means for: work rate (i.e., rowing speed and stroke rate), metabolic load as measured by mean heart rate, rowing cycle duration, or timing of the stroke in the cycle. 2-D motion analysis of hip and knee motion for the rowing cycle from the video footage taken during the test also revealed no significant differences in the joint range of motion between the ergometers. Ensemble average sEMG activity profiles based on 30+ strokes were obtained for each participant and normalised per 10% intervals of the cycle duration as well as for peak mean sEMG amplitude for each muscle. A repeated measures ANOVA on the sEMG activity per 10% interval for the four muscles contributing to hip and trunk motion during the rowing cycle revealed no significant differences between the Concept 2C and Rowperfect (F = 0.070, df = 1,5, p = 0.802). The outcome of this study suggests that the two different ergometer designs are equally useful for dry land training. Key Points The effects of endurance training on HR recovery after exercise and cardiac ANS modulation were investigated in female marathon runners by comparing with untrained controls. Time and frequency domain analysis of HRV was used to investigate cardiac ANS modulation. As compared with untrained controls, the female marathon runners showed faster HR recovery after exercise, which should result from their higher levels of HRV, higher aerobic capacity and exaggerated blood pressure response to exercise. PMID:24431957

Cell Type-Specific Gene Expression Analyses by RNA Sequencing Reveal Local High Nitrate-Triggered Lateral Root Initiation in Shoot-Borne Roots of Maize by Modulating Auxin-Related Cell Cycle Regulation1[OPEN

PubMed Central

Yu, Peng; Eggert, Kai; von Wirén, Nicolaus; Li, Chunjian; Hochholdinger, Frank

2015-01-01

Plants have evolved a unique plasticity of their root system architecture to flexibly exploit heterogeneously distributed mineral elements from soil. Local high concentrations of nitrate trigger lateral root initiation in adult shoot-borne roots of maize (Zea mays) by increasing the frequency of early divisions of phloem pole pericycle cells. Gene expression profiling revealed that, within 12 h of local high nitrate induction, cell cycle activators (cyclin-dependent kinases and cyclin B) were up-regulated, whereas repressors (Kip-related proteins) were down-regulated in the pericycle of shoot-borne roots. In parallel, a ubiquitin protein ligase S-Phase Kinase-Associated Protein1-cullin-F-box proteinS-Phase Kinase-Associated Protein 2B-related proteasome pathway participated in cell cycle control. The division of pericycle cells was preceded by increased levels of free indole-3-acetic acid in the stele, resulting in DR5-red fluorescent protein-marked auxin response maxima at the phloem poles. Moreover, laser-capture microdissection-based gene expression analyses indicated that, at the same time, a significant local high nitrate induction of the monocot-specific PIN-FORMED9 gene in phloem pole cells modulated auxin efflux to pericycle cells. Time-dependent gene expression analysis further indicated that local high nitrate availability resulted in PIN-FORMED9-mediated auxin efflux and subsequent cell cycle activation, which culminated in the initiation of lateral root primordia. This study provides unique insights into how adult maize roots translate information on heterogeneous nutrient availability into targeted root developmental responses. PMID:26198256

Microstructural characterization of ultra thin copper interconnects

NASA Astrophysics Data System (ADS)

Yang, Hee-Dong

The present study investigates the defects related to reliability issues, such as physical failures developed during processing and end use. In the first part of this study, kinetic analysis using the Johnson-Mehl-Avrami (JMA) model demonstrates that a self-annealing mechanism in electroplated Cu films depends on the film properties, such as thickness and the amount of crystal defects in an as-deposited state. In order to obtain the evidence of such defects, the microstructural characterization of defects in ultra thin copper interconnects using transmission electron microscopy (TEM) is presented. Examination of the defects using TEM reveals that voids filled with gas form as a lens shape along the {110} habit planes of the copper matrix. In the second part of this study, methodology and results of an electro-thermal-fatigue (ETF) testing, designed for early detection of process defects, are presented. Such ETF testing combines high-density current electrical stressing and thermal cycling to accelerate the evolution of defects in Cu interconnects. In ETF testing, the evolution of defects provides the nucleation sites for voids which open or close during thermal cycling. Then, the accumulation of voids creates the change in resistance when they reach a critical size. As a result of voids evolution, the high current density and high joule heating create a transient resistance increase. ETF testing reveals two failure modes, and the mode-I failure has the importance in detecting defects. The number of cycles to failure in ETF testing decreases with higher current density, but the rate of thermal cycling has no effect. Results from this investigation suggest that impurities in the copper electrodeposition process must be carefully controlled to achieve reliable ultra thin copper interconnects.

Thermomechanical Fatigue Damage/Failure Mechanisms in SCS-6/Timetal 21S [0/90](Sub S) Composite

NASA Technical Reports Server (NTRS)

Castelli, Michael G.

1994-01-01

The thermomechanical fatigue (TMF) deformation, damage, and life behaviors of SCS6/Timetal 21S (0/90)s were investigated under zero-tension conditions. In-phase (IP) and out-of-phase (OP) loadings were investigated with a temperature cycle from 150 to 650 deg C. An advanced TMF test technique was used to quantify mechanically damage progression. The technique incorporated explicit measurements of the macroscopic (1) isothermal static moduli at the temperature extremes of the TMF cycle and (2) coefficient of thermal expansion (CTE) as functions of the TMF cycles. The importance of thermal property degradation and its relevance to accurate post-test data analysis and interpretation is briefly addressed. Extensive fractography and metallography were conducted on specimens from failed and interrupted tests to characterize the extent of damage at the microstructure level. Fatigue life results indicated trends analogous to those established for similar unidirectional(0) reinforced titanium matrix composite systems. High stress IP and mid to low stress OP loading conditions were life-limiting in comparison to maximum temperature isothermal conditions. Dominant damage mechanisms changed with cycle type. Damage resulting from IP TMF conditions produced measurable decreases in static moduli but only minimal changes in the CTE. Metallography on interrupted and failed specimens revealed extensive (0) fiber cracking with sparse matrix damage. No surface initiated matrix cracks were present. Comparable OP TMF conditions initiated environment enhanced surface cracking and matrix cracking initiated at (90) fiber/matrix (F/M) interfaces. Notable static moduli and CTE degradations were measured. Fractography and metallography revealed that the transverse cracks originating from the surface and (90) F/M interfaces tended to converge and coalesce at the (0) fibers.

Isotope Label-Aided Mass Spectrometry Reveals the Influence of Environmental Factors on Metabolism in Single Eggs of Fruit Fly

PubMed Central

Tseng, Te-Wei; Wu, June-Tai; Chen, Yu-Chie; Urban, Pawel L.

2012-01-01

In order to investigate the influence of light/dark cycle on the biosynthesis of metabolites during oogenesis, here we demonstrate a simple experimental protocol which combines in-vivo isotopic labeling of primary metabolites with mass spectrometric analysis of single eggs of fruit fly (Drosophila melanogaster). First, fruit flies were adapted to light/dark cycle using artificial white light. Second, female flies were incubated with an isotopically labeled sugar (13C6-glucose) for 12 h – either during the circadian day or the circadian night, at light or at dark. Third, eggs were obtained from the incubated female flies, and analyzed individually by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS): this yielded information about the extent of labeling with carbon-13. Since the incorporation of carbon-13 to uridine diphosphate glucose (UDP-glucose) in fruit fly eggs is very fast, the labeling of this metabolite was used as an indicator of the biosynthesis of metabolites flies/eggs during 12-h periods, which correspond to circadian day or circadian night. The results reveal that once the flies adapted to the 12-h-light/12-h-dark cycle, the incorporation of carbon-13 to UDP-glucose present in fruit fly eggs was not markedly altered by an acute perturbation to this cycle. This effect may be due to a relationship between biosynthesis of primary metabolites in developing eggs and an alteration to the intake of the labeled substrate – possibly related to the change of the feeding habit. Overall, the study shows the possibility of using MALDI-MS in conjunction with isotopic labeling of small metazoans to unravel the influence of environmental cues on primary metabolism. PMID:23185587

Flow cytometric cell cycle analysis of muscle precursor cells cultured within 3D scaffolds in a perfusion bioreactor.

PubMed

Flaibani, Marina; Luni, Camilla; Sbalchiero, Elisa; Elvassore, Nicola

2009-01-01

It has been widely demonstrated that perfusion bioreactors improve in vitro three-dimensional (3D) cultures in terms of high cell density and uniformity of cell distribution; however, the studies reported in literature were primarily based on qualitative analysis (histology, immunofluorescent staining) or on quantitative data averaged on the whole population (DNA assay, PCR). Studies on the behavior, in terms of cell cycle, of a cell population growing in 3D scaffolds in static or dynamic conditions are still absent. In this work, a perfusion bioreactor suitable to culture C(2)C(12) muscle precursor cells within 3D porous collagen scaffolds was designed and developed and a method based on flowcytometric analyses for analyzing the cell cycle in the cell population was established. Cells were extracted by enzymatic digestion of the collagen scaffolds after 4, 7, and 10 days of culture, and flow cytometric live/dead and cell cycle analyses were performed with Propidium Iodide. A live/dead assay was used for validating the method for cell extraction and staining. Moreover, to investigate spatial heterogeneity of the cell population under perfusion conditions, two stacked scaffolds in the 3D domain, of which only the upstream layer was seeded, were analyzed separately. All results were compared with those obtained from static 3D cultures. The live/dead assay revealed the presence of less than 20% of dead cells, which did not affect the cell cycle analysis. Cell cycle analyses highlighted the increment of cell fractions in proliferating phases (S/G(2)/M) owing to medium perfusion in long-term cultures. After 7-10 days, the percentage of proliferating cells was 8-12% for dynamic cultures and 3-5% for the static controls. A higher fraction of proliferating cells was detected in the downstream scaffold. From a general perspective, this method provided data with a small standard deviation and detected the differences between static and dynamic cultures and between upper and lower scaffolds. Our methodology can be extended to other cell types to investigate the influence of 3D culture conditions on the expression of other relevant cell markers.

Precursor conditions related to Zimbabwe's summer droughts

NASA Astrophysics Data System (ADS)

Nangombe, Shingirai; Madyiwa, Simon; Wang, Jianhong

2018-01-01

Despite the increasing severity of droughts and their effects on Zimbabwe's agriculture, there are few tools available for predicting these droughts in advance. Consequently, communities and farmers are more exposed, and policy makers are always ill prepared for such. This study sought to investigate possible cycles and precursor meteorological conditions prior to drought seasons that could be used to predict impending droughts in Zimbabwe. The Single Z-Index was used to identify and grade drought years between 1951 and 2010 according to rainfall severity. Spectral analysis was used to reveal the cycles of droughts for possible use of these cycles for drought prediction. Composite analysis was used to investigate circulation and temperature anomalies associated with severe and extreme drought years. Results indicate that severe droughts are more highly correlated with circulation patterns and embedded weather systems in the Indian Ocean and equatorial Pacific Ocean than any other area. This study identified sea surface temperatures in the average period June to August, geopotential height and wind vector in July to September period, and air temperature in September to November period as precursors that can be used to predict a drought occurrence several months in advance. Therefore, in addition to sea surface temperature, which was identified through previous research for predicting Zimbabwean droughts, the other parameters identified in this study can aid in drought prediction. Drought cycles were established at 20-, 12.5-, 3.2-, and 2.7-year cycles. The spectral peaks, 12.5, 3.2, and 2.7, had a similar timescale with the luni-solar tide, El Niño Southern Oscillation and Quasi Biennial Oscillation, respectively, and hence, occurrence of these phenomena have a possibility of indicating when the next drought might be.

The influence of catalysts on biofuel life cycle analysis (LCA)

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

Benavides, Pahola Thathiana; Cronauer, Donald C.; Adom, Felix K.

Catalysts play an important role in biofuel production but are rarely included in biofuel life cycle analysis (LCA). In this work, we estimate the cradle-to-gate energy consumption and greenhouse gas (GHG) emissions of Pt/γ-Al 2O 3, CoMo/γ-Al 2O 3, and ZSM-5, catalysts that could be used in processes to convert biomass to biofuels. We also consider the potential impacts of catalyst recovery and recycling. Integrating the energy and environmental impacts of CoMo/γ-Al 2O 3 and ZSM-5 into an LCA of renewable gasoline produced via in-situ and ex-situ fast pyrolysis of a blended woody feedstock revealed that the ZSM-5, with cradle-to-gatemore » GHG emissions of 7.7 kg CO 2e/kg, could influence net life-cycle GHG emissions of the renewable gasoline (1.7 gCO 2e/MJ for the in-situ process, 1.2 gCO 2e/MJ for the ex-situ process) by up to 14% depending on the loading rate. CoMo/γ-Al 2O 3 had a greater GHG intensity (9.6 kg CO 2e/kg) than ZSM-5, however, it contributed approximately only 1% to the life-cycle GHG emissions of the renewable gasoline because of the small amount of this catalyst needed per kg of biofuel produced. As a result, given that catalysts can contribute significantly to biofuel life-cycle GHG emissions depending on the GHG intensity of their production and their consumption rates, biofuel LCAs should consider the potential influence of catalysts on LCA results.« less

The influence of catalysts on biofuel life cycle analysis (LCA)

DOE PAGES

Benavides, Pahola Thathiana; Cronauer, Donald C.; Adom, Felix K.; ...

2017-01-21

Catalysts play an important role in biofuel production but are rarely included in biofuel life cycle analysis (LCA). In this work, we estimate the cradle-to-gate energy consumption and greenhouse gas (GHG) emissions of Pt/γ-Al 2O 3, CoMo/γ-Al 2O 3, and ZSM-5, catalysts that could be used in processes to convert biomass to biofuels. We also consider the potential impacts of catalyst recovery and recycling. Integrating the energy and environmental impacts of CoMo/γ-Al 2O 3 and ZSM-5 into an LCA of renewable gasoline produced via in-situ and ex-situ fast pyrolysis of a blended woody feedstock revealed that the ZSM-5, with cradle-to-gatemore » GHG emissions of 7.7 kg CO 2e/kg, could influence net life-cycle GHG emissions of the renewable gasoline (1.7 gCO 2e/MJ for the in-situ process, 1.2 gCO 2e/MJ for the ex-situ process) by up to 14% depending on the loading rate. CoMo/γ-Al 2O 3 had a greater GHG intensity (9.6 kg CO 2e/kg) than ZSM-5, however, it contributed approximately only 1% to the life-cycle GHG emissions of the renewable gasoline because of the small amount of this catalyst needed per kg of biofuel produced. As a result, given that catalysts can contribute significantly to biofuel life-cycle GHG emissions depending on the GHG intensity of their production and their consumption rates, biofuel LCAs should consider the potential influence of catalysts on LCA results.« less

Cyanobacterial carbon metabolism: Fluxome plasticity and oxygen dependence: Cyanobacterial Carbon Metabolism

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

Wan, Ni; DeLorenzo, Drew M.; He, Lian

Synechocystis sp. strain PCC 6803 has been widely used as a photo-biorefinery chassis. Based on its genome annotation, this species contains a complete TCA cycle, an Embden-Meyerhof-Parnas pathway (EMPP), an oxidative pentose phosphate pathway (OPPP), and an Entner–Doudoroff pathway (EDP). To evaluate how Synechocystis 6803 catabolizes glucose under heterotrophic conditions, we performed 13C metabolic flux analysis, metabolite pool size analysis, gene knockouts, and heterologous expressions. The results revealed a cyclic mode of flux through the OPPP. Small, but non-zero, fluxes were observed through the TCA cycle and the malic shunt. Independent knockouts of 6-phosphogluconate dehydrogenase (gnd) and malic enzyme (me)more » corroborated these results, as neither mutant could grow under dark heterotrophic conditions. Our data also indicate that Synechocystis 6803 metabolism relies upon oxidative phosphorylation to generate ATP from NADPH under dark or insufficient light conditions. The pool sizes of intermediates in the TCA cycle, particularly acetyl-CoA, were found to be several fold lower in Synechocystis 6803 (compared to E. coli metabolite pool sizes), while its sugar phosphate intermediates were several-fold higher. Moreover, negligible flux was detected through the native, or heterologous, EDP in the wild type or Δgnd strains under heterotrophic conditions. Comparing photoautotrophic, photomixotrophic, and heterotrophic conditions, the Calvin cycle, OPPP, and EMPP in Synechocystis 6803 possess the ability to regulate their fluxes under various growth conditions (plastic), whereas its TCA cycle always maintains at low levels (rigid). This work also demonstrates how genetic profiles do not always reflect actual metabolic flux through native or heterologous pathways. Biotechnol. Bioeng. 2017;114: 1593–1602. © 2017 Wiley Periodicals, Inc.« less

Phaleria macrocarpa (Boerl.) fruit induce G0/G1 and G2/M cell cycle arrest and apoptosis through mitochondria-mediated pathway in MDA-MB-231 human breast cancer cell.

PubMed

Kavitha, Nowroji; Ein Oon, Chern; Chen, Yeng; Kanwar, Jagat R; Sasidharan, Sreenivasan

2017-04-06

Phaleria macrocarpa (Scheff) Boerl, is a well-known folk medicinal plant in Indonesia. Traditionally, P. macrocarpa has been used to control cancer, impotency, hemorrhoids, diabetes mellitus, allergies, liver and hearth disease, kidney disorders, blood diseases, acne, stroke, migraine, and various skin diseases. The purpose of this study was to determine the in situ cytotoxicity effect P. macrocarpa fruit ethyl acetate fraction (PMEAF) and the underlying molecular mechanism of cell death. MDA-MB-231 cells were incubated with PMEAF for 24h. Cell cycle and viability were examined using flow cytometry analysis. Apoptosis was determined using the Annexin V assay and also by fluorescence microscopy. Apoptosis protein profiling was detected by RayBio® Human Apoptosis Array. The AO/PI staining and flow cytometric analysis of MDA-MB-231 cells treated with PMEAF were showed apoptotic cell death. The cell cycle analysis by flow cytometry analysis revealed that the accumulation of PMEAF treated MDA-MB-231 cells in G 0 /G 1 and G 2 /M-phase of the cell cycle. Moreover, the PMEAF exert cytotoxicity by increased the ROS production in MDA-MB-231 cells consistently stimulated the loss of mitochondrial membrane potential (∆ Ψm ) and induced apoptosis cell death by activation of numerous signalling proteins. The results from apoptosis protein profiling array evidenced that PMEAF stimulated the expression of 9 pro-apoptotic proteins (Bax, Bid, caspase 3, caspase 8, cytochrome c, p21, p27, p53 and SMAC) and suppressed the 4 anti-apoptotic proteins (Bcl-2, Bcl-w, XIAP and survivin) in MDA-MB-231 cells. The results indicated that PMEAF treatment induced apoptosis in MDA-MB-231 cells through intrinsic mitochondrial related pathway with the participation of pro and anti-apoptotic proteins, caspases, G 0 /G 1 and G 2 /M-phases cell cycle arrest by p53-mediated mechanism. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

Empirical mode decomposition and long-range correlation analysis of sunspot time series

NASA Astrophysics Data System (ADS)

Zhou, Yu; Leung, Yee

2010-12-01

Sunspots, which are the best known and most variable features of the solar surface, affect our planet in many ways. The number of sunspots during a period of time is highly variable and arouses strong research interest. When multifractal detrended fluctuation analysis (MF-DFA) is employed to study the fractal properties and long-range correlation of the sunspot series, some spurious crossover points might appear because of the periodic and quasi-periodic trends in the series. However many cycles of solar activities can be reflected by the sunspot time series. The 11-year cycle is perhaps the most famous cycle of the sunspot activity. These cycles pose problems for the investigation of the scaling behavior of sunspot time series. Using different methods to handle the 11-year cycle generally creates totally different results. Using MF-DFA, Movahed and co-workers employed Fourier truncation to deal with the 11-year cycle and found that the series is long-range anti-correlated with a Hurst exponent, H, of about 0.12. However, Hu and co-workers proposed an adaptive detrending method for the MF-DFA and discovered long-range correlation characterized by H≈0.74. In an attempt to get to the bottom of the problem in the present paper, empirical mode decomposition (EMD), a data-driven adaptive method, is applied to first extract the components with different dominant frequencies. MF-DFA is then employed to study the long-range correlation of the sunspot time series under the influence of these components. On removing the effects of these periods, the natural long-range correlation of the sunspot time series can be revealed. With the removal of the 11-year cycle, a crossover point located at around 60 months is discovered to be a reasonable point separating two different time scale ranges, H≈0.72 and H≈1.49. And on removing all cycles longer than 11 years, we have H≈0.69 and H≈0.28. The three cycle-removing methods—Fourier truncation, adaptive detrending and the proposed EMD-based method—are further compared, and possible reasons for the different results are given. Two numerical experiments are designed for quantitatively evaluating the performances of these three methods in removing periodic trends with inexact/exact cycles and in detecting the possible crossover points.

Toward a mechanistic understanding of the damage evolution of SnAgCu solder joints in accelerated thermal cycling test

NASA Astrophysics Data System (ADS)

Mahin Shirazi, Sam

Accelerated thermal cycling (ATC) tests are the most commonly used tests for the thermo-mechanical performance assessment of microelectronics assemblies. Currently used reliability models have failed to incorporate the microstructural dependency of lead free solder joint behavior and its microstructure evolution during cycling. Thus, it is essential to have a mechanistic understanding of the effect of cycling parameters on damage evolution and failure of lead free solder joints in ATC. Recrystallization has been identified as the damage rate controlling mechanism in ATC. Usually it takes 1/3 of life for completion of recrystallization regardless of cycling parameters. Thus, the life of the solder joints can be predicted by estimating global recrystallization. The objective of the first part of the study was to examine whether the damage scenario applies in service is the same as the harsh thermal cycling tests (i.e. 0/100 °C and -40/125 °C) commonly used in industry. Microstructure analysis results on a variety of lead free solder SnAgCu assemblies subjected to the both harsh (0/100 °C) and mild (20/80 °C) ATC confirmed similar failure mechanism under the both testing conditions. Sn grain morphology (interlaced versus beach ball) has a significant effect on the thermo-mechanical performance (and thus the model) of the lead free solder joints. The longer thermal cycling lifetime observed in the interlaced solder joints subjected to the ATC compared to the beach ball structure was correlated to the different initial microstructure and the microstructure evolution during cycling. For the modeling proposes, the present study was focused on Sn-Ag-Cu solder joints with either a single Sn grain or beach ball structure. Microstructural analysis results of the simulated thermal cycling experiment revealed that, the life can be approximated as determined by the accumulation of a certain amount of work during the high temperature dwells. Finally the effect of precipitates spacing on acceleration factor was investigated. Results indicated that a smaller initial precipitate spacing would tend to result in a longer life in mild thermal cycling/service (where there is lower stresses). Accordingly, it is essential to incorporate the dependence of damage rate (i.e. recrystallization) on precipitate coarsening in any predictions.

Disentangling Intracycle Interferences in Photoelectron Momentum Distributions Using Orthogonal Two-Color Laser Fields

NASA Astrophysics Data System (ADS)

Xie, Xinhua; Wang, Tian; Yu, ShaoGang; Lai, XuanYang; Roither, Stefan; Kartashov, Daniil; Baltuška, Andrius; Liu, XiaoJun; Staudte, André; Kitzler, Markus

2017-12-01

We use orthogonally polarized two-color (OTC) laser pulses to separate quantum paths in the multiphoton ionization of Ar atoms. Our OTC pulses consist of 400 and 800 nm light at a relative intensity ratio of 10 ∶1 . We find a hitherto unobserved interference in the photoelectron momentum distribution, which exhibits a strong dependence on the relative phase of the OTC pulse. Analysis of model calculations reveals that the interference is caused by quantum pathways from nonadjacent quarter cycles.

Structure-phase states evolution in Al-Si alloy under electron-beam treatment and high-cycle fatigue

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

Konovalov, Sergey, E-mail: konovserg@gmail.com; Alsaraeva, Krestina, E-mail: gromov@physics.sibsiu.ru; Gromov, Victor, E-mail: gromov@physics.sibsiu.ru

By methods of scanning and transmission electron diffraction microscopy the analysis of structure-phase states and defect substructure of silumin subjected to high-intensity electron beam irradiation in various regimes and subsequent fatigue loading up to failure was carried out. It is revealed that the sources of fatigue microcracks are silicon plates of micron and submicron size are not soluble in electron beam processing. The possible reasons of the silumin fatigue life increase under electron-beam treatment are discussed.

Genome-wide characterization reveals complex interplay between TP53 and TP63 in response to genotoxic stress

PubMed Central

McDade, Simon S.; Patel, Daksha; Moran, Michael; Campbell, James; Fenwick, Kerry; Kozarewa, Iwanka; Orr, Nicholas J.; Lord, Christopher J.; Ashworth, Alan A.; McCance, Dennis J.

2014-01-01

In response to genotoxic stress the TP53 tumour suppressor activates target gene expression to induce cell cycle arrest or apoptosis depending on the extent of DNA damage. These canonical activities can be repressed by TP63 in normal stratifying epithelia to maintain proliferative capacity or drive proliferation of squamous cell carcinomas, where TP63 is frequently overexpressed/amplified. Here we use ChIP-sequencing, integrated with microarray analysis, to define the genome-wide interplay between TP53 and TP63 in response to genotoxic stress in normal cells. We reveal that TP53 and TP63 bind to overlapping, but distinct cistromes of sites through utilization of distinctive consensus motifs and that TP53 is constitutively bound to a number of sites. We demonstrate that cisplatin and adriamycin elicit distinct effects on TP53 and TP63 binding events, through which TP53 can induce or repress transcription of an extensive network of genes by direct binding and/or modulation of TP63 activity. Collectively, this results in a global TP53-dependent repression of cell cycle progression, mitosis and DNA damage repair concomitant with activation of anti-proliferative and pro-apoptotic canonical target genes. Further analyses reveal that in the absence of genotoxic stress TP63 plays an important role in maintaining expression of DNA repair genes, loss of which results in defective repair. PMID:24823795

Curcumin inhibits growth potential by G1 cell cycle arrest and induces apoptosis in p53-mutated COLO 320DM human colon adenocarcinoma cells.

PubMed

Dasiram, Jade Dhananjay; Ganesan, Ramamoorthi; Kannan, Janani; Kotteeswaran, Venkatesan; Sivalingam, Nageswaran

2017-02-01

Curcumin, a natural polyphenolic compound and it is isolated from the rhizome of Curcuma longa, have been reported to possess anticancer effect against stage I and II colon cancer. However, the effect of curcumin on colon cancer at Dukes' type C metastatic stage III remains still unclear. In the present study, we have investigated the anticancer effects of curcumin on p53 mutated COLO 320DM human colon adenocarcinoma cells derived from Dukes' type C metastatic stage. The cellular viability and proliferation were assessed by trypan blue exclusion assay and MTT assay, respectively. The cytotoxicity effect was examined by lactate dehydrogenase (LDH) cytotoxicity assay. Apoptosis was analyzed by DNA fragmentation analysis, Hoechst and propidium iodide double fluorescent staining and confocal microscopy analysis. Cell cycle distribution was performed by flow cytometry analysis. Here we have observed that curcumin treatment significantly inhibited the cellular viability and proliferation potential of p53 mutated COLO 320DM cells in a dose- and time-dependent manner. In addition, curcumin treatment showed no cytotoxic effects to the COLO 320DM cells. DNA fragmentation analysis, Hoechst and propidium iodide double fluorescent staining and confocal microscopy analysis revealed that curcumin treatment induced apoptosis in COLO 320DM cells. Furthermore, curcumin caused cell cycle arrest at the G1 phase, decreased the cell population in the S phase and induced apoptosis in COLO 320DM colon adenocarcinoma cells. Together, these data suggest that curcumin exerts anticancer effects and induces apoptosis in p53 mutated COLO 320DM human colon adenocarcinoma cells derived from Dukes' type C metastatic stage. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Interannual variations of middle atmospheric temperature as measured by the JPL lidar at Mauna Loa Observatory, Hawaii (19.5°N, 155.6°W)

NASA Astrophysics Data System (ADS)

Li, Tao; Leblanc, Thierry; McDermid, I. Stuart

2008-07-01

The Jet Propulsion Laboratory Rayleigh-Raman lidar at Mauna Loa Observatory (MLO), Hawaii (19.5°N, 155.6°W) has been measuring atmospheric temperature vertical profiles routinely since 1993. Linear regression analysis was applied to the 13.5-yearlong (January 1994 to June 2007) deseasonalized monthly mean lidar temperature time series for each 1-km altitude bin between 15 and 85 km. The regression analysis included components representing the Quasi-Biennial Oscillation (QBO), El Niño-Southern Oscillation (ENSO), and the 11-year solar cycle. Where overlapping was possible, the results were compared to those obtained from the twice-daily National Weather Service (NWS) radiosonde profiles at Hilo (5-30 km) located 60 km east-north-east of the lidar site, and the four-times-daily temperature analysis of the European Centre for Medium Range Weather Forecast (ECMWF). The analysis revealed the dominance of the QBO (1-3 K) in the stratosphere and mesosphere, and a strong winter signature of ENSO in the troposphere and lowermost stratosphere (˜1.5 K/MEI). Additionally, and for the first time, a statistically significant signature of ENSO was observed in the mesosphere, consistent with the findings of recent model simulations. The annual mean response to the solar cycle shows two statistically significant maxima of ˜1.3 K/100 F10.7 units at 35 and 55 km. The temperature responses to QBO, ENSO, and solar cycle are all maximized in winter. Comparisons with the global ECMWF temperature analysis clearly showed that the middle atmosphere above MLO is under a subtropical/extratropical regime, i.e., generally out-of-phase with that in the equatorial regions, and synchronized to the northern hemisphere winter/spring.

Effects of Cycling vs. Running Training on Endurance Performance in Preparation for Inline Speed Skating.

PubMed

Stangier, Carolin; Abel, Thomas; Hesse, Clemens; Claen, Stephanie; Mierau, Julia; Hollmann, Wildor; Strüder, Heiko K

2016-06-01

Winter weather conditions restrict regular sport-specific endurance training in inline speed skating. As a result, this study was designed to compare the effects of cycling and running training programs on inline speed skaters' endurance performance. Sixteen (8 men, 8 women) high-level athletes (mean ± SD 24 ± 8 years) were randomly assigned to 1 of 2 groups (running and cycling). Both groups trained twice a week for 8 weeks, one group on a treadmill and the other on a cycle ergometer. Training intensity and duration was individually calculated (maximal fat oxidation: ∼52% of V[Combining Dot Above]O2peak: 500 kcal per session). Before and after the training intervention, all athletes performed an incremental specific (inline speed skating) and 1 nonspecific (cycling or running) step test according to the group affiliation. In addition to blood lactate concentration, oxygen uptake (V[Combining Dot Above]O2), ventilatory equivalent (VE/V[Combining Dot Above]O2), respiratory exchange ratio (RER), and heart rate were measured. The specific posttest revealed significantly increased absolute V[Combining Dot Above]O2peak values (2.9 ± 0.4, 3.4 ± 0.7, p = 0.01) and submaximal V[Combining Dot Above]O2 values (p ≤ 0.01). VE/V[Combining Dot Above]O2 and RER significantly decreased at maximal (46.6 ± 6.6, 38.5 ± 3.4, p = 0.005; 1.1 ± 0.03, 1.0 ± 0.04, p = 0.001) and submaximal intensities (p ≤ 0.04). None of the analysis revealed a significant group effect (p ≥ 0.15). The results indicate that both cycling vs. running exercise at ∼52% of V[Combining Dot Above]O2peak had a positive effect on the athletes' endurance performance. The increased submaximal V[Combining Dot Above]O2 values indicate a reduction in athletes' inline speed skating technique. Therefore, athletes would benefit from a focus on technique training in the subsequent period.

Thermochemical cycle analysis using linked CECS72 and HYDRGN computer programs

NASA Technical Reports Server (NTRS)

Donovan, L. F.

1977-01-01

A combined thermochemical cycle analysis computer program was designed. Input to the combined program is the same as input to the thermochemical cycle analysis program except that the extent of the reactions need not be specified. The combined program is designed to be run interactively from a computer time-sharing terminal. This mode of operation allows correction or modification of the cycle to take place during cycle analysis. A group of 13 thermochemical cycles was used to test the combined program.

Reduction of In-Stent Restenosis Risk on Nickel-Free Stainless Steel by Regulating Cell Apoptosis and Cell Cycle

PubMed Central

Li, Liming; Pan, Shuang; Zhou, Xiaohang; Meng, Xin; Han, Xiaoxi; Ren, Yibin; Yang, Ke; Guan, Yifu

2013-01-01

High nitrogen nickel-free austenitic stainless steel (HNNF SS) is one of the biomaterials developed recently for circumventing the in-stent restenosis (ISR) in coronary stent applications. To understand the ISR-resistance mechanism, we have conducted a comparative study of cellular and molecular responses of human umbilical vein endothelial cells (HUVECs) to HNNF SS and 316L SS (nickel-containing austenitic 316L stainless steel) which is the stent material used currently. CCK-8 analysis and flow cytometric analysis were used to assess the cellular responses (proliferation, apoptosis, and cell cycle), and quantitative real-time PCR (qRT-PCR) was used to analyze the gene expression profile of HUVECs exposed to HNNF SS and 316L SS, respectively. Flow cytometry analysis revealed that 316L SS could activate the cellular apoptosis more efficiently and initiate an earlier entry into the S-phase of cell cycle than HNNF SS. At the molecular level, qRT-PCR results showed that the genes regulating cell apoptosis and autophagy were overexpressed on 316L SS. Further examination indicated that nickel released from 316L SS triggered the cell apoptosis via Fas-Caspase8-Caspase3 exogenous pathway. These molecular mechanisms of HUVECs present a good model for elucidating the observed cellular responses. The findings in this study furnish valuable information for understanding the mechanism of ISR-resistance on the cellular and molecular basis as well as for developing new biomedical materials for stent applications. PMID:23638002

Analysis of Bufo arenarum oviductal secretion during the sexual cycle.

PubMed

Crespo, Claudia A; Ramos, Inés; Medina, Marcela F; Fernández, Silvia N

2009-11-01

SummaryBufo arenarum oocytes are oviposited surrounded by jelly coats, one component of the extracellular matrix required for fertilization. The secretion, released to the oviductal lumen, was analysed by SDS-PAGE. The coomassie blue staining evidenced an electrophoretic pattern with molecules ranging between 300 and 19 kDa that showed variations in their secretion profiles during the sexual cycle. In the preovulatory period the densitometric analysis showed the presence of nine peaks with marked predominance of the 74 kDa molecule. Once ovulation has occurred, the jelly coats become arranged around the oocytes during their transit throughout the oviductal pars convoluta (PC), revealing the addition of three proteins only observed during this period, which suggests a differential secretion. Some of these proteins could not diffuse under any extraction treatment, indicating for them a structural or in situ function. Proteins of low molecular mass diffused totally while others showed a partial diffusing capacity. After ovulation a marked decrease in the relative amount of all the proteins released to the lumen, especially the 74 kDa protein, could be detected. During this period, unlike the other stages of the sexual cycle, a differential secretion pattern was observed along the PC. The histochemical analysis performed during the ovulatory period showed the presence of glycoconjugates including both acidic and neutral groups. The present results are in agreement with previous ultrastructural and histochemical studies that describe the role of Bufo arenarum jelly coats in fertilization.

Activation of PPARγ mediates icaritin-induced cell cycle arrest and apoptosis in glioblastoma multiforme.

PubMed

Liu, Yongji; Shi, Ling; Liu, Yuan; Li, Peng; Jiang, Guoping; Gao, Xiaoning; Zhang, Yongbin; Jiang, Chuanwu; Zhu, Weiping; Han, Hongxing; Ju, Fang

2018-04-01

Glioblastoma multiforme (GBM) is the most prevalent primary malignancy of the brain. This study was designed to investigate whether icaritin exerts anti-neoplastic activity against GBM in vitro. Cell Counting Kit-8 (CCK-8) assay was utilized to examine the viability of GBM cells. The apoptotic cell population was measured by flow cytometry analysis. Cell cycle distribution was detected by flow cytometry as well. Western blot analysis was performed to examine the level of biomarker proteins in GBM cells. Levels of PPARγ mRNA and protein were detected by qPCR and western blot analysis, respectively. To examine the role of PPARγ in the anti-neoplastic activity of icaritin, PPARγ antagonist GW9662 or PPARγ siRNA was used. The activity of PPARγ was determined by DNA binding and luciferase assays. Our findings revealed that icaritin markedly suppresses cell growth in a dose-dependent and time-dependent fashion. The cell population at the G0/G1 phase of the cell cycle was significantly increased following icaritin treatment. Meanwhile, icaritin promoted apoptotic cell death in T98G and U87MG cells. Further investigation showed upregulation of PPARγ played a key role in the anti-neoplastic activities of icaritin. Moreover, our result demonstrated activation of AMPK signaling by icaritin mediated the modulatory effect of icaritin on PPARγ. Our results suggest the PPARγ may mediate anti-neoplastic activities against GBM. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

Hormones and Dichotic Listening: Evidence from the Study of Menstrual Cycle Effects

ERIC Educational Resources Information Center

Cowell, Patricia E.; Ledger, William L.; Wadnerkar, Meghana B.; Skilling, Fiona M.; Whiteside, Sandra P.

2011-01-01

This report presents evidence for changes in dichotic listening asymmetries across the menstrual cycle, which replicate studies from our laboratory and others. Increases in the right ear advantage (REA) were present in women at phases of the menstrual cycle associated with higher levels of ovarian hormones. The data also revealed correlations…

Analysis of hepatic transcript profile and plasma lipid profile in early lactating dairy cows fed grape seed and grape marc meal extract.

PubMed

Gessner, Denise K; Winkler, Anne; Koch, Christian; Dusel, Georg; Liebisch, Gerhard; Ringseis, Robert; Eder, Klaus

2017-03-23

It was recently reported that dairy cows fed a polyphenol-rich grape seed and grape marc meal extract (GSGME) during the transition period had an increased milk yield, but the underlying reasons remained unclear. As polyphenols exert a broad spectrum of metabolic effects, we hypothesized that feeding of GSGME influences metabolic pathways in the liver which could account for the positive effects of GSGME in dairy cows. In order to identify these pathways, we performed genome-wide transcript profiling in the liver and lipid profiling in plasma of dairy cows fed GSGME during the transition period at 1 week postpartum. Transcriptomic analysis of the liver revealed 207 differentially expressed transcripts, from which 156 were up- and 51 were down-regulated, between cows fed GSGME and control cows. Gene set enrichment analysis of the 155 up-regulated mRNAs showed that the most enriched gene ontology (GO) biological process terms were dealing with cell cycle regulation and the most enriched Kyoto Encyclopedia of Genes and Genomes pathways were p53 signaling and cell cycle. Functional analysis of the 43 down-regulated mRNAs revealed that a great part of these genes are involved in endoplasmic reticulum (ER) stress-induced unfolded protein response (UPR) and inflammatory processes. Accordingly, protein folding, response to unfolded protein, unfolded protein binding, chemokine activity and heat shock protein binding were identified as one of the most enriched GO biological process and molecular function terms assigned to the down-regulated genes. In line with the transcriptomics data the plasma concentrations of the acute phase proteins serum amyloid A (SAA) and haptoglobin were reduced in cows fed GSGME compared to control cows. Lipidomic analysis of plasma revealed no differences in the concentrations of individual species of major and minor lipid classes between cows fed GSGME and control cows. Analysis of hepatic transcript profile in cows fed GSGME during the transition period at 1 week postpartum indicates that polyphenol-rich feed components are able to inhibit ER stress-induced UPR and inflammatory processes, both of which are considered to contribute to liver-associated diseases and to impair milk performance in dairy cows, in the liver of dairy cows during early lactation.

Defect propagation in NiTi rotary instruments: a noncontact optical profilometry analysis.

PubMed

Barbosa, I; Ferreira, F; Scelza, P; Neff, J; Russano, D; Montagnana, M; Zaccaro Scelza, M

2018-04-10

To evaluate the presence and propagation of defects and their effects on surfaces of nickel-titanium (NiTi) instruments using noncontact, three-dimensional optical profilometry, and to assess the accuracy of this method of investigation. The flute surface areas of instruments from two commercial instrumentation systems, namely Reciproc R25 (n = 5) and WaveOne Primary (n = 5), were assessed and compared before and after performing two instrumentation cycles in simulated root canals in clear resin blocks. All the analyses were conducted on areas measuring 211 × 211 μm, located 3 mm from the tips of the instruments. A quantitative analysis was conducted before and after the first and second instrumentation cycles, using the Sa (average roughness over the measurement field), Sq (root mean square roughness) and Sz (average height over the measurement field) amplitude parameters. All the data were submitted to statistical analysis at a 5% level of significance. There was a significant increase (P = 0.007) in wear in both groups, especially between baseline and the second instrumentation cycle, with significantly higher wear values being observed on WaveOne instruments (Sz median values = 33.68 and 2.89 μm, respectively, for WO and RP groups). A significant increase in surface roughness (P = 0.016 and P = 0.008, respectively, for Sa and Sq) was observed in both groups from the first to the second instrumentation cycle, mostly in WaveOne specimens. Qualitative analysis revealed a greater number of defects on the flute topography of all the instruments after use. More defects were identified in WaveOne Primary instruments compared to Reciproc R25, irrespective of the evaluation stage. The investigation method provided an accurate, repeatable and reproducible assessment of NiTi instruments at different time-points. © 2018 International Endodontic Journal. Published by John Wiley & Sons Ltd.

Drivers of multi-century trends in the atmospheric CO2 mean annual cycle in a prognostic ESM

NASA Astrophysics Data System (ADS)

Liptak, Jessica; Keppel-Aleks, Gretchen; Lindsay, Keith

2017-03-01

The amplitude of the mean annual cycle of atmospheric CO2 is a diagnostic of seasonal surface-atmosphere carbon exchange. Atmospheric observations show that this quantity has increased over most of the Northern Hemisphere (NH) extratropics during the last 3 decades, likely from a combination of enhanced atmospheric CO2, climate change, and anthropogenic land use change. Accurate climate prediction requires accounting for long-term interactions between the environment and carbon cycling; thus, analysis of the evolution of the mean annual cycle in a fully prognostic Earth system model may provide insight into the multi-decadal influence of environmental change on the carbon cycle. We analyzed the evolution of the mean annual cycle in atmospheric CO2 simulated by the Community Earth System Model (CESM) from 1950 to 2300 under three scenarios designed to separate the effects of climate change, atmospheric CO2 fertilization, and land use change. The NH CO2 seasonal amplitude increase in the CESM mainly reflected enhanced primary productivity during the growing season due to climate change and the combined effects of CO2 fertilization and nitrogen deposition over the mid- and high latitudes. However, the simulations revealed shifts in key climate drivers of the atmospheric CO2 seasonality that were not apparent before 2100. CO2 fertilization and nitrogen deposition in boreal and temperate ecosystems were the largest contributors to mean annual cycle amplification over the midlatitudes for the duration of the simulation (1950-2300). Climate change from boreal ecosystems was the main driver of Arctic CO2 annual cycle amplification between 1950 and 2100, but CO2 fertilization had a stronger effect on the Arctic CO2 annual cycle amplitude during 2100-2300. Prior to 2100, the NH CO2 annual cycle amplitude increased in conjunction with an increase in the NH land carbon sink. However, these trends decoupled after 2100, underscoring that an increasing atmospheric CO2 annual cycle amplitude does not necessarily imply a strengthened terrestrial carbon sink.

Endometrial thickness as a predictor of the reproductive outcomes in fresh and frozen embryo transfer cycles

PubMed Central

Zhang, Tao; Li, Zhou; Ren, Xinling; Huang, Bo; Zhu, Guijin; Yang, Wei; Jin, Lei

2018-01-01

Abstract To evaluate the relationship between endometrial thickness during fresh in vitro fertilization (IVF) cycles and the clinical outcomes of subsequent frozen embryo transfer (FET) cycles. FET cycles using at least one morphological good-quality blastocyst conducted between 2012 and 2013 at a university-based reproductive center were reviewed retrospectively. Endometrial ultrasonographic characteristics were recorded both on the oocyte retrieval day and on the day of progesterone supplementation in FET cycles. Clinical pregnancy rate, spontaneous abortion rate, and live birth rate were analyzed. One thousand five hundred twelve FET cycles was included. The results showed that significant difference in endometrial thickness on day of oocyte retrieval (P = .03) was observed between the live birth group (n = 844) and no live birth group (n = 668), while no significant difference in FET endometrial thickness was found (P = .261) between the live birth group and no live birth group. For endometrial thickness on oocyte retrieval day, clinical pregnancy rate ranged from 50.0% among patients with an endometrial thickness of ≤6 mm to 84.2% among patients with an endometrial thickness of >16 mm, with live birth rate from 33.3% to 63.2%. Multiple logistic regression analysis of factors related to live birth indicated endometrial thickness on oocyte retrieval day was associated with improved live birth rate (OR was 1.069, 95% CI: 1.011–1.130, P = .019), while FET endometrial thickness did not contribute significantly to pregnancy outcomes following FET cycles. The ROC curves revealed the cut-off points of endometrial thickness on oocyte retrieval day was 8.75 mm for live birth. Endometrial thickness during fresh IVF cycles was a better predictor of endometrial receptivity in subsequent FET cycles than FET cycle endometrial thickness. For those females with thin endometrium in fresh cycles, additional estradiol stimulation might be helpful for adequate endometrial development. PMID:29369190

High preservation of DNA standards diluted in 50% glycerol.

PubMed

Schaudien, Dirk; Baumgärtner, Wolfgang; Herden, Christiane

2007-09-01

Standard curves are important tools in real-time quantitative polymerase chain reaction (PCR) to precisely analyze gene expression patterns under physiologic and pathologic conditions. Handling of DNA standards often implies multiple cycles of freezing and thawing that might affect DNA stability and integrity. This in turn might influence the reliability and reproducibility of quantitative measurements in real-time PCR assays. In this study, 3 DNA standards such as murine tumor necrosis factor (TNF) alpha, interferon (IFN) gamma, and kainat-1 receptor were diluted in 50% glycerol or water after 1, 4, and 16 cycles of freezing and thawing and amplified copy numbers after real-time PCR were compared. The standards diluted in water showed a reduction to 83%, 55%, and 50% after 4 cycles, to 24%, 5%, and 4% after 16 cycles for kainat-1 receptor, TNFalpha, and IFNgamma standards, respectively, when compared with a single cycle of freezing and thawing. Interestingly, all cDNA samples diluted in 50% glycerol were amplified in comparable copy numbers even after 16 cycles of freezing and thawing. The effect of the standards undergoing different cycles of freezing and thawing on sample values was demonstrated by amplifying cDNA obtained from Borna disease virus infected and noninfected TNF-transgenic mice brain. This revealed significant differences of measured cDNA copy numbers using water-diluted DNA standards. In contrast, sample values did not vary using glycerol-diluted standards that were frozen and thawed for 16 times. In conclusion, glycerol storage of DNA standards represents a suitable tool for the accurate and reproducible quantification of cDNA samples in real-time PCR analysis.

The effect of gradient boracic polyanion-doping on structure, morphology, and cycling performance of Ni-rich LiNi0.8Co0.15Al0.05O2 cathode material

NASA Astrophysics Data System (ADS)

Chen, Tao; Li, Xiang; Wang, Hao; Yan, Xinxiu; Wang, Lei; Deng, Bangwei; Ge, Wujie; Qu, Meizhen

2018-01-01

A gradient boracic polyanion-doping method is applied to Ni-rich LiNi0.8Co0.15Al0.05O2 (NCA) cathode material in this study to suppress the capacity/potential fade during charge-discharge cycling. Scanning electron microscope (SEM) results show that all samples present spherical morphology and the secondary particle size increases with increasing boron content. X-ray diffraction (XRD), transmission electron microscopy (TEM), and X-ray photoelectron spectroscopy (XPS) results demonstrate that boracic polyanions are successfully introduced into the bulk material and more enriched in the outer layer. XPS analysis further reveals that the valence state of Ni3+ is partly reduced to Ni2+ at the surface due to the incorporation of boracic polyanions. From the electrochemical measurements, B0.015-NCA electrode exhibits excellent cycling performance, even at high potential and elevated temperature. Moreover, the SEM images illustrate the presence of cracks and a thick SEI layer on pristine particles after 100 cycles at high temperature, while the B0.015-NCA particles show an intact structure and thin SEI layer. Electrochemical impedance spectroscopy confirms that the boracic polyanion doping could hinder the impedance increase during cycling at elevated temperature. These results clearly indicate that the gradient boracic polyanion-doping contributes to the remarkable enhancement of structure stability and cycling performance of NCA.

Induction of Apoptosis and Antiproliferative Activity of Naringenin in Human Epidermoid Carcinoma Cell through ROS Generation and Cell Cycle Arrest

PubMed Central

Jafri, Asif; Ahmad, Sheeba; Afzal, Mohammad; Arshad, Md

2014-01-01

A natural predominant flavanone naringenin, especially abundant in citrus fruits, has a wide range of pharmacological activities. The search for antiproliferative agents that reduce skin carcinoma is a task of great importance. The objective of this study was to analyze the anti-proliferative and apoptotic mechanism of naringenin using MTT assay, DNA fragmentation, nuclear condensation, change in mitochondrial membrane potential, cell cycle kinetics and caspase-3 as biomarkers and to investigate the ability to induce reactive oxygen species (ROS) initiating apoptotic cascade in human epidermoid carcinoma A431 cells. Results showed that naringenin exposure significantly reduced the cell viability of A431 cells (p<0.01) with a concomitant increase in nuclear condensation and DNA fragmentation in a dose dependent manner. The intracellular ROS generation assay showed statistically significant (p<0.001) dose-related increment in ROS production for naringenin. It also caused naringenin-mediated epidermoid carcinoma apoptosis by inducing mitochondrial depolarization. Cell cycle study showed that naringenin induced cell cycle arrest in G0/G1 phase of cell cycle and caspase-3 analysis revealed a dose dependent increment in caspase-3 activity which led to cell apoptosis. This study confirms the efficacy of naringenin that lead to cell death in epidermoid carcinoma cells via inducing ROS generation, mitochondrial depolarization, nuclear condensation, DNA fragmentation, cell cycle arrest in G0/G1 phase and caspase-3 activation. PMID:25330158

Development of high-rise buildings: digitalization of life cycle management

NASA Astrophysics Data System (ADS)

Gusakova, Elena

2018-03-01

The analysis of the accumulated long-term experience in the construction and operation of high-rise buildings reveals not only the engineering specificity of such projects, but also systemic problems in the field of project management. Most of the project decisions are made by the developer and the investor in the early stages of the life cycle - from the acquisition of the site to the start of operation, so most of the participants in the construction and operation of the high-rise building are far from the strategic life-cycle management of the project. The solution of these tasks due to the informatization of management has largely exhausted its efficiency resource. This is due to the fact that the applied IT-systems automated traditional "inherited" processes and management structures, and, in addition, they were focused on informatization of the activities of the construction company, rather than the construction project. Therefore, in the development of high-rise buildings, the tasks of researching approaches and methods for managing the full life cycle of projects that will improve their competitiveness become topical. For this purpose, the article substantiates the most promising approaches and methods of informational modeling of high-rise construction as a basis for managing the full life cycle of this project. Reengineering of information interaction schemes for project participants is considered; formation of a unified digital environment for the life cycle of the project; the development of systems for integrating data management and project management.

Impacts of mesoscale eddies on biogeochemical cycles in the South China Sea

NASA Astrophysics Data System (ADS)

Xiu, P.; Chai, F.; Guo, M.

2016-02-01

Biogeochemical cycles associated with mesoscale eddies in the South China Sea (SCS) are investigated by using satellite surface chlorophyll concentration, altimeter data, satellite sea surface temperature, and a coupled physical-biogeochemical Pacific Ocean model (ROMS-CoSiNE) simulation for the period from 1991 to 2007. Considering the annual mean, composite analysis reveals that cyclonic eddies are associated with higher concentrations of nutrients, phytoplankton and zooplankton while the anticyclonic eddies are with lower concentrations compared with surrounding waters, which is generally controlled by the eddy pumping mechanism. Dipole structures of vertical fluxes with net upward motion in cyclonic eddies and net downward motion in anticyclonic eddies are also revealed. During the lifetime of an eddy, the evolutions of physical, biological, and chemical structures are not linearly coupled at the eddy core where plankton grow and composition of the community depend not only on the physical and chemical processes but also on the adjustments by the predator-prey relationship. Considering the seasonal variability, we find eddy pumping mechanisms are generally dominant in winter and eddy advection effects are dominant in summer. Over the space, variability of chlorophyll to the west of Luzon Strait and off northwest of Luzon Island are mainly controlled by eddy pumping mechanism. In regions off the Vietnam coast, chlorophyll distributions are generally associated with horizontal eddy advection. This research highlights different mesoscale mechanisms affecting biological structures that can potentially disturb ocean biogeochemical cycling processes in the South China Sea.

Sarcocyst Development in Raccoons (Procyon lotor) Inoculated with Different Strains of Sarcocystis neurona Culture-Derived Merozoites.

PubMed

Dryburgh, E L; Marsh, A E; Dubey, J P; Howe, D K; Reed, S M; Bolten, K E; Pei, W; Saville, W J A

2015-08-01

Sarcocystis neurona is considered the major etiologic agent of equine protozoal myeloencephalitis (EPM), a neurological disease in horses. Raccoon ( Procyon lotor ) is considered the most important intermediate host in the life cycle of S. neurona in the United States; S. neurona sarcocysts do mature in raccoon muscles, and raccoons also develop clinical signs simulating EPM. The focus of this study was to determine if sarcocysts would develop in raccoons experimentally inoculated with different host-derived strains of in vitro-cultivated S. neurona merozoites. Four raccoons were inoculated with strains derived from a raccoon, a sea otter, a cat, and a horse. Raccoon tissues were fed to laboratory-raised opossums ( Didelphis virginiana ), the definitive host of S. neurona . Intestinal scraping revealed sporocysts in opossums who received muscle tissue from raccoons inoculated with the raccoon-derived or the sea otter-derived isolates. These results demonstrate that sarcocysts can mature in raccoons inoculated with in vitro-derived S. neurona merozoites. In contrast, the horse and cat-derived isolates did not produce microscopically or biologically detected sarcocysts. Immunoblot analysis revealed both antigenic and antibody differences when testing the inoculated raccoons. Immunohistochemical staining indicated differences in staining between the merozoite and sarcocyst stages. The successful infections achieved in this study indicates that the life cycle can be manipulated in the laboratory without affecting subsequent stage development, thereby allowing further purification of strains and artificial maintenance of the life cycle.

Two Chimeric Regulators of G-protein Signaling (RGS) Proteins Differentially Modulate Soybean Heterotrimeric G-protein Cycle*

PubMed Central

Roy Choudhury, Swarup; Westfall, Corey S.; Laborde, John P.; Bisht, Naveen C.; Jez, Joseph M.; Pandey, Sona

2012-01-01

Heterotrimeric G-proteins and the regulator of G-protein signaling (RGS) proteins, which accelerate the inherent GTPase activity of Gα proteins, are common in animals and encoded by large gene families; however, in plants G-protein signaling is thought to be more limited in scope. For example, Arabidopsis thaliana contains one Gα, one Gβ, three Gγ, and one RGS protein. Recent examination of the Glycine max (soybean) genome reveals a larger set of G-protein-related genes and raises the possibility of more intricate G-protein networks than previously observed in plants. Stopped-flow analysis of GTP-binding and GDP/GTP exchange for the four soybean Gα proteins (GmGα1–4) reveals differences in their kinetic properties. The soybean genome encodes two chimeric RGS proteins with an N-terminal seven transmembrane domain and a C-terminal RGS box. Both GmRGS interact with each of the four GmGα and regulate their GTPase activity. The GTPase-accelerating activities of GmRGS1 and -2 differ for each GmGα, suggesting more than one possible rate of the G-protein cycle initiated by each of the Gα proteins. The differential effects of GmRGS1 and GmRGS2 on GmGα1–4 result from a single valine versus alanine difference. The emerging picture suggests complex regulation of the G-protein cycle in soybean and in other plants with expanded G-protein networks. PMID:22474294

Relationship of Estimated SHIV Acquisition Time Points During the Menstrual Cycle and Thinning of Vaginal Epithelial Layers in Pigtail Macaques.

PubMed

Kersh, Ellen N; Ritter, Jana; Butler, Katherine; Ostergaard, Sharon Dietz; Hanson, Debra; Ellis, Shanon; Zaki, Sherif; McNicholl, Janet M

2015-12-01

HIV acquisition in the female genital tract remains incompletely understood. Quantitative data on biological HIV risk factors, the influence of reproductive hormones, and infection risk are lacking. We evaluated vaginal epithelial thickness during the menstrual cycle in pigtail macaques (Macaca nemestrina). This model previously revealed increased susceptibility to vaginal infection during and after progesterone-dominated periods in the menstrual cycle. Nucleated and nonnucleated (superficial) epithelial layers were quantitated throughout the menstrual cycle of 16 macaques. We examined the relationship with previously estimated vaginal SHIVSF162P3 acquisition time points in the cycle of 43 different animals repeatedly exposed to low virus doses. In the luteal phase (days 17 to cycle end), the mean vaginal epithelium thinned to 66% of mean follicular thickness (days 1-16; P = 0.007, Mann-Whitney test). Analyzing 4-day segments, the epithelium was thickest on days 9 to 12 and thinned to 31% thereof on days 29 to 32, with reductions of nucleated and nonnucleated layers to 36% and 15% of their previous thickness, respectively. The proportion of animals with estimated SHIV acquisition in each cycle segment correlated with nonnucleated layer thinning (Pearson r = 0.7, P < 0.05, linear regression analysis), but not nucleated layer thinning (Pearson r = 0.6, P = 0.15). These data provide a detailed picture of dynamic cycle-related changes in the vaginal epithelium of pigtail macaques. Substantial thinning occurred in the superficial, nonnucleated layer, which maintains the vaginal microbiome. The findings support vaginal tissue architecture as susceptibility factor for infection and contribute to our understanding of innate resistance to SHIV infection.

Adult active transport in the Netherlands: an analysis of its contribution to physical activity requirements.

PubMed

Fishman, Elliot; Böcker, Lars; Helbich, Marco

2015-01-01

Modern, urban lifestyles have engineered physical activity out of everyday life and this presents a major threat to human health. The Netherlands is a world leader in active travel, particularly cycling, but little research has sought to quantify the cumulative amount of physical activity through everyday walking and cycling. Using data collected as part of the Dutch National Travel Survey (2010 - 2012), this paper determines the degree to which Dutch walking and cycling contributes to meeting minimum level of physical activity of 150 minutes of moderate intensity aerobic activity throughout the week. The sample includes 74,465 individuals who recorded at least some travel on the day surveyed. As physical activity benefits are cumulative, all walking and cycling trips are analysed, including those to and from public transport. These trips are then converted into an established measure of physical activity intensity, known as metabolic equivalents of tasks. Multivariate Tobit regression models were performed on a range of socio-demographic, transport resources, urban form and meteorological characteristics. The results reveal that Dutch men and women participate in 24 and 28 minutes of daily physical activity through walking and cycling, which is 41% and 55% more than the minimum recommended level. It should be noted however that some 57% of the entire sample failed to record any walking or cycling, and an investigation of this particular group serves as an important topic of future research. Active transport was positively related with age, income, bicycle ownership, urban density and air temperature. Car ownership had a strong negative relationship with physically active travel. The results of this analysis demonstrate the significance of active transport to counter the emerging issue of sedentary lifestyle disease. The Dutch experience provides other countries with a highly relevant case study in the creation of environments and cultures that support healthy, active living.

Afferent control of central pattern generators: experimental analysis of scratching in the decerebrate cat.

PubMed

Baev, K V; Esipenko, V B; Shimansky, Y P

1991-01-01

Systematic quantitative analysis of changes in the spinal scratching generator motor activity evoked by tonic and phasic peripheral afferent signals during "fictitious" scratching was carried out in the cat. Correlations between the kinematics of hindlimb scratching movement, sensory inflow, and primary afferent depolarization were investigated. Reliable correlations between the parameters of generator motor activity during fictitious scratching were revealed: they depended on tonic peripheral afferent inflow. The functional role of these dependencies consists of providing stability for aiming the hindlimb to the itch site. It was shown that scratching generator reaction to a phasic sensory signal depended significantly on afferent input, signal intensity, and its arrival phase in the cycle of motor activity. Phase correction of "scratching" rhythm was performed by inhibition of the current stage of "scratching" cycle, the inhibition magnitude depending on the intensity of a sensory signal run along high threshold afferent fibers. The moments in the scratching cycle, in which the afferent signal caused no rearrangement in scratching generator activity, were discovered for all investigated afferent inputs. These moments corresponded to the transitions from one scratching cycle phase to another. Integral afferent activity was distributed unevenly in the cycle during real scratching. The main part of it was observed just in that scratching cycle part which included the above mentioned no rearrangement phase points. The data obtained allowed us to conclude that the scratching generator should be considered as a working program for the motor optimal control system containing the intrinsic model of the controlled object dynamics (e.g. hindlimb scratching movement dynamics), which produces an inner analog of peripheral flow. This inner flow interacts with peripheral afferent inflow just as one of the latter components. Centrally originated modulation of primary afferent depolarization is a result of affecting the depolarization generating system by this inner "sensory" activity. It is the model, with the aid of which the generator can work after deafferentation. The functional organization of a central pattern generator is considered.

The nexus between geopolitical uncertainty and crude oil markets: An entropy-based wavelet analysis

NASA Astrophysics Data System (ADS)

Uddin, Gazi Salah; Bekiros, Stelios; Ahmed, Ali

2018-04-01

The global financial crisis and the subsequent geopolitical turbulence in energy markets have brought increased attention to the proper statistical modeling especially of the crude oil markets. In particular, we utilize a time-frequency decomposition approach based on wavelet analysis to explore the inherent dynamics and the casual interrelationships between various types of geopolitical, economic and financial uncertainty indices and oil markets. Via the introduction of a mixed discrete-continuous multiresolution analysis, we employ the entropic criterion for the selection of the optimal decomposition level of a MODWT as well as the continuous-time coherency and phase measures for the detection of business cycle (a)synchronization. Overall, a strong heterogeneity in the revealed interrelationships is detected over time and across scales.

Phosphate cycling on the basic protein of Plodia interpunctella granulosis virus

NASA Technical Reports Server (NTRS)

Funk, C. J.; Consigli, R. A.; Spooner, B. S. (Principal Investigator)

1993-01-01

The presence of infected cell-specific phosphoproteins was investigated in Plodia interpunctella granulosis virus (PiGV)-infected fat body using [32P]orthophosphoric acid labeling. One infected cell-specific phosphoprotein had a mobility similar to that of the basic protein (VP12) of PiGV. Further analysis, using immunoblotting and acid-urea gel analysis of infected fat body, confirmed that this phosphoprotein was VP12. However we did not detect phosphorylated VP12 in 32P-labeled nucleocapsids. Phosphoamino acid analysis of 32P-labeled VP12 revealed that phosphoserine was present in the basic protein. Since VP12 is phosphorylated in the infected cell, but not in the nucleocapsid, it appears that dephosphorylation of VP12 is a critical event in the life cycle of the virus. We therefore assayed virus nucleocapsids and infected fat body for the presence of phosphatase activity. Phosphatase activity was not detected in the virus, but the infected fat body had more activity than uninfected fat body. A model for nucleocapsid assembly and uncoating is presented which takes into account the phosphorylation state of VP12, the role of Zn2+ in the nucleocapsid, and the role of the capsid-associated kinase.

Identification of critical equipment and determination of operational limits in helium refrigerators under pulsed heat load

NASA Astrophysics Data System (ADS)

Dutta, Rohan; Ghosh, Parthasarathi; Chowdhury, Kanchan

2014-01-01

Large-scale helium refrigerators are subjected to pulsed heat load from tokamaks. As these plants are designed for constant heat loads, operation under such varying load may lead to instability in plants thereby tripping the operation of different equipment. To understand the behavior of the plant subjected to pulsed heat load, an existing plant of 120 W at 4.2 K and another large-scale plant of 18 kW at 4.2 K have been analyzed using a commercial process simulator Aspen Hysys®. A similar heat load characteristic has been applied in both quasi steady state and dynamic analysis to determine critical stages and equipment of these plants from operational point of view. It has been found that the coldest part of both the cycles consisting JT-stage and its preceding reverse Brayton stage are the most affected stages of the cycles. Further analysis of the above stages and constituting equipment revealed limits of operation with respect to variation of return stream flow rate resulted from such heat load variations. The observations on the outcome of the analysis can be used for devising techniques for steady operation of the plants subjected to pulsed heat load.

Molecular characterization of a peritrophic membrane protein from the silkworm, Bombyx mori.

PubMed

Hu, Xiaolong; Chen, Lin; Yang, Rui; Xiang, Xingwei; Wu, Xiaofeng

2013-02-01

The peritrophic membrane lines the gut of most insects at one or more stages of their life cycles. It facilitates the digestive processes in the guts and protects from invasion by pathogens or food particles. In the current study, a novel PM protein, designated as BmMtch, was identified from the silkworm, Bombyx mori. The open reading frame of BmMtch is 888 bp in length, encoding 295 amino acid residues consisting of two domains (Mito_carr domains) and three transmembrane regions. They are localized on the 11th chromosome as single copy with one exon only. Quantitative real time PCR analysis (qRT-PCR) revealed that BmMtch was mainly expressed in larval fat bodies, Malpighian tubules, testis and ovaries, and could be detected through all stages of the life cycle of silkworm. Immuno-fluorescence analysis indicated that BmMtch was localized within the goblet cell of larval midgut. Western blotting analysis showed that BmMtch were detected in total proteins of PM and larval midgut. The characteristics of BmMtch indicated that BmMtch represents a novel member of insect PM proteins, without chitin-binding domains.

Quantitative proteomics reveals the mechanism and consequence of gliotoxin-mediated dysregulation of the methionine cycle in Aspergillus niger.

PubMed

Manzanares-Miralles, Lara; Sarikaya-Bayram, Özlem; Smith, Elizabeth B; Dolan, Stephen K; Bayram, Özgür; Jones, Gary W; Doyle, Sean

2016-01-10

Gliotoxin (GT) is a redox-active metabolite, produced by Aspergillus fumigatus, which inhibits the growth of other fungi. Here we demonstrate how Aspergillus niger responds to GT exposure. Quantitative proteomics revealed that GT dysregulated the abundance of 378 proteins including those involved in methionine metabolism and induced de novo abundance of two S-adenosylmethionine (SAM)-dependent methyltransferases. Increased abundance of enzymes S-adenosylhomocysteinase (p=0.0018) required for homocysteine generation from S-adenosylhomocysteine (SAH), and spermidine synthase (p=0.0068), involved in the recycling of Met, was observed. Analysis of Met-related metabolites revealed significant increases in the levels of Met and adenosine, in correlation with proteomic data. Methyltransferase MT-II is responsible for bisthiobis(methylthio)gliotoxin (BmGT) formation, deletion of MT-II abolished BmGT formation and led to increased GT sensitivity in A. niger. Proteomic analysis also revealed that GT exposure also significantly (p<0.05) increased hydrolytic enzyme abundance, including glycoside hydrolases (n=22) and peptidases (n=16). We reveal that in an attempt to protect against the detrimental affects of GT, methyltransferase-mediated GT thiomethylation alters cellular pathways involving Met and SAM, with consequential dysregulation of hydrolytic enzyme abundance in A. niger. Thus, it provides new opportunities to exploit the response of GT-naïve fungi to GT. Copyright © 2015 Elsevier B.V. All rights reserved.

Gene Set−Based Integrative Analysis Revealing Two Distinct Functional Regulation Patterns in Four Common Subtypes of Epithelial Ovarian Cancer

PubMed Central

Chang, Chia-Ming; Chuang, Chi-Mu; Wang, Mong-Lien; Yang, Yi-Ping; Chuang, Jen-Hua; Yang, Ming-Jie; Yen, Ming-Shyen; Chiou, Shih-Hwa; Chang, Cheng-Chang

2016-01-01

Clear cell (CCC), endometrioid (EC), mucinous (MC) and high-grade serous carcinoma (SC) are the four most common subtypes of epithelial ovarian carcinoma (EOC). The widely accepted dualistic model of ovarian carcinogenesis divided EOCs into type I and II categories based on the molecular features. However, this hypothesis has not been experimentally demonstrated. We carried out a gene set-based analysis by integrating the microarray gene expression profiles downloaded from the publicly available databases. These quantified biological functions of EOCs were defined by 1454 Gene Ontology (GO) term and 674 Reactome pathway gene sets. The pathogenesis of the four EOC subtypes was investigated by hierarchical clustering and exploratory factor analysis. The patterns of functional regulation among the four subtypes containing 1316 cases could be accurately classified by machine learning. The results revealed that the ERBB and PI3K-related pathways played important roles in the carcinogenesis of CCC, EC and MC; while deregulation of cell cycle was more predominant in SC. The study revealed that two different functional regulation patterns exist among the four EOC subtypes, which were compatible with the type I and II classifications proposed by the dualistic model of ovarian carcinogenesis. PMID:27527159

Si-FeSi2/C nanocomposite anode materials produced by two-stage high-energy mechanical milling

NASA Astrophysics Data System (ADS)

Yang, Yun Mo; Loka, Chadrasekhar; Kim, Dong Phil; Joo, Sin Yong; Moon, Sung Whan; Choi, Yi Sik; Park, Jung Han; Lee, Kee-Sun

2017-05-01

High capacity retention Silicon-based nanocomposite anode materials have been extensively explored for use in lithium-ion rechargeable batteries. Here we report the preparation of Si-FeSi2/C nanocomposite through scalable a two-stage high-energy mechanical milling process, in which nano-scale Si-FeSi2 powders are besieged by the carbon (graphite/amorphous phase) layer; and investigation of their structure, morphology and electrochemical performance. Raman analysis revealed that the carbon layer structure comprised of graphitic and amorphous phase rather than a single amorphous phase. Anodes fabricated with the Si-FeSi2/C showed excellent electrochemical behavior such as a first discharge capacity of 1082 mAh g-1 and a high capacity retention until the 30th cycle. A remarkable coulombic efficiency of 99.5% was achieved within a few cycles. Differential capacity plots of the Si-FeSi2/C anodes revealed a stable lithium reaction with Si for lithiation/delithiation. The enhanced electrochemical properties of the Si-FeSi2/C nanocomposite are mainly attributed to the nano-size Si and stable solid electrolyte interface formation and highly conductive path driven by the carbon layer.

Raman spectrum reveals the cell cycle arrest of Triptolide-induced leukemic T-lymphocytes apoptosis

NASA Astrophysics Data System (ADS)

Zhang, Daosen; Feng, Yanyan; Zhang, Qinnan; Su, Xin; Lu, Xiaoxu; Liu, Shengde; Zhong, Liyun

2015-04-01

Triptolide (TPL), a traditional Chinese medicine extract, possesses anti-inflammatory and anti-tumor properties. Though some research results have implicated that Triptolide (TPL) can be utilized in the treatment of leukemia, it remains controversial about the mechanism of TPL-induced leukemic T-lymphocytes apoptosis. In this study, combining Raman spectroscopic data, principal component analysis (PCA) and atomic force microscopy (AFM) imaging, both the biochemical changes and morphological changes during TPL-induced cell apoptosis were presented. In contrast, the corresponding data during Daunorubicin (DNR)-induced cell apoptosis was also exhibited. The obtained results showed that Raman spectral changes during TPL-induced cell apoptosis were greatly different from DNR-induced cell apoptosis in the early stage of apoptosis but revealed the high similarity in the late stage of apoptosis. Moreover, above Raman spectral changes were respectively consistent with the morphological changes of different stages during TPL-induced apoptosis or DNR-induced apoptosis, including membrane shrinkage and blebbing, chromatin condensation and the formation of apoptotic bodies. Importantly, it was found that Raman spectral changes with TPL-induced apoptosis or DNR-induced apoptosis were respectively related with the cell cycle G1 phase arrest or G1 and S phase arrest.

Effect of oxygen minimum zone formation on communities of marine protists.

PubMed

Orsi, William; Song, Young C; Hallam, Steven; Edgcomb, Virginia

2012-08-01

Changes in ocean temperature and circulation patterns compounded by human activities are leading to oxygen minimum zone (OMZ) expansion with concomitant alteration in nutrient and climate active trace gas cycling. Here, we report the response of microbial eukaryote populations to seasonal changes in water column oxygen-deficiency using Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island British Columbia, as a model ecosystem. We combine small subunit ribosomal RNA gene sequencing approaches with multivariate statistical methods to reveal shifts in operational taxonomic units during successive stages of seasonal stratification and renewal. A meta-analysis is used to identify common and unique patterns of community composition between Saanich Inlet and the anoxic/sulfidic Cariaco Basin (Venezuela) and Framvaren Fjord (Norway) to show shared and unique responses of microbial eukaryotes to oxygen and sulfide in these three environments. Our analyses also reveal temporal fluctuations in rare populations of microbial eukaryotes, particularly anaerobic ciliates, that may be of significant importance to the biogeochemical cycling of methane in OMZs. Eukaryotic 18S rRNA gene sequences recovered from the Saanich Inlet water column on were deposited in Genbank under accession numbers HQ864863–HQ871151.

Electrochemical behaviour of manganese & ruthenium mixed oxide@ reduced graphene oxide nanoribbon composite in symmetric and asymmetric supercapacitor

NASA Astrophysics Data System (ADS)

Ahuja, Preety; Ujjain, Sanjeev Kumar; Kanojia, Rajni

2018-01-01

This paper reports the interaction of 3d-4d transition metal mixed oxide as simultaneous existence of M(3d) and M(4d) expectedly enhance the electrochemical performance of the resulting composite. Electrochemical performance of MnO2-RuO2 nanoflakes reduced graphene oxide nanoribbon composite (MnO2-RuO2@GNR) is intensively explored in symmetric and asymmetric supercapacitor assembly. In situ incorporation of graphene oxide nanoribbon (GONR) during synthesis provides efficient binding sites for growth of MnO2-RuO2 nanoflakes via their surface functionalities. The interconnected MnO2-RuO2 nanoflakes via GNR form a network with enhanced diffusion kinetics leading to efficient supercapacitor performance. Fabricated asymmetric supercapacitor reveals energy density 60 Wh kg-1 at power density 14 kW kg-1. Based on the analysis of impedance data in terms of complex power, quick response time of supercapacitor reveals excellent power delivery of the device. Improved cycling stability after 7000 charge discharge cycles for symmetric and asymmetric supercapacitor highlights the buffering action of GNR and can be generalized for next generation high performance supercapacitor.

Hepatoid Adenocarcinoma of the Stomach: A Challenging Diagnostic and Therapeutic Disease through a Case Report and Review of the Literature.

PubMed

Fakhruddin, Najla; Bahmad, Hisham F; Aridi, Tarek; Yammine, Yara; Mahfouz, Rami; Boulos, Fouad; Awada, Ahmad; Farhat, Fadi

2017-01-01

Hepatoid adenocarcinoma of the stomach (HAS) is a rare aggressive tumor with hepatocellular differentiation. HAS often produces alpha fetoprotein (AFP) and metastasizes to the lymph nodes and the liver. Molecular studies revealed Her2 amplification and overexpression, association with p53 mutations, but no association with KRAS mutations. EGFR and BRAF mutations have not yet been evaluated in hepatoid carcinoma of the stomach so far. Hereby, we present a case of a 41-year-old female patient with HAS with high AFP level and liver metastases. Molecular analysis revealed Her2 overexpression by immunohistochemistry (IHC), but no EGFR, KRAS , or BRAF mutations were detected. The patient underwent chemotherapy type DCX (docetaxel, cisplatinum, and capecitabine) every 3 weeks with partial response after two cycles, maintained for eight cycles, and then was on maintenance therapy with trastuzumab for 7 months before relapsing and dying 18 months from the day of diagnosis. Conclusively, HAS may be misdiagnosed as hepatocellular carcinoma; therefore, it should be considered in the differential diagnosis of multiple hepatic nodules with high AFP and no history of hepatitis, liver fibrosis or cirrhosis.

Similarity of vegetation dynamics during interglacial periods

PubMed Central

Cheddadi, Rachid; de Beaulieu, Jacques-Louis; Jouzel, Jean; Andrieu-Ponel, Valérie; Laurent, Jeanne-Marine; Reille, Maurice; Raynaud, Dominique; Bar-Hen, Avner

2005-01-01

The Velay sequence (France) provides a unique, continuous, palynological record spanning the last four climatic cycles. A pollen-based reconstruction of temperature and precipitation displays marked climatic cycles. An analysis of the climate and vegetation changes during the interglacial periods reveals comparable features and identical major vegetation successions. Although Marine Isotope Stage (MIS) 11.3 and the Holocene had similar earth precessional variations, their correspondence in terms of vegetation dynamics is low. MIS 9.5, 7.5, and especially 5.5 display closer correlation to the Holocene than MIS 11.3. Ecological factors, such as the distribution and composition of glacial refugia or postglacial migration patterns, may explain these discrepancies. Comparison of ecosystem dynamics during the past five interglacials suggests that vegetation development in the current interglacial has no analogue from the past 500,000 years. PMID:16162676

Solar forcing of drought frequency in the Maya lowlands.

PubMed

Hodell, D A; Brenner, M; Curtis, J H; Guilderson, T

2001-05-18

We analyzed lake-sediment cores from the Yucatan Peninsula, Mexico, to reconstruct the climate history of the region over the past 2600 years. Time series analysis of sediment proxies, which are sensitive to the changing ratio of evaporation to precipitation (oxygen isotopes and gypsum precipitation), reveal a recurrent pattern of drought with a dominant periodicity of 208 years. This cycle is similar to the documented 206-year period in records of cosmogenic nuclide production (carbon-14 and beryllium-10) that is thought to reflect variations in solar activity. We conclude that a significant component of century-scale variability in Yucatan droughts is explained by solar forcing. Furthermore, some of the maxima in the 208-year drought cycle correspond with discontinuities in Maya cultural evolution, suggesting that the Maya were affected by these bicentennial oscillations in precipitation.

Data supporting the comparative life cycle assessment of different municipal solid waste management scenarios

PubMed Central

Ali Rajaeifar, Mohammad; Tabatabaei, Meisam; Ghanavati, Hossein

2015-01-01

Environmental assessment of municipal solid waste (MSW) management scenarios would help to select eco-friendly scenarios. In this study, the inventory data in support of life cycle assessment of different MSW are presented. The scenarios were defined as: anaerobic digestion (AD, Sc-0), landfilling combined with composting (Sc-1), incineration (Sc-2), incineration combined with composting (Sc-3), and AD combined with incineration (Sc-4). The current article contains flowcharts of the different scenarios. Additionally, six supplementary files including inventory data on the different scenarios, data on the different damage assessment categories, normalization, and single scores are presented (Supplementary files 1–6). The analysis of the different scenarios revealed that the most eco-friendly scenario to be implemented in the future would be the combination of AD and incineration (Sc-4). PMID:26217743

STAT5 Activation in the Dermal Papilla Is Important for Hair Follicle Growth Phase Induction.

PubMed

Legrand, Julien M D; Roy, Edwige; Ellis, Jonathan J; Francois, Mathias; Brooks, Andrew J; Khosrotehrani, Kiarash

2016-09-01

Hair follicles are skin appendages that undergo periods of growth (anagen), regression (catagen), and rest (telogen) regulated by their mesenchymal component, the dermal papilla (DP). On the basis of the reports of its specific expression in the DP, we investigated signal transducer and activator of transcription (STAT5) activation during hair development and cycling. STAT5 activation in the DP began in late catagen, reaching a peak in early anagen before disappearing for the rest of the cycle. This was confirmed by the expression profile of suppressor of cytokine signaling 2, a STAT5 target in the DP. This pattern of expression starts after the first postnatal hair cycle. Quantification of hair cycling using the Flash canonical Wnt signaling in vivo bioluminescence reporter found that conditional knockout of STAT5A/B in the DP targeted through Cre-recombinase under the control of the Sox18 promoter resulted in delayed anagen entry compared with control. Microarray analysis of STAT5 deletion versus control revealed key changes in tumor necrosis factor-α, Wnt, and fibroblast growth factor ligands, known for their role in inducing anagen entry. We conclude that STAT5 activation acts as a mesenchymal switch to trigger natural anagen entry in postdevelopmental hair follicle cycling. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

A record of astronomically forced climate change in a late Ordovician (Sandbian) deep marine sequence, Ordos Basin, North China

NASA Astrophysics Data System (ADS)

Fang, Qiang; Wu, Huaichun; Hinnov, Linda A.; Wang, Xunlian; Yang, Tianshui; Li, Haiyan; Zhang, Shihong

2016-07-01

The late Ordovician Pingliang Formation on the southwestern margin of the Ordos Basin, North China, consists of rhythmic alternations of shale, limestone, and siliceous beds. To explore the possible astronomical forcing preserved in this lithological record, continuous lithological rank and magnetic susceptibility (MS) stratigraphic series were obtained from a 34 m thick section of the Pingliang Formation at Guanzhuang. Power spectral analysis of the MS and rank series reveal 85.5 cm to 124 cm, 23 cm to 38 cm, and 15 cm to 27 cm thick sedimentary cycles that in ratio match that of late Ordovician short eccentricity, obliquity and precession astronomical cycles. The power spectrum of the MS time series, calibrated to interpreted short orbital eccentricity cycles, aligns with spectral peaks to astronomical parameters, including 95 kyr short orbital eccentricity, 35.3 kyr and 30.6 kyr obliquity, and 19.6 kyr and 16.3 kyr precession cycles. The 15 cm to 27 cm thick limestone-shale couplets mainly represent precession cycles, and siliceous bed deposition may be related to both precession and obliquity forcing. We propose that precession-forced sea-level fluctuations mainly controlled production of lime mud in a shallow marine environment, and transport to the basin. Precession and obliquity controlled biogenic silica productivity, and temperature-dependent preservation of silica may have been influenced by obliquity forcing.

Controllable Electrochemical Synthesis of Copper Sulfides as Sodium-Ion Battery Anodes with Superior Rate Capability and Ultralong Cycle Life.

PubMed

Li, Haomiao; Wang, Kangli; Cheng, Shijie; Jiang, Kai

2018-03-07

Sodium-ion batteries (SIBs) are prospective alternative to lithium-ion batteries for large-scale energy-storage applications, owing to the abundant resources of sodium. Metal sulfides are deemed to be promising anode materials for SIBs due to their low-cost and eco-friendliness. Herein, for the first time, series of copper sulfides (Cu 2 S, Cu 7 S 4 , and Cu 7 KS 4 ) are controllably synthesized via a facile electrochemical route in KCl-NaCl-Na 2 S molten salts. The as-prepared Cu 2 S with micron-sized flakes structure is first investigated as anode of SIBs, which delivers a capacity of 430 mAh g -1 with a high initial Coulombic efficiency of 84.9% at a current density of 100 mA g -1 . Moreover, the Cu 2 S anode demonstrates superior capability (337 mAh g -1 at 20 A g -1 , corresponding to 50 C) and ultralong cycle performance (88.2% of capacity retention after 5000 cycles at 5 A g -1 , corresponding to 0.0024% of fade rate per cycle). Meanwhile, the pseudocapacitance contribution and robust porous structure in situ formed during cycling endow the Cu 2 S anodes with outstanding rate capability and enhanced cyclic performance, which are revealed by kinetics analysis and ex situ characterization.

Phosphatidylcholine catabolism in the MCF-7 cell cycle.

PubMed

Lin, Weiyang; Arthur, Gilbert

2006-10-01

The catabolism of phosphatidylcholine (PtdCho) appears to play a key role in regulating the net accumulation of the lipid in the cell cycle. Current protocols for measuring the degradation of PtdCho at specific cell-cycle phases require prolonged periods of incubation with radiolabelled choline. To measure the degradation of PtdCho at the S and G2 phases in the MCF-7 cell cycle, protocols were developed with radiolabelled lysophosphatidylcholine (lysoPtdCho), which reduces the labelling period and minimizes the recycling of labelled components. Although most of the incubated lysoPtdCho was hydrolyzed to glycerophosphocholine (GroPCho) in the medium, the kinetics of the incorporation of label into PtdCho suggests that the labelled GroPCho did not contribute significantly to cellular PtdCho formation. A protocol which involved exposing the cells twice to hydroxyurea, was also developed to produce highly synchronized MCF-7 cells with a profile of G1:S:G2/M of 90:5:5. An analysis of PtdCho catabolism in the synchronized cells following labelling with lysoPtdCho revealed that there was increased degradation of PtdCho in early to mid-S phase, which was attenuated in the G2/M phase. The results suggest that the net accumulation of PtdCho in MCF-7 cells may occur in the G2 phase of the cell cycle.

The budding yeast Rad9 checkpoint protein is subjected to Mec1/Tel1-dependent hyperphosphorylation and interacts with Rad53 after DNA damage.

PubMed

Vialard, J E; Gilbert, C S; Green, C M; Lowndes, N F

1998-10-01

The Saccharomyces cerevisiae RAD9 checkpoint gene is required for transient cell-cycle arrests and transcriptional induction of DNA repair genes in response to DNA damage. Polyclonal antibodies raised against the Rad9 protein recognized several polypeptides in asynchronous cultures, and in cells arrested in S or G2/M phases while a single form was observed in G1-arrested cells. Treatment with various DNA damaging agents, i.e. UV, ionizing radiation or methyl methane sulfonate, resulted in the appearance of hypermodified forms of the protein. All modifications detected during a normal cell cycle and after DNA damage were sensitive to phosphatase treatment, indicating that they resulted from phosphorylation. Damage-induced hyperphosphorylation of Rad9 correlated with checkpoint functions (cell-cycle arrest and transcriptional induction) and was cell-cycle stage- and progression-independent. In asynchronous cultures, Rad9 hyperphosphorylation was dependent on MEC1 and TEL1, homologues of the ATR and ATM genes. In G1-arrested cells, damage-dependent hyperphosphorylation required functional MEC1 in addition to RAD17, RAD24, MEC3 and DDC1, demonstrating cell-cycle stage specificity of the checkpoint genes in this response to DNA damage. Analysis of checkpoint protein interactions after DNA damage revealed that Rad9 physically associates with Rad53.

Multiple timescales of cyclical behaviour observed at two dome-forming eruptions

NASA Astrophysics Data System (ADS)

Lamb, Oliver D.; Varley, Nick R.; Mather, Tamsin A.; Pyle, David M.; Smith, Patrick J.; Liu, Emma J.

2014-09-01

Cyclic behaviour over a range of timescales is a well-documented feature of many dome-forming volcanoes, but has not previously been identified in high resolution seismic data from Volcán de Colima (Mexico). Using daily seismic count datasets from Volcán de Colima and Soufrière Hills volcano (Montserrat), this study explores parallels in the long-term behaviour of seismicity at two long-lived systems. Datasets are examined using multiple techniques, including Fast-Fourier Transform, Detrended Fluctuation Analysis and Probabilistic Distribution Analysis, and the comparison of results from two systems reveals interesting parallels in sub-surface processes operating at both systems. Patterns of seismicity at both systems reveal complex but broadly similar long-term temporal patterns with cycles on the order of ~ 50- to ~ 200-days. These patterns are consistent with previously published spectral analyses of SO2 flux time-series at Soufrière Hills volcano, and are attributed to variations in the movement of magma in each system. Detrended Fluctuation Analysis determined that both volcanic systems showed a systematic relationship between the number of seismic events and the relative ‘roughness' of the time-series, and explosions at Volcán de Colima showed a 1.5-2 year cycle; neither observation has a clear explanatory mechanism. At Volcán de Colima, analysis of repose intervals between seismic events shows long-term behaviour that responds to changes in activity at the system. Similar patterns for both volcanic systems suggest a common process or processes driving the observed signal but it is not clear from these results alone what those processes may be. Further attempts to model conduit processes at each volcano must account for the similarities and differences in activity within each system. The identification of some commonalities in the patterns of behaviour during long-lived dome-forming eruptions at andesitic volcanoes provides a motivation for investigating further use of time-series analysis as a monitoring tool.

Gene-expression profiles of epithelial cells treated with EMD in vitro: analysis using complementary DNA arrays.

PubMed

Kapferer, I; Schmidt, S; Gstir, R; Durstberger, G; Huber, L A; Vietor, I

2011-02-01

During surgical periodontal treatment, EMD is topically applied in order to facilitate regeneration of the periodontal ligament, acellular cementum and alveolar bone. Suppresion of epithelial down-growth is essential for successful periodontal regeneration; however, the underlying mechanisms of how EMD influences epithelial wound healing are poorly understood. In the present study, the effects of EMD on gene-expression profiling in an epithelial cell line (HSC-2) model were investigated. Gene-expression modifications, determined using a comparative genome-wide expression-profiling strategy, were independently validated by quantitative real-time RT-PCR. Additionally, cell cycle, cell growth and in vitro wound-healing assays were conducted. A set of 43 EMD-regulated genes was defined, which may be responsible for the reduced epithelial down-growth upon EMD application. Gene ontology analysis revealed genes that could be attributed to pathways of locomotion, developmental processes and associated processes such as regulation of cell size and cell growth. Additionally, eight regulated genes have previously been reported to take part in the process of epithelial-to-mesenchymal transition. Several independent experimental assays revealed significant inhibition of cell migration, growth and cell cycle by EMD. The set of EMD-regulated genes identified in this study offers the opportunity to clarify mechanisms underlying the effects of EMD on epithelial cells. Reduced epithelial repopulation of the dental root upon periodontal surgery may be the consequence of reduced migration and cell growth, as well as epithelial-to-mesenchymal transition. © 2010 John Wiley & Sons A/S.

Climate Prediction Center global monthly soil moisture data set at 0.5° resolution for 1948 to present

NASA Astrophysics Data System (ADS)

Fan, Yun; van den Dool, Huug

2004-05-01

We have produced a 0.5° × 0.5° monthly global soil moisture data set for the period from 1948 to the present. The land model is a one-layer "bucket" water balance model, while the driving input fields are Climate Prediction Center monthly global precipitation over land, which uses over 17,000 gauges worldwide, and monthly global temperature from global Reanalysis. The output consists of global monthly soil moisture, evaporation, and runoff, starting from January 1948. A distinguishing feature of this data set is that all fields are updated monthly, which greatly enhances utility for near-real-time purposes. Data validation shows that the land model does well; both the simulated annual cycle and interannual variability of soil moisture are reasonably good against the limited observations in different regions. A data analysis reveals that, on average, the land surface water balance components have a stronger annual cycle in the Southern Hemisphere than those in the Northern Hemisphere. From the point of view of soil moisture, climates can be characterized into two types, monsoonal and midlatitude climates, with the monsoonal ones covering most of the low-latitude land areas and showing a more prominent annual variation. A global soil moisture empirical orthogonal function analysis and time series of hemisphere means reveal some interesting patterns (like El Niño-Southern Oscillation) and long-term trends in both regional and global scales.

Downregulation of p16(ink4a) inhibits cell proliferation and induces G1 cell cycle arrest in cervical cancer cells.

PubMed

Zhang, Chu-Yue; Bao, Wei; Wang, Li-Hua

2014-06-01

Studies have suggested that p16(ink4a) may be a surrogate biomarker for the diagnosis of cervical cancer; however, the function of p16(ink4a) in human cervical cancer cells remains largely unknown. Therefore, in this study, we aimed to investigate the role of p16(ink4a) in human cervical cancer cells. Immunocytochemistry was used to examine invasive squamous cell carcinoma and its precancerous lesions. p16(ink4a)-siRNA was transfected into SiHa and HeLa cells to deplete its expression. The cellular levels of p16(ink4a) mRNA and protein were detected by qRT-PCR and western blot analysis. Proliferation rates were assessed by methyl thiazolyl tetrazolium (MTT) and plate colony formation assays. Cellular migration and invasion ability were assessed by a wound healing assay and Transwell assay. Cellular apoptosis and the cell cycle were measured by flow cytometry. The protein levels of retinoblastoma (Rb), phosphorylated Rb (phospho-Rb), cyclin D1 and caspase-3 were determined by western blot analysis. The results revealed that p16(ink4a) was overexpressed in the cervical cancer and precancerous lesions (P<0.05). The downregulation of p16(ink4a) in the SiHa and HeLa cells inhibited their proliferation, migration and invasion. In the SiHa cells, p16(ink4a)-siRNA also induced G1 cell cycle arrest and apoptosis. Western blot analysis revealed that the downregulation of p16(ink4a) in the SiHa cells markedly induced caspase-3 activation and decreased cyclin D1 expression. These data suggest that the overexpression of p16(ink4a) appears to be useful in monitoring cervical precancerous lesions, which supports that the hypothesis that p16(ink4a) is a surrogate biomarker for the diagnosis of cervical cancer. The therapeutic targeting of overexpressed p16(ink4a) in the p16(ink4a)-cyclin-Rb pathway may be a useful strategy in the treatment of cervical cancer.

Redistribution of cell cycle by arsenic trioxide is associated with demethylation and expression changes of cell cycle related genes in acute promyelocytic leukemia cell line (NB4).

PubMed

Hassani, Saeed; Khaleghian, Ali; Ahmadian, Shahin; Alizadeh, Shaban; Alimoghaddam, Kamran; Ghavamzadeh, Ardeshir; Ghaffari, Seyed H

2018-01-01

PML-RARα perturbs the normal epigenetic setting, which is essential to oncogenic transformation in acute promyelocytic leukemia (APL). Transcription induction and recruitment of DNA methyltransferases (DNMTs) by PML-RARα and subsequent hypermethylation are components of this perturbation. Arsenic trioxide (ATO), an important drug in APL therapy, concurrent with degradation of PML-RARα induces cell cycle change and apoptosis. How ATO causes cell cycle alteration has remained largely unexplained. Here, we investigated DNA methylation patterns of cell cycle regulatory genes promoters, the effects of ATO on the methylated genes and cell cycle distribution in an APL cell line, NB4. Analysis of promoter methylation status of 22 cell cycle related genes in NB4 revealed that CCND1, CCNE1, CCNF, CDKN1A, GADD45α, and RBL1 genes were methylated 60.7, 84.6, 58.6, 8.7, 33.4, and 73.7%, respectively, that after treatment with 2 μM ATO for 48 h, turn into 0.6, 13.8, 0.1, 6.6, 10.7, and 54.5% methylated. ATO significantly reduced the expression of DNMT1, 3A, and 3B. ATO induced the expression of CCND1, CCNE1, and GADD45α genes, suppressed the expression of CCNF and CDKN1A genes, which were consistent with decreased number of cells in G1 and S phases and increased number of cells in G2/M phase. In conclusion, demethylation and alteration in the expression level of the cell cycle related genes may be possible mechanisms in ATO-induced cell cycle arrest in APL cells. It may suggest that ATO by demethylation of CCND1 and CCNE1 and their transcriptional activation accelerates G1 and S transition into the G2/M cell cycle arrest.

Comparison of Extensive Thermal Cycling Effects on Microstructure Development in Micro-alloyed Sn-Ag-Cu Solder Joints

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

Anderson, Iver E.; Boesenberg, Adam; Harringa, Joel

2011-09-28

Pb-free solder alloys based on the Sn-Ag-Cu (SAC) ternary eutectic have promise for widespread adoption across assembly conditions and operating environments, but enhanced microstructural control is needed. Micro-alloying with elements such as Zn was demonstrated for promoting a preferred solidification path and joint microstructure earlier in simple (Cu/Cu) solder joints studies for different cooling rates. This beneficial behavior now has been verified in reworked ball grid array (BGA) joints, using dissimilar SAC305 (Sn-3.0Ag-0.5Cu, wt.%) solder paste. After industrial assembly, BGA components joined with Sn-3.5Ag-0.74Cu-0.21Zn solder were tested in thermal cycling (-55 C/+125 C) along with baseline SAC305 BGA joints beyondmore » 3000 cycles with continuous failure monitoring. Weibull analysis of the results demonstrated that BGA components joined with SAC + Zn/SAC305 have less joint integrity than SAC305 joints, but their lifetime is sufficient for severe applications in consumer, defense, and avionics electronic product field environments. Failure analysis of the BGA joints revealed that cracking did not deviate from the typical top area (BGA component side) of each joint, in spite of different Ag3Sn blade content. Thus, SAC + Zn solder has not shown any advantage over SAC305 solder in these thermal cycling trials, but other characteristics of SAC + Zn solder may make it more attractive for use across the full range of harsh conditions of avionics or defense applications.« less

A yeast gene essential for regulation of spindle pole duplication.

PubMed Central

Baum, P; Yip, C; Goetsch, L; Byers, B

1988-01-01

In eucaryotic cells, duplication of spindle poles must be coordinated with other cell cycle functions. We report here the identification in Saccharomyces cerevisiae of a temperature-sensitive lethal mutation, esp1, that deregulates spindle pole duplication. Mutant cells transferred to the nonpermissive temperature became unable to continue DNA synthesis and cell division but displayed repeated duplication of their spindle pole bodies. Although entry into this state after transient challenge by the nonpermissive temperature was largely lethal, rare survivors were recovered and found to have become increased in ploidy. If the mutant cells were held in G0 or G1 during exposure to the elevated temperature, they remained viable and maintained normal numbers of spindle poles. These results suggest dual regulation of spindle pole duplication, including a mechanism that promotes duplication as cells enter the division cycle and a negative regulatory mechanism, controlled by ESP1, that limits duplication to a single occurrence in each cell division cycle. Tetrad analysis has revealed that ESP1 resides at a previously undescribed locus on the right arm of chromosome VII. Images PMID:3072479

Carbon budgets of biological soil crusts at micro-, meso-, and global scales

USGS Publications Warehouse

Sancho, Leopoldo G; Belnap, Jayne; Colesie, Claudia; Raggio, Jose; Weber, Bettina

2016-01-01

The importance of biocrusts in the ecology of arid lands across all continents is widely recognized. In spite of this broad distribution, contributions of biocrusts to the global biogeochemical cycles have only recently been considered. While these studies opened a new view on the global role of biocrusts, they also clearly revealed the lack of data for many habitats and of overall standards for measurements and analysis. In order to understand carbon cycling in biocrusts and the progress which has been made during the last 15 years, we offer a multi-scale approach covering different climatic regions. We also include a discussion on available measurement techniques at each scale: A micro-scale section focuses on the individual organism level, including modeling based on the combination of field and lab data. The meso-scale section addresses the CO2 exchange of a complete ecosystem or at the community level. Finally, we consider the contribution of biocrusts at a global scale, giving a general perspective of the most relevant findings regarding the role of biological soil crusts in the global terrestrial carbon cycle.

A unified nonlinear stochastic time series analysis for climate science

PubMed Central

Moon, Woosok; Wettlaufer, John S.

2017-01-01

Earth’s orbit and axial tilt imprint a strong seasonal cycle on climatological data. Climate variability is typically viewed in terms of fluctuations in the seasonal cycle induced by higher frequency processes. We can interpret this as a competition between the orbitally enforced monthly stability and the fluctuations/noise induced by weather. Here we introduce a new time-series method that determines these contributions from monthly-averaged data. We find that the spatio-temporal distribution of the monthly stability and the magnitude of the noise reveal key fingerprints of several important climate phenomena, including the evolution of the Arctic sea ice cover, the El Nio Southern Oscillation (ENSO), the Atlantic Nio and the Indian Dipole Mode. In analogy with the classical destabilising influence of the ice-albedo feedback on summertime sea ice, we find that during some time interval of the season a destabilising process operates in all of these climate phenomena. The interaction between the destabilisation and the accumulation of noise, which we term the memory effect, underlies phase locking to the seasonal cycle and the statistical nature of seasonal predictability. PMID:28287128

SABRE observations of a sequence of Pc 5 micropulsations

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

Waldock, J.A.; Thomas, E.C.

Observations of a Pc 5 micropulsation event, using the Wick half of the new SABRE auroral radar, are presented. During a 3-hour period in the early morning of September 18, 1981, a train of pulsations were recorded. Analysis revealed that there were three main events, rather than one continuous disturbance. The first event appeared as a perturbation of only one or two cycles, extending throughout the latitude of the viewing area. It was also visible in the STARE region, but the perturbation drift velocity was in the north-south direction as opposed to the east-west perturbation drift of a more conventional,more » toroidal mode field line resonance. The second disturbance was an isolated, one-cycle perturbation, also visible throughout both SABRE and STARE viewing areas and also having a dominant north-south velocity component. Finally, a very localized monochromatic event, lasting five cycles or more, with a period of about 5 min, was recorded. The characteristics of the third event were found to be consistent with those predicted by field line resonance theory. 18 references.« less

A unified nonlinear stochastic time series analysis for climate science.

PubMed

Moon, Woosok; Wettlaufer, John S

2017-03-13

Earth's orbit and axial tilt imprint a strong seasonal cycle on climatological data. Climate variability is typically viewed in terms of fluctuations in the seasonal cycle induced by higher frequency processes. We can interpret this as a competition between the orbitally enforced monthly stability and the fluctuations/noise induced by weather. Here we introduce a new time-series method that determines these contributions from monthly-averaged data. We find that the spatio-temporal distribution of the monthly stability and the magnitude of the noise reveal key fingerprints of several important climate phenomena, including the evolution of the Arctic sea ice cover, the El Nio Southern Oscillation (ENSO), the Atlantic Nio and the Indian Dipole Mode. In analogy with the classical destabilising influence of the ice-albedo feedback on summertime sea ice, we find that during some time interval of the season a destabilising process operates in all of these climate phenomena. The interaction between the destabilisation and the accumulation of noise, which we term the memory effect, underlies phase locking to the seasonal cycle and the statistical nature of seasonal predictability.

A unified nonlinear stochastic time series analysis for climate science

NASA Astrophysics Data System (ADS)

Moon, Woosok; Wettlaufer, John

2017-04-01

Earth's orbit and axial tilt imprint a strong seasonal cycle on climatological data. Climate variability is typically viewed in terms of fluctuations in the seasonal cycle induced by higher frequency processes. We can interpret this as a competition between the orbitally enforced monthly stability and the fluctuations/noise induced by weather. Here we introduce a new time-series method that determines these contributions from monthly-averaged data. We find that the spatio-temporal distribution of the monthly stability and the magnitude of the noise reveal key fingerprints of several important climate phenomena, including the evolution of the Arctic sea ice cover, the El Niño Southern Oscillation (ENSO), the Atlantic Niño and the Indian Dipole Mode. In analogy with the classical destabilising influence of the ice-albedo feedback on summertime sea ice, we find that during some period of the season a destabilising process operates in all of these climate phenomena. The interaction between the destabilisation and the accumulation of noise, which we term the memory effect, underlies phase locking to the seasonal cycle and the statistical nature of seasonal predictability.

Ethanolic extract of Ferula gummosa is cytotoxic against cancer cells by inducing apoptosis and cell cycle arrest.

PubMed

Gudarzi, Hoda; Salimi, Mona; Irian, Saeed; Amanzadeh, Amir; Mostafapour Kandelous, Hirsa; Azadmanesh, Keyhan; Salimi, Misha

2015-01-01

Ferula gummosa Boiss. has medicinal applications in treating a wide range of diseases including cancer. The objective of this study was to evaluate the antiproliferative activities of the seed and gum extracts of F. gummosa as well as to study the effect of the potent extract on the induction of apoptosis and cell cycle arrest. Our results demonstrated that the ethanolic extract had the lowest IC50 value at 72 h (0.001 ± 1.2 mg/mL) in BHY cells. Moreover, flowcytometry and annexin-V analysis revealed that the ethanolic extract induced apoptosis and cell-cycle arrest in BHY cells at G1/S phase. In addition, colorimetric methods exhibited the highest amount of total phenolics and flavonoids in the aqueous and gum extracts (0.12 ± 0.037, 0.01 ± 2.51 mg/g of dry powder). Generally, the results obtained indicate that F. gummosa ethanol extract may contain effective compounds which can be used as a chemotherapeutic agent.

Unsteady surface pressure measurements on a slender delta wing undergoing limit cycle wing rock

NASA Technical Reports Server (NTRS)

Arena, Andrew S., Jr.; Nelson, Robert C.

1991-01-01

An experimental investigation of slender wing limit cycle motion known as wing rock was investigated using two unique experimental systems. Dynamic roll moment measurements and visualization data on the leading edge vortices were obtained using a free to roll apparatus that incorporates an airbearing spindle. In addition, both static and unsteady surface pressure data was measured on the top and bottom surfaces of the model. To obtain the unsteady surface pressure data a new computer controller drive system was developed to accurately reproduce the free to roll time history motions. The data from these experiments include, roll angle time histories, vortex trajectory data on the position of the vortices relative to the model's surface, and surface pressure measurements as a function of roll angle when the model is stationary or undergoing a wing rock motion. The roll time history data was numerically differentiated to determine the dynamic roll moment coefficient. An analysis of these data revealed that the primary mechanism for the limit cycle behavior was a time lag in the position of the vortices normal to the wing surface.

Hormonal regulation of delta opioid receptor immunoreactivity in interneurons and pyramidal cells in the rat hippocampus

PubMed Central

Williams, Tanya J.; Torres-Reveron, Annelyn; Chapleau, Jeanette D.; Milner, Teresa A.

2011-01-01

Clinical and preclinical studies indicate that women and men differ in relapse vulnerability to drug-seeking behavior during abstinence periods. As relapse is frequently triggered by exposure of the recovered addict to objects previously associated with drug use and the formation of these associations requires memory systems engaged by the hippocampal formation (HF), studies exploring ovarian hormone modulation of hippocampal function are warranted. Previous studies revealed that ovarian steroids alter endogenous opioid peptide levels and trafficking of mu opioid receptors in the HF, suggesting cooperative interaction between opioids and estrogens in modulating hippocampal excitability. However, whether ovarian steroids affect the levels or trafficking of delta opioid receptors (DORs) in the HF is unknown. Here, hippocampal sections of adult male and normal cycling female Sprague-Dawley rats were processed for quantitative immunoperoxidase light microscopy and dual label fluorescence or immunoelectron microscopy using antisera directed against the DOR and neuropeptide Y (NPY). Consistent with previous studies in males, DOR-immunoreactivity (-ir) localized to select interneurons and principal cells in the female HF. In comparison to males, females, regardless of estrous cycle phase, show reduced DOR-ir in the granule cell layer of the dentate gyrus and proestrus (high estrogen) females, in particular, display reduced DOR-ir in the CA1 pyramidal cell layer. Ultrastructural analysis of DOR-labeled profiles in CA1 revealed that while females generally show fewer DORs in the distal apical dendrites of pyramidal cells, proestrus females, in particular, exhibit DOR internalization and trafficking towards the soma. Dual label studies revealed that DORs are found in NPY-labeled interneurons in the hilus, CA3, and CA1. While DOR colocalization frequency in NPY-labeled neuron somata was similar between animals in the hilus, proestrus females had fewer NPY-labeled neurons that co-labeled with DOR in stratum oriens of CA1 and CA3 when compared to males. Ultrastructural analysis of NPY-labeled axon terminals within stratum radiatum of CA1 revealed that NPY-labeled axon terminals contain DORs that are frequently found at or near the plasma membrane. As no differences were noted by sex or estrous cycle phase, DOR activation on NPY-labeled axon terminals would inhibit GABA release probability equally in males and females. Taken together, these findings suggest that ovarian steroids can impact hippocampal function through direct effects on DOR levels and trafficking in principal cells and broad indirect effects through reductions in DOR-ir in NPY-labeled interneurons, particularly in CA1. PMID:21224009

An Integrated Multi-Omics Study Revealed Metabolic Alterations Underlying the Effects of Coffee Consumption

PubMed Central

Takahashi, Shoko; Saito, Kenji; Jia, Huijuan; Kato, Hisanori

2014-01-01

Many epidemiological studies have indicated that coffee consumption may reduce the risks of developing obesity and diabetes, but the underlying mechanisms of these effects are poorly understood. Our previous study revealed the changes on gene expression profiles in the livers of C57BL/6J mice fed a high-fat diet containing three types of coffee (caffeinated, decaffeinated and green unroasted coffee), using DNA microarrays. The results revealed remarkable alterations in lipid metabolism-related molecules which may be involved in the anti-obesity effects of coffee. We conducted the present study to further elucidate the metabolic alterations underlying the effects of coffee consumption through comprehensive proteomic and metabolomic analyses. Proteomics revealed an up-regulation of isocitrate dehydrogenase (a key enzyme in the TCA cycle) and its related proteins, suggesting increased energy generation. The metabolomics showed an up-regulation of metabolites involved in the urea cycle, with which the transcriptome data were highly consistent, indicating accelerated energy expenditure. The TCA cycle and the urea cycle are likely be accelerated in a concerted manner, since they are directly connected by mutually providing each other's intermediates. The up-regulation of these pathways might result in a metabolic shift causing increased ATP turnover, which is related to the alterations of lipid metabolism. This mechanism may play an important part in the suppressive effects of coffee consumption on obesity, inflammation, and hepatosteatosis. This study newly revealed global metabolic alterations induced by coffee intake, providing significant insights into the association between coffee intake and the prevention of type 2 diabetes, utilizing the benefits of multi-omics analyses. PMID:24618914

A Rice PECTATE LYASE-LIKE Gene Is Required for Plant Growth and Leaf Senescence1[OPEN

PubMed Central

Leng, Yujia; Yang, Yaolong; Ren, Deyong; Dai, Liping; Wang, Yuqiong; Chen, Long; Tu, Zhengjun; Gao, Yihong; Zhu, Li; Hu, Jiang; Gao, Zhenyu; Guo, Longbiao; Lin, Yongjun

2017-01-01

To better understand the molecular mechanisms behind plant growth and leaf senescence in monocot plants, we identified a mutant exhibiting dwarfism and an early-senescence leaf phenotype, termed dwarf and early-senescence leaf1 (del1). Histological analysis showed that the abnormal growth was caused by a reduction in cell number. Further investigation revealed that the decline in cell number in del1 was affected by the cell cycle. Physiological analysis, transmission electron microscopy, and TUNEL assays showed that leaf senescence was triggered by the accumulation of reactive oxygen species. The DEL1 gene was cloned using a map-based approach. It was shown to encode a pectate lyase (PEL) precursor that contains a PelC domain. DEL1 contains all the conserved residues of PEL and has strong similarity with plant PelC. DEL1 is expressed in all tissues but predominantly in elongating tissues. Functional analysis revealed that mutation of DEL1 decreased the total PEL enzymatic activity, increased the degree of methylesterified homogalacturonan, and altered the cell wall composition and structure. In addition, transcriptome assay revealed that a set of cell wall function- and senescence-related gene expression was altered in del1 plants. Our research indicates that DEL1 is involved in both the maintenance of normal cell division and the induction of leaf senescence. These findings reveal a new molecular mechanism for plant growth and leaf senescence mediated by PECTATE LYASE-LIKE genes. PMID:28455404

A Rice PECTATE LYASE-LIKE Gene Is Required for Plant Growth and Leaf Senescence.

PubMed

Leng, Yujia; Yang, Yaolong; Ren, Deyong; Huang, Lichao; Dai, Liping; Wang, Yuqiong; Chen, Long; Tu, Zhengjun; Gao, Yihong; Li, Xueyong; Zhu, Li; Hu, Jiang; Zhang, Guangheng; Gao, Zhenyu; Guo, Longbiao; Kong, Zhaosheng; Lin, Yongjun; Qian, Qian; Zeng, Dali

2017-06-01

To better understand the molecular mechanisms behind plant growth and leaf senescence in monocot plants, we identified a mutant exhibiting dwarfism and an early-senescence leaf phenotype, termed dwarf and early-senescence leaf1 ( del1 ). Histological analysis showed that the abnormal growth was caused by a reduction in cell number. Further investigation revealed that the decline in cell number in del1 was affected by the cell cycle. Physiological analysis, transmission electron microscopy, and TUNEL assays showed that leaf senescence was triggered by the accumulation of reactive oxygen species. The DEL1 gene was cloned using a map-based approach. It was shown to encode a pectate lyase (PEL) precursor that contains a PelC domain. DEL1 contains all the conserved residues of PEL and has strong similarity with plant PelC. DEL1 is expressed in all tissues but predominantly in elongating tissues. Functional analysis revealed that mutation of DEL1 decreased the total PEL enzymatic activity, increased the degree of methylesterified homogalacturonan, and altered the cell wall composition and structure. In addition, transcriptome assay revealed that a set of cell wall function- and senescence-related gene expression was altered in del1 plants. Our research indicates that DEL1 is involved in both the maintenance of normal cell division and the induction of leaf senescence. These findings reveal a new molecular mechanism for plant growth and leaf senescence mediated by PECTATE LYASE-LIKE genes. © 2017 American Society of Plant Biologists. All Rights Reserved.

Thermal control systems for low-temperature heat rejection on a lunar base

NASA Technical Reports Server (NTRS)

Sridhar, K. R.; Gottmann, Matthias

1992-01-01

In this report, Rankine-cycle heat pumps and absorption heat pumps (ammonia-water and lithium bromide-water) have been analyzed and optimized for a lunar base cooling load of 100 kW. For the Rankine cycle, a search of several commonly used commercial refrigerants provided R11 and R717 as possible working fluids. Hence, the Rankine-cycle analysis has been performed for both R11 and R717. Two different configurations were considered for the system--one in which the heat pump is directly connected to the rejection loop and another in which a heat exchanger connects the heat pump to the rejection loop. For a marginal increase in mass, the decoupling of the rejection loop and the radiator from the heat pump provides greater reliability of the system and better control. Hence, the decoupled system is the configuration of choice. The optimal TCS mass for a 100 kW cooling load at 270 K was 5940 kg at a radiator temperature of 362 K. R11 was the working fluid in the heat pump, and R717 was the transport fluid in the rejection loop. Two TCS's based on an absorption-cycle heat pump were considered, one with an ammonia-water mixture and the other with a lithium bromide-water mixture as the working fluid. A complete cycle analysis was performed for these systems. The system components were approximated as heat exchangers with no internal pressure drop for the mass estimate. This simple approach underpredicts the mass of the systems, but is a good 'optimistic' first approximation to the TCS mass in the absence of reliable component mass data. The mass estimates of the two systems reveal that, in spite of this optimistic estimate, the absorption heat pumps are not competitive with the Rankine-cycle heat pumps. Future work at the systems level will involve similar analyses for the Brayton- and Stirling-cycle heat pumps. The analyses will also consider the operation of the pump under partial-load conditions. On the component level, a capillary evaporator will be designed, built, and tested in order to investigate its suitability in lunar base TCS and microgravity two-phase applications.

Survivin is a novel transcription regulator of KIT and is downregulated by miRNA-494 in gastrointestinal stromal tumors.

PubMed

Yun, SeongJu; Kim, Won Kyu; Kwon, Yujin; Jang, Mi; Bauer, Sebastian; Kim, Hoguen

2018-05-15

Gain-of-function mutations of KIT are pathognomonic in sporadic gastrointestinal stromal tumors (GISTs). Several microRNAs have been shown to be dysregulated in GISTs and impact KIT expression. Little is known though on KIT-independent targets of KIT-regulating mRNAs. We sought to investigate how miR-494 inhibits GIST proliferation and to identify novel target gene. We used microarray-based gene expression analyses to identify pathways and target genes affected by miR-494. The expressional relationship between survivin and miR-494 was determined in 35 GIST tissues. Cell proliferation assay, FACS analysis, colony formation assay, promoter assays and chromatin immunoprecipitation (ChiP) were performed to clarify the roles of survivin in GIST progression. Gene expression microarray analysis revealed that miR-494 inhibited GISTs by affecting multiple genes in the cell cycle pathway. Survivin (BIRC5) was a key target of miR-494, and its expression showed an inverse correlation with miR-494 expression in 35 GIST tissues (Pearson's correlation coefficient, r = -0.418, p = 0.012). Downregulation of survivin inhibited proliferation and colony formation, and resulted in cell cycle alteration. Induced survivin overexpression relieved miR-494-mediated inhibition of GIST progression. Targeting PI3K effectively suppressed proliferation of GISTs with downregulation of survivin. Survivin also regulated KIT expression at the transcription level. Immunohistochemical analysis using 113 GISTs revealed that survivin expression was significantly correlated with overall survival of GIST patients (p = 0.004). Our findings indicated that miR-494 synergistically suppressed GISTs by concomitantly targeting survivin and KIT. © 2017 The Authors International Journal of Cancer published by John Wiley & Sons Ltd on behalf of UICC.

Survivin is a novel transcription regulator of KIT and is downregulated by miRNA‐494 in gastrointestinal stromal tumors

PubMed Central

Yun, SeongJu; Kim, Won Kyu; Kwon, Yujin; Jang, Mi; Bauer, Sebastian

2018-01-01

Gain‐of‐function mutations of KIT are pathognomonic in sporadic gastrointestinal stromal tumors (GISTs). Several microRNAs have been shown to be dysregulated in GISTs and impact KIT expression. Little is known though on KIT‐independent targets of KIT‐regulating mRNAs. We sought to investigate how miR‐494 inhibits GIST proliferation and to identify novel target gene. We used microarray‐based gene expression analyses to identify pathways and target genes affected by miR‐494. The expressional relationship between survivin and miR‐494 was determined in 35 GIST tissues. Cell proliferation assay, FACS analysis, colony formation assay, promoter assays and chromatin immunoprecipitation (ChiP) were performed to clarify the roles of survivin in GIST progression. Gene expression microarray analysis revealed that miR‐494 inhibited GISTs by affecting multiple genes in the cell cycle pathway. Survivin (BIRC5) was a key target of miR‐494, and its expression showed an inverse correlation with miR‐494 expression in 35 GIST tissues (Pearson's correlation coefficient, r = −0.418, p = 0.012). Downregulation of survivin inhibited proliferation and colony formation, and resulted in cell cycle alteration. Induced survivin overexpression relieved miR‐494‐mediated inhibition of GIST progression. Targeting PI3K effectively suppressed proliferation of GISTs with downregulation of survivin. Survivin also regulated KIT expression at the transcription level. Immunohistochemical analysis using 113 GISTs revealed that survivin expression was significantly correlated with overall survival of GIST patients (p = 0.004). Our findings indicated that miR‐494 synergistically suppressed GISTs by concomitantly targeting survivin and KIT. PMID:29277888

²H enrichment distribution of hepatic glycogen from ²H₂O reveals the contribution of dietary fructose to glycogen synthesis.

PubMed

Delgado, Teresa C; Martins, Fátima O; Carvalho, Filipa; Gonçalves, Ana; Scott, Donald K; O'Doherty, Robert; Macedo, M Paula; Jones, John G

2013-02-15

Dietary fructose can benefit or hinder glycemic control, depending on the quantity consumed, and these contrasting effects are reflected by alterations in postprandial hepatic glycogen synthesis. Recently, we showed that ²H enrichment of glycogen positions 5 and 2 from deuterated water (²H₂O) informs direct and indirect pathway contributions to glycogenesis in naturally feeding rats. Inclusion of position 6(S) ²H enrichment data allows indirect pathway sources to be further resolved into triose phosphate and Krebs cycle precursors. This analysis was applied to six rats that had fed on standard chow (SC) and six rats that had fed on SC plus 35% sucrose in their drinking water (HS). After 2 wk, hepatic glycogenesis sources during overnight feeding were determined by ²H₂O administration and postmortem analysis of glycogen ²H enrichment at the conclusion of the dark period. Net overnight hepatic glycogenesis was similar between SC and HS rodents. Whereas direct pathway contributions were similar (403 ± 71 μmol/g dry wt HS vs. 578 ± 76 μmol/g dry wt SC), triose phosphate contributions were significantly higher for HS compared with SC (382 ± 61 vs. 87 ± 24 μmol/g dry wt, P < 0.01) and Krebs cycle inputs lower for HS compared with SC (110 ± 9 vs. 197 ± 32 μmol/g dry wt, P < 0.05). Analysis of plasma glucose ²H enrichments at the end of the feeding period also revealed a significantly higher fractional contribution of triose phosphate to plasma glucose levels in HS vs. SC. Hence, the ²H enrichment distributions of hepatic glycogen and glucose from ²H₂O inform the contribution of dietary fructose to hepatic glycogen and glucose synthesis.

Lithofacies, paleoenvironment and high-resolution stratigraphy of the D5 and D6 members of the Middle Jurassic carbonates Dhruma Formation, outcrop analog, central Saudi Arabia

NASA Astrophysics Data System (ADS)

Yousif, Ibrahim M.; Abdullatif, Osman M.; Makkawi, Mohammad H.; Bashri, Mazin A.; Abdulghani, Waleed M.

2018-03-01

This study characterizes the lithofacies, paleoenvironment and stratigraphic architecture of the D5 and D6 members of carbonates Dhruma Formation outcrops in central Saudi Arabia. The study integrates detailed lithofacies analysis based on vertical and lateral profiles, in addition to thin-sections petrography to reveal the high-resolution architecture framework. Nine lithofacies types (LFTs) were defined namely: (1) skeletal peletal spiculitic wackestone (15%), (2) peloidal echinoderm packstone (19%), (3) fissile shale (36%), (4) peloidal spiculitic echinoderm pack-grainstone (5%), (5) cross-bedded peloidal skeletal oolitic grainstone (7%), (6) oolitic grainstone (2%), (7) intraformational rudstone (<1%), (8) skeletal peloidal foraminiferal packstone (12%) and (9) skeletal foraminiferal wackestone (4%). These lithofacies types were grouped into five major carbonate paleoenvironments that range from distal-to-proximal carbonate ramp setting. The detailed stratigraphic analysis revealed around 53 cycles and cycle sets with 5th to 6th orders magnitude, and thickness ranges from a few centimeters up to 6 m with an average of 1.5 m. Those are stacked to form four high-frequency sequences with thickness range from 1 m up to 14 m. The latter were grouped into a single depositional sequence of 3rd order magnitude. The architectural analysis also shows that the potential reservoir units were intensively affected by muddy-textured rocks which act as reservoir seals. These variations in the stratigraphic sequences in Middle Jurassic Dhruma Formation and its equivalents could be attributed to the eustatic sea-level changes, climate, tectonics, and local paleoenvironments. This study attempts to provide detailed insight into reservoir heterogeneity and architecture. The analog may help to understand and predict lithofacies heterogeneity, architecture, and quality in the subsurface equivalent reservoirs.

Synergy between (13)C-metabolic flux analysis and flux balance analysis for understanding metabolic adaptation to anaerobiosis in E. coli.

PubMed

Chen, Xuewen; Alonso, Ana P; Allen, Doug K; Reed, Jennifer L; Shachar-Hill, Yair

2011-01-01

Genome-based Flux Balance Analysis (FBA) and steady-state isotopic-labeling-based Metabolic Flux Analysis (MFA) are complimentary approaches to predicting and measuring the operation and regulation of metabolic networks. Here, genome-derived models of Escherichia coli (E. coli) metabolism were used for FBA and ¹³C-MFA analyses of aerobic and anaerobic growths of wild-type E. coli (K-12 MG1655) cells. Validated MFA flux maps reveal that the fraction of maintenance ATP consumption in total ATP production is about 14% higher under anaerobic (51.1%) than aerobic conditions (37.2%). FBA revealed that an increased ATP utilization is consumed by ATP synthase to secrete protons from fermentation. The TCA cycle is shown to be incomplete in aerobically growing cells and submaximal growth is due to limited oxidative phosphorylation. An FBA was successful in predicting product secretion rates in aerobic culture if both glucose and oxygen uptake measurement were constrained, but the most-frequently predicted values of internal fluxes yielded from sampling the feasible space differ substantially from MFA-derived fluxes. © 2010 Elsevier Inc. All rights reserved.

Teaching Human Genetics with Mustard: Rapid Cycling Brassica rapa (Fast Plants Type) as a Model for Human Genetics in the Classroom Laboratory

PubMed Central

Pickard, Dawn

2007-01-01

We have developed experiments and materials to model human genetics using rapid cycling Brassica rapa, also known as Fast Plants. Because of their self-incompatibility for pollination and the genetic diversity within strains, B. rapa can serve as a relevant model for human genetics in teaching laboratory experiments. The experiment presented here is a paternity exclusion project in which a child is born with a known mother but two possible alleged fathers. Students use DNA markers (microsatellites) to perform paternity exclusion on these subjects. Realistic DNA marker analysis can be challenging to implement within the limitations of an instructional lab, but we have optimized the experimental methods to work in a teaching lab environment and to maximize the “hands-on” experience for the students. The genetic individuality of each B. rapa plant, revealed by analysis of polymorphic microsatellite markers, means that each time students perform this project, they obtain unique results that foster independent thinking in the process of data interpretation. PMID:17548880

Urea Amendment Decreases Microbial Diversity and Selects for Specific Nitrifying Strains in Eight Contrasting Agricultural Soils

PubMed Central

Staley, Christopher; Breuillin-Sessoms, Florence; Wang, Ping; Kaiser, Thomas; Venterea, Rodney T.; Sadowsky, Michael J.

2018-01-01

Application of nitrogen (N) fertilizers, predominantly as urea, is a major source of reactive N in the environment, with wide ranging effects including increased greenhouse gas accumulation in the atmosphere and aquatic eutrophication. The soil microbial community is the principal driver of soil N cycling; thus, improved understanding of microbial community responses to urea addition has widespread implications. We used next-generation amplicon sequencing of the 16S rRNA gene to characterize bacterial and archaeal communities in eight contrasting agricultural soil types amended with 0, 100, or 500 μg N g-1 of urea and incubated for 21 days. We hypothesized that urea amendment would have common, direct effects on the abundance and diversity of members of the microbial community associated with nitrification, across all soils, and would further affect the broader heterotrophic community resulting in decreased diversity and variation in abundances of specific taxa. Significant (P < 0.001) differences in bacterial community diversity and composition were observed by site, but amendment with only the greatest urea concentration significantly decreased Shannon indices. Expansion in the abundances of members of the families Microbacteriaceae, Chitinophagaceae, Comamonadaceae, Xanthomonadaceae, and Nitrosomonadaceae were also consistently observed among all soils (linear discriminant analysis score ≥ 3.0). Analysis of nitrifier genera revealed diverse, soil-specific distributions of oligotypes (strains), but few were correlated with nitrification gene abundances that were reported in a previous study. Our results suggest that the majority of the bacterial and archaeal community are likely unassociated with N cycling, but are significantly negatively impacted by urea application. Furthermore, these results reveal that amendment with high concentrations of urea may reduce nitrifier diversity, favoring specific strains, specifically those within the nitrifying genera Nitrobacter, Nitrospira, and Nitrosospira, that may play significant roles related to N cycling in soils receiving intensive urea inputs. PMID:29670600

Exergy analysis of helium liquefaction systems based on modified Claude cycle with two-expanders

NASA Astrophysics Data System (ADS)

Thomas, Rijo Jacob; Ghosh, Parthasarathi; Chowdhury, Kanchan

2011-06-01

Large-scale helium liquefaction systems, being energy-intensive, demand judicious selection of process parameters. An effective tool for design and analysis of thermodynamic cycles for these systems is exergy analysis, which is used to study the behavior of a helium liquefaction system based on modified Claude cycle. Parametric evaluation using process simulator Aspen HYSYS® helps to identify the effects of cycle pressure ratio and expander flow fraction on the exergetic efficiency of the liquefaction cycle. The study computes the distribution of losses at different refrigeration stages of the cycle and helps in selecting optimum cycle pressures, operating temperature levels of expanders and mass flow rates through them. Results from the analysis may help evolving guidelines for designing appropriate thermodynamic cycles for practical helium liquefaction systems.

Microbial mediation of biogeochemical cycles revealed by simulation of global changes with soil transplant and cropping

PubMed Central

Zhao, Mengxin; Xue, Kai; Wang, Feng; Liu, Shanshan; Bai, Shijie; Sun, Bo; Zhou, Jizhong; Yang, Yunfeng

2014-01-01

Despite microbes' key roles in driving biogeochemical cycles, the mechanism of microbe-mediated feedbacks to global changes remains elusive. Recently, soil transplant has been successfully established as a proxy to simulate climate changes, as the current trend of global warming coherently causes range shifts toward higher latitudes. Four years after southward soil transplant over large transects in China, we found that microbial functional diversity was increased, in addition to concurrent changes in microbial biomass, soil nutrient content and functional processes involved in the nitrogen cycle. However, soil transplant effects could be overridden by maize cropping, which was attributed to a negative interaction. Strikingly, abundances of nitrogen and carbon cycle genes were increased by these field experiments simulating global change, coinciding with higher soil nitrification potential and carbon dioxide (CO2) efflux. Further investigation revealed strong correlations between carbon cycle genes and CO2 efflux in bare soil but not cropped soil, and between nitrogen cycle genes and nitrification. These findings suggest that changes of soil carbon and nitrogen cycles by soil transplant and cropping were predictable by measuring microbial functional potentials, contributing to a better mechanistic understanding of these soil functional processes and suggesting a potential to incorporate microbial communities in greenhouse gas emission modeling. PMID:24694714

Integrated Analysis of the Effects of Cold and Dehydration on Rice Metabolites, Phytohormones, and Gene Transcripts1[W][OPEN

PubMed Central

Maruyama, Kyonoshin; Urano, Kaoru; Yoshiwara, Kyouko; Morishita, Yoshihiko; Sakurai, Nozomu; Suzuki, Hideyuki; Kojima, Mikiko; Sakakibara, Hitoshi; Shibata, Daisuke; Saito, Kazuki; Shinozaki, Kazuo; Yamaguchi-Shinozaki, Kazuko

2014-01-01

Correlations between gene expression and metabolite/phytohormone levels under abiotic stress conditions have been reported for Arabidopsis (Arabidopsis thaliana). However, little is known about these correlations in rice (Oryza sativa ‘Nipponbare’), despite its importance as a model monocot. We performed an integrated analysis to clarify the relationships among cold- and dehydration-responsive metabolites, phytohormones, and gene transcription in rice. An integrated analysis of metabolites and gene expression indicated that several genes encoding enzymes involved in starch degradation, sucrose metabolism, and the glyoxylate cycle are up-regulated in rice plants exposed to cold or dehydration and that these changes are correlated with the accumulation of glucose (Glc), fructose, and sucrose. In particular, high expression levels of genes encoding isocitrate lyase and malate synthase in the glyoxylate cycle correlate with increased Glc levels in rice, but not in Arabidopsis, under dehydration conditions, indicating that the regulation of the glyoxylate cycle may be involved in Glc accumulation under dehydration conditions in rice but not Arabidopsis. An integrated analysis of phytohormones and gene transcripts revealed an inverse relationship between abscisic acid (ABA) signaling and cytokinin (CK) signaling under cold and dehydration stresses; these stresses increase ABA signaling and decrease CK signaling. High levels of Oryza sativa 9-cis-epoxycarotenoid dioxygenase transcripts correlate with ABA accumulation, and low levels of Cytochrome P450 (CYP) 735A transcripts correlate with decreased levels of a CK precursor in rice. This reduced expression of CYP735As occurs in rice but not Arabidopsis. Therefore, transcriptional regulation of CYP735As might be involved in regulating CK levels under cold and dehydration conditions in rice but not Arabidopsis. PMID:24515831

High expression of Polycomb group protein EZH2 predicts poor survival in salivary gland adenoid cystic carcinoma.

PubMed

Vékony, H; Raaphorst, F M; Otte, A P; van Lohuizen, M; Leemans, C R; van der Waal, I; Bloemena, E

2008-06-01

The prognosis of adenoid cystic carcinoma (ACC), a malignant salivary gland tumour, depends on clinicopathological parameters. To decipher the biological behaviour of ACC, and to identify patients at risk of developing metastases, additional markers are needed. Expression of the cell cycle proteins p53, cyclin D1, p16(INK4a), E2F1 and Ki-67, together with the Polycomb group (PcG) proteins BMI-1, MEL-18, EZH2 and EED was investigated immunohistochemically 21 formalin-fixed, paraffin-embedded primary ACCs in relation to tumour characteristics. ACC revealed significantly increased expression of the cell cycle proteins compared to normal salivary tissue (n = 17). Members of the two PcG complexes displayed mutually exclusive expression in normal salivary gland tissue, with BMI-1 and MEL-18 being abundantly present. In ACC, this expression pattern was disturbed, with EZH2 and EED showing significantly increased expression levels. In univariate analysis, presence of recurrence, poor differentiation and high EZH2 levels (>25% immunopositivity) significantly correlated with unfavourable outcome. ACCs with high proliferative rate (>25% Ki-67 immunopositivity) significantly correlated with high levels of EZH2 and p16. Only the development of recurrence was an independent prognostic factor of survival in multivariate analysis. Expression of PcG complexes and of essential cell cycle proteins is highly deregulated in ACC. Also, EZH2 expression has prognostic relevance in this malignancy.

Differential expression of lncRNAs during the HIV replication cycle: an underestimated layer in the HIV-host interplay.

PubMed

Trypsteen, Wim; Mohammadi, Pejman; Van Hecke, Clarissa; Mestdagh, Pieter; Lefever, Steve; Saeys, Yvan; De Bleser, Pieter; Vandesompele, Jo; Ciuffi, Angela; Vandekerckhove, Linos; De Spiegelaere, Ward

2016-10-26

Studying the effects of HIV infection on the host transcriptome has typically focused on protein-coding genes. However, recent advances in the field of RNA sequencing revealed that long non-coding RNAs (lncRNAs) add an extensive additional layer to the cell's molecular network. Here, we performed transcriptome profiling throughout a primary HIV infection in vitro to investigate lncRNA expression at the different HIV replication cycle processes (reverse transcription, integration and particle production). Subsequently, guilt-by-association, transcription factor and co-expression analysis were performed to infer biological roles for the lncRNAs identified in the HIV-host interplay. Many lncRNAs were suggested to play a role in mechanisms relying on proteasomal and ubiquitination pathways, apoptosis, DNA damage responses and cell cycle regulation. Through transcription factor binding analysis, we found that lncRNAs display a distinct transcriptional regulation profile as compared to protein coding mRNAs, suggesting that mRNAs and lncRNAs are independently modulated. In addition, we identified five differentially expressed lncRNA-mRNA pairs with mRNA involvement in HIV pathogenesis with possible cis regulatory lncRNAs that control nearby mRNA expression and function. Altogether, the present study demonstrates that lncRNAs add a new dimension to the HIV-host interplay and should be further investigated as they may represent targets for controlling HIV replication.

Global Analysis of Palmitoylated Proteins in Toxoplasma gondii.

PubMed

Foe, Ian T; Child, Matthew A; Majmudar, Jaimeen D; Krishnamurthy, Shruthi; van der Linden, Wouter A; Ward, Gary E; Martin, Brent R; Bogyo, Matthew

2015-10-14

Post-translational modifications (PTMs) such as palmitoylation are critical for the lytic cycle of the protozoan parasite Toxoplasma gondii. While palmitoylation is involved in invasion, motility, and cell morphology, the proteins that utilize this PTM remain largely unknown. Using a chemical proteomic approach, we report a comprehensive analysis of palmitoylated proteins in T. gondii, identifying a total of 282 proteins, including cytosolic, membrane-associated, and transmembrane proteins. From this large set of palmitoylated targets, we validate palmitoylation of proteins involved in motility (myosin light chain 1, myosin A), cell morphology (PhIL1), and host cell invasion (apical membrane antigen 1, AMA1). Further studies reveal that blocking AMA1 palmitoylation enhances the release of AMA1 and other invasion-related proteins from apical secretory organelles, suggesting a previously unrecognized role for AMA1. These findings suggest that palmitoylation is ubiquitous throughout the T. gondii proteome and reveal insights into the biology of this important human pathogen. Copyright © 2015 Elsevier Inc. All rights reserved.

10 CFR 434.607 - Life cycle cost analysis criteria.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 3 2011-01-01 2011-01-01 false Life cycle cost analysis criteria. 434.607 Section 434.607... HIGH RISE RESIDENTIAL BUILDINGS Building Energy Compliance Alternative § 434.607 Life cycle cost analysis criteria. 607.1 The following life cycle cost criteria applies to the fuel selection requirements...

10 CFR 434.607 - Life cycle cost analysis criteria.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 3 2010-01-01 2010-01-01 false Life cycle cost analysis criteria. 434.607 Section 434.607... HIGH RISE RESIDENTIAL BUILDINGS Building Energy Compliance Alternative § 434.607 Life cycle cost analysis criteria. 607.1 The following life cycle cost criteria applies to the fuel selection requirements...

Developmental stage-specific regulation of the circadian clock by temperature in zebrafish.

PubMed

Lahiri, Kajori; Froehlich, Nadine; Heyd, Andreas; Foulkes, Nicholas S; Vallone, Daniela

2014-01-01

The circadian clock enables animals to adapt their physiology and behaviour in anticipation of the day-night cycle. Light and temperature represent two key environmental timing cues (zeitgebers) able to reset this mechanism and so maintain its synchronization with the environmental cycle. One key challenge is to unravel how the regulation of the clock by zeitgebers matures during early development. The zebrafish is an ideal model for studying circadian clock ontogeny since the process of development occurs ex utero in an optically transparent chorion and many tools are available for genetic analysis. However, the role played by temperature in regulating the clock during zebrafish development is poorly understood. Here, we have established a clock-regulated luciferase reporter transgenic zebrafish line (Tg (-3.1) per1b::luc) to study the effects of temperature on clock entrainment. We reveal that under complete darkness, from an early developmental stage onwards (48 to 72 hpf), exposure to temperature cycles is a prerequisite for the establishment of self-sustaining rhythms of zfper1b, zfaanat2, and zfirbp expression and also for circadian cell cycle rhythms. Furthermore, we show that following the 5-9 somite stage, the expression of zfper1b is regulated by acute temperature shifts.