Comparative Activity-Based Flavin-Dependent Oxidase Profiling.

PubMed

Krysiak, Joanna; Breinbauer, Rolf

2017-01-01

Activity-based protein profiling (ABPP) has become a powerful chemoproteomic technology allowing for the dissection of complex ligand-protein interactions in their native cellular environment. One of the biggest challenges for ABPP is the extension of the proteome coverage. In this chapter a new ABPP strategy dedicated to monoamine oxidases (MAO) is presented. These enzymes are representative examples of flavin-dependent oxidases, playing a crucial role in the regulation of nervous system signaling.

Proteomic data from human cell cultures refine mechanisms of chaperone-mediated protein homeostasis.

PubMed

Finka, Andrija; Goloubinoff, Pierre

2013-09-01

In the crowded environment of human cells, folding of nascent polypeptides and refolding of stress-unfolded proteins is error prone. Accumulation of cytotoxic misfolded and aggregated species may cause cell death, tissue loss, degenerative conformational diseases, and aging. Nevertheless, young cells effectively express a network of molecular chaperones and folding enzymes, termed here "the chaperome," which can prevent formation of potentially harmful misfolded protein conformers and use the energy of adenosine triphosphate (ATP) to rehabilitate already formed toxic aggregates into native functional proteins. In an attempt to extend knowledge of chaperome mechanisms in cellular proteostasis, we performed a meta-analysis of human chaperome using high-throughput proteomic data from 11 immortalized human cell lines. Chaperome polypeptides were about 10% of total protein mass of human cells, half of which were Hsp90s and Hsp70s. Knowledge of cellular concentrations and ratios among chaperome polypeptides provided a novel basis to understand mechanisms by which the Hsp60, Hsp70, Hsp90, and small heat shock proteins (HSPs), in collaboration with cochaperones and folding enzymes, assist de novo protein folding, import polypeptides into organelles, unfold stress-destabilized toxic conformers, and control the conformal activity of native proteins in the crowded environment of the cell. Proteomic data also provided means to distinguish between stable components of chaperone core machineries and dynamic regulatory cochaperones.

Interwoven Aligned Conductive Nanofiber Yarn/Hydrogel Composite Scaffolds for Engineered 3D Cardiac Anisotropy.

PubMed

Wu, Yaobin; Wang, Ling; Guo, Baolin; Ma, Peter X

2017-06-27

Mimicking the anisotropic cardiac structure and guiding 3D cellular orientation play a critical role in designing scaffolds for cardiac tissue regeneration. Significant advances have been achieved to control cellular alignment and elongation, but it remains an ongoing challenge for engineering 3D cardiac anisotropy using these approaches. Here, we present a 3D hybrid scaffold based on aligned conductive nanofiber yarns network (NFYs-NET, composition: polycaprolactone, silk fibroin, and carbon nanotubes) within a hydrogel shell for mimicking the native cardiac tissue structure, and further demonstrate their great potential for engineering 3D cardiac anisotropy for cardiac tissue engineering. The NFYs-NET structures are shown to control cellular orientation and enhance cardiomyocytes (CMs) maturation. 3D hybrid scaffolds were then fabricated by encapsulating NFYs-NET layers within hydrogel shell, and these 3D scaffolds performed the ability to promote aligned and elongated CMs maturation on each layer and individually control cellular orientation on different layers in a 3D environment. Furthermore, endothelialized myocardium was constructed by using this hybrid strategy via the coculture of CMs on NFYs-NET layer and endothelial cells within hydrogel shell. Therefore, these 3D hybrid scaffolds, containing NFYs-NET layer inducing cellular orientation, maturation, and anisotropy and hydrogel shell providing a suitable 3D environment for endothelialization, has great potential in engineering 3D cardiac anisotropy.

Non-native Soluble Oligomers of Cu/Zn Superoxide Dismutase (SOD1) Contain a Conformational Epitope Linked to Cytotoxicity in Amyotrophic Lateral Sclerosis (ALS)

PubMed Central

2015-01-01

Soluble misfolded Cu/Zn superoxide dismutase (SOD1) is implicated in motor neuron death in amyotrophic lateral sclerosis (ALS); however, the relative toxicities of the various non-native species formed by SOD1 as it misfolds and aggregates are unknown. Here, we demonstrate that early stages of SOD1 aggregation involve the formation of soluble oligomers that contain an epitope specific to disease-relevant misfolded SOD1; this epitope, recognized by the C4F6 antibody, has been proposed as a marker of toxic species. Formation of potentially toxic oligomers is likely to be exacerbated by an oxidizing cellular environment, as evidenced by increased oligomerization propensity and C4F6 reactivity when oxidative modification by glutathione is present at Cys-111. These findings suggest that soluble non-native SOD1 oligomers, rather than native-like dimers or monomers, share structural similarity to pathogenic misfolded species found in ALS patients and therefore represent potential cytotoxic agents and therapeutic targets in ALS. PMID:24660965

Fluorescent Reporters and Biosensors for Probing the Dynamic Behavior of Protein Kinases

PubMed Central

González-Vera, Juan A.; Morris, May C.

2015-01-01

Probing the dynamic activities of protein kinases in real-time in living cells constitutes a major challenge that requires specific and sensitive tools tailored to meet the particular demands associated with cellular imaging. The development of genetically-encoded and synthetic fluorescent biosensors has provided means of monitoring protein kinase activities in a non-invasive fashion in their native cellular environment with high spatial and temporal resolution. Here, we review existing technologies to probe different dynamic features of protein kinases and discuss limitations where new developments are required to implement more performant tools, in particular with respect to infrared and near-infrared fluorescent probes and strategies which enable improved signal-to-noise ratio and controlled activation of probes. PMID:28248276

Considering the Lives of Microbes in Microbial Communities.

PubMed

Shank, Elizabeth A

2018-01-01

Over the last decades, sequencing technologies have transformed our ability to investigate the composition and functional capacity of microbial communities. Even so, critical questions remain about these complex systems that cannot be addressed by the bulk, community-averaged data typically provided by sequencing methods. In this Perspective, I propose that future advances in microbiome research will emerge from considering "the lives of microbes": we need to create methods to explicitly interrogate how microbes exist and interact in native-setting-like microenvironments. This approach includes developing approaches that expose the phenotypic heterogeneity of microbes; exploring the effects of coculture cues on cellular differentiation and metabolite production; and designing visualization systems that capture features of native microbial environments while permitting the nondestructive observation of microbial interactions over space and time with single-cell resolution.

Towards native-state imaging in biological context in the electron microscope

PubMed Central

Weston, Anne E.; Armer, Hannah E. J.

2009-01-01

Modern cell biology is reliant on light and fluorescence microscopy for analysis of cells, tissues and protein localisation. However, these powerful techniques are ultimately limited in resolution by the wavelength of light. Electron microscopes offer much greater resolution due to the shorter effective wavelength of electrons, allowing direct imaging of sub-cellular architecture. The harsh environment of the electron microscope chamber and the properties of the electron beam have led to complex chemical and mechanical preparation techniques, which distance biological samples from their native state and complicate data interpretation. Here we describe recent advances in sample preparation and instrumentation, which push the boundaries of high-resolution imaging. Cryopreparation, cryoelectron microscopy and environmental scanning electron microscopy strive to image samples in near native state. Advances in correlative microscopy and markers enable high-resolution localisation of proteins. Innovation in microscope design has pushed the boundaries of resolution to atomic scale, whilst automatic acquisition of high-resolution electron microscopy data through large volumes is finally able to place ultrastructure in biological context. PMID:19916039

Rearrangement of Upstream Sequences of the hTERT Gene During Cellular Immortalization

PubMed Central

Zhao, Yuanjun; Wang, Shuwen; Popova, Evgenya Y.; Grigoryev, Sergei A.; Zhu, Jiyue

2010-01-01

Telomerase expression, resulting from transcriptional activation of the hTERT gene, allows cells to acquire indefinite proliferative potential during cellular immortalization and tumorigenesis. However, mechanisms of hTERT gene activation in many immortal cell lines and cancer cells are poorly understood. Here, we report our studies on hTERT activation using genetically related pairs of telomerase-negative (Tel−) and -positive (Tel+) fibroblast lines. First, whereas transiently transfected plasmid reporters did not recapitulate the endogenous hTERT promoter, the promoter in chromosomally integrated bacterial artificial chromosome (BAC) reporters was activated in a subset of Tel+ cells, indicating that activation of the hTERT promoter required native chromatin context and/or distal regulatory elements. Second, the hTERT gene, located near the telomere of chromosome 5p, was translocated in all three Tel+ cell lines but not in their parental pre-crisis cells and Tel− immortal siblings. The breakage points were mapped to regions upstream of the hTERT promoter, indicating that the hTERT gene was the target of these chromosomal rearrangements. In two Tel+ cell lines, translocation of the endogenous hTERT gene appeared to be the major mechanism of its activation as the activity of hTERT promoter in many chromosomally integrated BAC reporters, with intact upstream and downstream neighboring loci, remained relatively low. Therefore, our results suggest that rearrangement of upstream sequences is an important new mechanism of hTERT promoter activation during cellular immortalization. The chromosomal rearrangements likely occurred during cellular crisis and facilitated by telomere dysfunction. Such translocations allowed the hTERT promoter to escape from the native condensed chromatin environment. PMID:19672873

Pharmacological profiling of the TRPV3 channel in recombinant and native assays.

PubMed

Grubisha, Olivera; Mogg, Adrian J; Sorge, Jessica L; Ball, Laura-Jayne; Sanger, Helen; Ruble, Cara L A; Folly, Elizabeth A; Ursu, Daniel; Broad, Lisa M

2014-05-01

Transient receptor potential vanilloid subtype 3 (TRPV3) is implicated in nociception and certain skin conditions. As such, it is an attractive target for pharmaceutical research. Understanding of endogenous TRPV3 function and pharmacology remains elusive as selective compounds and native preparations utilizing higher throughput methodologies are lacking. In this study, we developed medium-throughput recombinant and native cellular assays to assess the detailed pharmacological profile of human, rat and mouse TRPV3 channels. Medium-throughput cellular assays were developed using a Ca(2+) -sensitive dye and a fluorescent imaging plate reader. Human and rat TRPV3 pharmacology was examined in recombinant cell lines, while the mouse 308 keratinocyte cell line was used to assess endogenous TRPV3 activity. A recombinant rat TRPV3 cellular assay was successfully developed after solving a discrepancy in the published rat TRPV3 protein sequence. A medium-throughput, native, mouse TRPV3 keratinocyte assay was also developed and confirmed using genetic approaches. Whereas the recombinant human and rat TRPV3 assays exhibited similar agonist and antagonist profiles, the native mouse assay showed important differences, namely, TRPV3 activity was detected only in the presence of potentiator or during agonist synergy. Furthermore, the native assay was more sensitive to block by some antagonists. Our findings demonstrate similarities but also notable differences in TRPV3 pharmacology between recombinant and native systems. These findings offer insights into TRPV3 function and these assays should aid further research towards developing TRPV3 therapies. © 2013 The British Pharmacological Society.

Histone modifications controlling native and induced neural stem cell identity.

PubMed

Broccoli, Vania; Colasante, Gaia; Sessa, Alessandro; Rubio, Alicia

2015-10-01

During development, neural progenitor cells (NPCs) that are capable of self-renewing maintain a proliferative cellular pool while generating all differentiated neural cell components. Although the genetic network of transcription factors (TFs) required for neural specification has been well characterized, the unique set of histone modifications that accompanies this process has only recently started to be investigated. In vitro neural differentiation of pluripotent stem cells is emerging as a powerful system to examine epigenetic programs. Deciphering the histone code and how it shapes the chromatin environment will reveal the intimate link between epigenetic changes and mechanisms for neural fate determination in the developing nervous system. Furthermore, it will offer a molecular framework for a stringent comparison between native and induced neural stem cells (iNSCs) generated by direct neural cell conversion. Copyright © 2015 Elsevier Ltd. All rights reserved.

Live-Cell Imaging of the Adult Drosophila Ovary Using Confocal Microscopy.

PubMed

Shalaby, Nevine A; Buszczak, Michael

2017-01-01

The Drosophila ovary represents a key in vivo model used to study germline stem cell (GSC) maintenance and stem cell daughter differentiation because these cells and their somatic cell neighbors can be identified at single-cell resolution within their native environment. Here we describe a fluorescent-based technique for the acquisition of 4D datasets of the Drosophila ovariole for periods that can exceed 12 consecutive hours. Live-cell imaging facilitates the investigation of molecular and cellular dynamics that were not previously possible using still images.

Control of Scar Tissue Formation in the Cornea: Strategies in Clinical and Corneal Tissue Engineering

PubMed Central

Wilson, Samantha L.; El Haj, Alicia J.; Yang, Ying

2012-01-01

Corneal structure is highly organized and unified in architecture with structural and functional integration which mediates transparency and vision. Disease and injury are the second most common cause of blindness affecting over 10 million people worldwide. Ninety percent of blindness is permanent due to scarring and vascularization. Scarring caused via fibrotic cellular responses, heals the tissue, but fails to restore transparency. Controlling keratocyte activation and differentiation are key for the inhibition and prevention of fibrosis. Ophthalmic surgery techniques are continually developing to preserve and restore vision but corneal regression and scarring are often detrimental side effects and long term continuous follow up studies are lacking or discouraging. Appropriate corneal models may lead to a reduced need for corneal transplantation as presently there are insufficient numbers or suitable tissue to meet demand. Synthetic optical materials are under development for keratoprothesis although clinical use is limited due to implantation complications and high rejection rates. Tissue engineered corneas offer an alternative which more closely mimic the morphological, physiological and biomechanical properties of native corneas. However, replication of the native collagen fiber organization and retaining the phenotype of stromal cells which prevent scar-like tissue formation remains a challenge. Careful manipulation of culture environments are under investigation to determine a suitable environment that simulates native ECM organization and stimulates keratocyte migration and generation. PMID:24955637

Ligand-directed tosyl chemistry for in situ native protein labeling and engineering in living systems: from basic properties to applications.

PubMed

Tsukiji, Shinya; Hamachi, Itaru

2014-08-01

The ability to introduce any chemical probe to any endogenous target protein in its native environment, that is in cells and in vivo, is anticipated to provide various new exciting tools for biological and biomedical research. Although still at the prototype stage, the ligand-directed tosyl (LDT) chemistry is a novel type of affinity labeling technique that we developed for such a dream. This chemistry allows for modifying native proteins by various chemical probes with high specificity in various biological settings ranging from in vitro (in test tubes) to in living cells and in vivo. Since the first report, the list of proteins that are successfully labeled by the LDT chemistry has been increasing. A growing number of studies have demonstrated its utility to create semisynthetic proteins directly in cellular contexts. The in situ generated semisynthetic proteins are applicable for various types of analysis and imaging of intracellular biological processes. In this review, we summarize the basic properties of the LDT chemistry and its applications toward in situ engineering and analysis of native proteins in living systems. Current limitations and future challenges of this area are also described. Copyright © 2014 Elsevier Ltd. All rights reserved.

Amyloid Oligomers and Protofibrils, but Not Filaments, Self-Replicate from Native Lysozyme

PubMed Central

2015-01-01

Self-assembly of amyloid fibrils is the molecular mechanism best known for its connection with debilitating human disorders such as Alzheimer’s disease but is also associated with various functional cellular responses. There is increasing evidence that amyloid formation proceeds along two distinct assembly pathways involving either globular oligomers and protofibrils or rigid monomeric filaments. Oligomers, in particular, have been implicated as the dominant molecular species responsible for pathogenesis. Yet the molecular mechanisms regulating their self-assembly have remained elusive. Here we show that oligomers/protofibrils and monomeric filaments, formed along distinct assembly pathways, display critical differences in their ability to template amyloid growth at physiological vs denaturing temperatures. At physiological temperatures, amyloid filaments remained stable but could not seed growth of native monomers. In contrast, oligomers and protofibrils not only remained intact but were capable of self-replication using native monomers as the substrate. Kinetic data further suggested that this prion-like growth mode of oligomers/protofibrils involved two distinct activities operating orthogonal from each other: autocatalytic self-replication of oligomers from native monomers and nucleated polymerization of oligomers into protofibrils. The environmental changes to stability and templating competence of these different amyloid species in different environments are likely to be important for understanding the molecular mechanisms underlying both pathogenic and functional amyloid self-assembly. PMID:24884889

Amyloid oligomers and protofibrils, but not filaments, self-replicate from native lysozyme.

PubMed

Mulaj, Mentor; Foley, Joseph; Muschol, Martin

2014-06-25

Self-assembly of amyloid fibrils is the molecular mechanism best known for its connection with debilitating human disorders such as Alzheimer's disease but is also associated with various functional cellular responses. There is increasing evidence that amyloid formation proceeds along two distinct assembly pathways involving either globular oligomers and protofibrils or rigid monomeric filaments. Oligomers, in particular, have been implicated as the dominant molecular species responsible for pathogenesis. Yet the molecular mechanisms regulating their self-assembly have remained elusive. Here we show that oligomers/protofibrils and monomeric filaments, formed along distinct assembly pathways, display critical differences in their ability to template amyloid growth at physiological vs denaturing temperatures. At physiological temperatures, amyloid filaments remained stable but could not seed growth of native monomers. In contrast, oligomers and protofibrils not only remained intact but were capable of self-replication using native monomers as the substrate. Kinetic data further suggested that this prion-like growth mode of oligomers/protofibrils involved two distinct activities operating orthogonal from each other: autocatalytic self-replication of oligomers from native monomers and nucleated polymerization of oligomers into protofibrils. The environmental changes to stability and templating competence of these different amyloid species in different environments are likely to be important for understanding the molecular mechanisms underlying both pathogenic and functional amyloid self-assembly.

3D printing for the design and fabrication of polymer-based gradient scaffolds.

PubMed

Bracaglia, Laura G; Smith, Brandon T; Watson, Emma; Arumugasaamy, Navein; Mikos, Antonios G; Fisher, John P

2017-07-01

To accurately mimic the native tissue environment, tissue engineered scaffolds often need to have a highly controlled and varied display of three-dimensional (3D) architecture and geometrical cues. Additive manufacturing in tissue engineering has made possible the development of complex scaffolds that mimic the native tissue architectures. As such, architectural details that were previously unattainable or irreproducible can now be incorporated in an ordered and organized approach, further advancing the structural and chemical cues delivered to cells interacting with the scaffold. This control over the environment has given engineers the ability to unlock cellular machinery that is highly dependent upon the intricate heterogeneous environment of native tissue. Recent research into the incorporation of physical and chemical gradients within scaffolds indicates that integrating these features improves the function of a tissue engineered construct. This review covers recent advances on techniques to incorporate gradients into polymer scaffolds through additive manufacturing and evaluate the success of these techniques. As covered here, to best replicate different tissue types, one must be cognizant of the vastly different types of manufacturing techniques available to create these gradient scaffolds. We review the various types of additive manufacturing techniques that can be leveraged to fabricate scaffolds with heterogeneous properties and discuss methods to successfully characterize them. Additive manufacturing techniques have given tissue engineers the ability to precisely recapitulate the native architecture present within tissue. In addition, these techniques can be leveraged to create scaffolds with both physical and chemical gradients. This work offers insight into several techniques that can be used to generate graded scaffolds, depending on the desired gradient. Furthermore, it outlines methods to determine if the designed gradient was achieved. This review will help to condense the abundance of information that has been published on the creation and characterization of gradient scaffolds and to provide a single review discussing both methods for manufacturing gradient scaffolds and evaluating the establishment of a gradient. Copyright © 2017. Published by Elsevier Ltd.

Pharmacological profiling of the TRPV3 channel in recombinant and native assays

PubMed Central

Grubisha, Olivera; Mogg, Adrian J; Sorge, Jessica L; Ball, Laura-Jayne; Sanger, Helen; Ruble, Cara L A; Folly, Elizabeth A; Ursu, Daniel; Broad, Lisa M

2014-01-01

Background and Purpose Transient receptor potential vanilloid subtype 3 (TRPV3) is implicated in nociception and certain skin conditions. As such, it is an attractive target for pharmaceutical research. Understanding of endogenous TRPV3 function and pharmacology remains elusive as selective compounds and native preparations utilizing higher throughput methodologies are lacking. In this study, we developed medium-throughput recombinant and native cellular assays to assess the detailed pharmacological profile of human, rat and mouse TRPV3 channels. Experimental Approach Medium-throughput cellular assays were developed using a Ca2+-sensitive dye and a fluorescent imaging plate reader. Human and rat TRPV3 pharmacology was examined in recombinant cell lines, while the mouse 308 keratinocyte cell line was used to assess endogenous TRPV3 activity. Key Results A recombinant rat TRPV3 cellular assay was successfully developed after solving a discrepancy in the published rat TRPV3 protein sequence. A medium-throughput, native, mouse TRPV3 keratinocyte assay was also developed and confirmed using genetic approaches. Whereas the recombinant human and rat TRPV3 assays exhibited similar agonist and antagonist profiles, the native mouse assay showed important differences, namely, TRPV3 activity was detected only in the presence of potentiator or during agonist synergy. Furthermore, the native assay was more sensitive to block by some antagonists. Conclusions and Implications Our findings demonstrate similarities but also notable differences in TRPV3 pharmacology between recombinant and native systems. These findings offer insights into TRPV3 function and these assays should aid further research towards developing TRPV3 therapies. Linked Articles This article is part of a themed section on the pharmacology of TRP channels. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2014.171.issue-10 PMID:23848361

Dynamic nuclear polarization methods in solids and solutions to explore membrane proteins and membrane systems.

PubMed

Cheng, Chi-Yuan; Han, Songi

2013-01-01

Membrane proteins regulate vital cellular processes, including signaling, ion transport, and vesicular trafficking. Obtaining experimental access to their structures, conformational fluctuations, orientations, locations, and hydration in membrane environments, as well as the lipid membrane properties, is critical to understanding their functions. Dynamic nuclear polarization (DNP) of frozen solids can dramatically boost the sensitivity of current solid-state nuclear magnetic resonance tools to enhance access to membrane protein structures in native membrane environments. Overhauser DNP in the solution state can map out the local and site-specific hydration dynamics landscape of membrane proteins and lipid membranes, critically complementing the structural and dynamics information obtained by electron paramagnetic resonance spectroscopy. Here, we provide an overview of how DNP methods in solids and solutions can significantly increase our understanding of membrane protein structures, dynamics, functions, and hydration in complex biological membrane environments.

Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies

PubMed Central

2018-01-01

Membrane proteins perform a host of vital cellular functions. Deciphering the molecular mechanisms whereby they fulfill these functions requires detailed biophysical and structural investigations. Detergents have proven pivotal to extract the protein from its native surroundings. Yet, they provide a milieu that departs significantly from that of the biological membrane, to the extent that the structure, the dynamics, and the interactions of membrane proteins in detergents may considerably vary, as compared to the native environment. Understanding the impact of detergents on membrane proteins is, therefore, crucial to assess the biological relevance of results obtained in detergents. Here, we review the strengths and weaknesses of alkyl phosphocholines (or foscholines), the most widely used detergent in solution-NMR studies of membrane proteins. While this class of detergents is often successful for membrane protein solubilization, a growing list of examples points to destabilizing and denaturing properties, in particular for α-helical membrane proteins. Our comprehensive analysis stresses the importance of stringent controls when working with this class of detergents and when analyzing the structure and dynamics of membrane proteins in alkyl phosphocholine detergents. PMID:29488756

Comparison of alpha 1A- and alpha 1B-adrenoceptor coupling to inositol phosphate formation in rat kidney.

PubMed

Büscher, R; Erdbrügger, W; Philipp, T; Brodde, O E; Michel, M C

1994-12-01

We have compared the coupling mechanisms of rat renal alpha 1A- and alpha 1B-like adrenoceptors to inositol phosphate formation. The experiments were performed in parallel in native renal tissue preparations and in those where alpha 1B-adrenoceptors had been inactivated by treatment with 10 mumol/l chloroethylclonidine for 30 min at 37 degrees C; renal slices were used in most experiments but isolated renal cells were also used in some cases. The Ca2+ chelating agent, EGTA (5 mmol/l), reduced noradrenaline-stimulated inositol phosphate formation in native but enhanced it in chloroethylclonidine-treated renal slices. The inhibitory effect of EGTA was not mimicked by 100 nmol/l nifedipine. Inactivation of 87% of cellular Gi by 16-20 h treatment with 500 ng/ml pertussis toxin did not significantly affect noradrenaline-stimulated inositol phosphate formation in isolated renal cells but abolished the inhibitory effect of chloroethylclonidine. The adenylate cyclase activator, forskolin (20 mumol/l), inhibited noradrenaline-stimulated inositol phosphate formation in native and chloroethylclonidine-treated slices, and the inhibitory effects of chloroethylclonidine treatment and forskolin were additive. We conclude that in rat kidney inositol phosphate formation via alpha 1B-like adrenoceptors may involve the influx of extracellular Ca2+ and a pertussis toxin-sensitive G-protein but is insensitive to inhibition by forskolin. In contrast alpha 1A-like adrenoceptor-mediated inositol phosphate formation does not require the presence of extracellular Ca2+ or of Gi and is sensitive to inhibition by forskolin. In comparison to published data from other model systems we further conclude that the signaling mechanisms of alpha 1-adrenoceptor subtypes may depend on their cellular environment.

Customizing cell signaling using engineered genetic logic circuits.

PubMed

Wang, Baojun; Buck, Martin

2012-08-01

Cells live in an ever-changing environment and continuously sense, process and react to environmental signals using their inherent signaling and gene regulatory networks. Recently, there have been great advances on rewiring the native cell signaling and gene networks to program cells to sense multiple noncognate signals and integrate them in a logical manner before initiating a desired response. Here, we summarize the current state-of-the-art of engineering synthetic genetic logic circuits to customize cellular signaling behaviors, and discuss their promising applications in biocomputing, environmental, biotechnological and biomedical areas as well as the remaining challenges in this growing field. Copyright © 2012 Elsevier Ltd. All rights reserved.

Glycosaminoglycan-Mimetic Signals Direct the Osteo/Chondrogenic Differentiation of Mesenchymal Stem Cells in a Three-Dimensional Peptide Nanofiber Extracellular Matrix Mimetic Environment.

PubMed

Arslan, Elif; Guler, Mustafa O; Tekinay, Ayse B

2016-04-11

Recent efforts in bioactive scaffold development focus strongly on the elucidation of complex cellular responses through the use of synthetic systems. Designing synthetic extracellular matrix (ECM) materials must be based on understanding of cellular behaviors upon interaction with natural and artificial scaffolds. Hence, due to their ability to mimic both the biochemical and mechanical properties of the native tissue environment, supramolecular assemblies of bioactive peptide nanostructures are especially promising for development of bioactive ECM-mimetic scaffolds. In this study, we used glycosaminoglycan (GAG) mimetic peptide nanofiber gel as a three-dimensional (3D) platform to investigate how cell lineage commitment is altered by external factors. We observed that amount of fetal bovine serum (FBS) presented in the cell media had synergistic effects on the ability of GAG-mimetic nanofiber gel to mediate the differentiation of mesenchymal stem cells into osteogenic and chondrogenic lineages. In particular, lower FBS concentration in the culture medium was observed to enhance osteogenic differentiation while higher amount FBS promotes chondrogenic differentiation in tandem with the effects of the GAG-mimetic 3D peptide nanofiber network, even in the absence of externally administered growth factors. We therefore demonstrate that mesenchymal stem cell differentiation can be specifically controlled by the combined influence of growth medium components and a 3D peptide nanofiber environment.

Cryo-FIB-SEM serial milling and block face imaging: Large volume structural analysis of biological tissues preserved close to their native state.

PubMed

Vidavsky, Netta; Akiva, Anat; Kaplan-Ashiri, Ifat; Rechav, Katya; Addadi, Lia; Weiner, Steve; Schertel, Andreas

2016-12-01

Many important biological questions can be addressed by studying in 3D large volumes of intact, cryo fixed hydrated tissues (⩾10,000μm 3 ) at high resolution (5-20nm). This can be achieved using serial FIB milling and block face surface imaging under cryo conditions. Here we demonstrate the unique potential of the cryo-FIB-SEM approach using two extensively studied model systems; sea urchin embryos and the tail fin of zebrafish larvae. We focus in particular on the environment of mineral deposition sites. The cellular organelles, including mitochondria, Golgi, ER, nuclei and nuclear pores are made visible by the image contrast created by differences in surface potential of different biochemical components. Auto segmentation and/or volume rendering of the image stacks and 3D reconstruction of the skeleton and the cellular environment, provides a detailed view of the relative distribution in space of the tissue/cellular components, and thus of their interactions. Simultaneous acquisition of secondary and back-scattered electron images adds additional information. For example, a serial view of the zebrafish tail reveals the presence of electron dense mineral particles inside mitochondrial networks extending more than 20μm in depth in the block. Large volume imaging using cryo FIB SEM, as demonstrated here, can contribute significantly to the understanding of the structures and functions of diverse biological tissues. Copyright © 2016 Elsevier Inc. All rights reserved.

Biomaterials for 4D stem cell culture

PubMed Central

Hilderbrand, Amber M.; Ovadia, Elisa M.; Rehmann, Matthew S.; Kharkar, Prathamesh M.; Guo, Chen; Kloxin, April M.

2017-01-01

Stem cells reside in complex three-dimensional (3D) environments within the body that change with time, promoting various cellular functions and processes such as migration and differentiation. These complex changes in the surrounding environment dictate cell fate yet, until recently, have been challenging to mimic within cell culture systems. Hydrogel-based biomaterials are well suited to mimic aspects of these in vivo environments, owing to their high water content, soft tissue-like elasticity, and often-tunable biochemical content. Further, hydrogels can be engineered to achieve changes in matrix properties over time to better mimic dynamic native microenvironments for probing and directing stem cell function and fate. This review will focus on techniques to form hydrogel-based biomaterials and modify their properties in time during cell culture using select addition reactions, cleavage reactions, or non-covalent interactions. Recent applications of these techniques for the culture of stem cells in four dimensions (i.e., in three dimensions with changes over time) also will be discussed for studying essential stem cell processes. PMID:28717344

A MODELING AND SIMULATION LANGUAGE FOR BIOLOGICAL CELLS WITH COUPLED MECHANICAL AND CHEMICAL PROCESSES

PubMed Central

Somogyi, Endre; Glazier, James A.

2017-01-01

Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical properties, chemical uptake and secretion, cell differentiation, proliferation, death, and migration. Modeling and simulation of such dynamic phenomena poses a number of computational challenges. A modeling language describing cellular dynamics must naturally represent complex intra and extra-cellular spatial structures and coupled mechanical, chemical and electrical processes. Domain experts will find a modeling language most useful when it is based on concepts, terms and principles native to the problem domain. A compiler must then be able to generate an executable model from this physically motivated description. Finally, an executable model must efficiently calculate the time evolution of such dynamic and inhomogeneous phenomena. We present a spatial hybrid systems modeling language, compiler and mesh-free Lagrangian based simulation engine which will enable domain experts to define models using natural, biologically motivated constructs and to simulate time evolution of coupled cellular, mechanical and chemical processes acting on a time varying number of cells and their environment. PMID:29303160

A MODELING AND SIMULATION LANGUAGE FOR BIOLOGICAL CELLS WITH COUPLED MECHANICAL AND CHEMICAL PROCESSES.

PubMed

Somogyi, Endre; Glazier, James A

2017-04-01

Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical properties, chemical uptake and secretion, cell differentiation, proliferation, death, and migration. Modeling and simulation of such dynamic phenomena poses a number of computational challenges. A modeling language describing cellular dynamics must naturally represent complex intra and extra-cellular spatial structures and coupled mechanical, chemical and electrical processes. Domain experts will find a modeling language most useful when it is based on concepts, terms and principles native to the problem domain. A compiler must then be able to generate an executable model from this physically motivated description. Finally, an executable model must efficiently calculate the time evolution of such dynamic and inhomogeneous phenomena. We present a spatial hybrid systems modeling language, compiler and mesh-free Lagrangian based simulation engine which will enable domain experts to define models using natural, biologically motivated constructs and to simulate time evolution of coupled cellular, mechanical and chemical processes acting on a time varying number of cells and their environment.

Visualizing Viral Protein Structures in Cells Using Genetic Probes for Correlated Light and Electron Microscopy

PubMed Central

Ou, Horng D.; Deerinck, Thomas J.; Bushong, Eric; Ellisman, Mark H.; O’Shea, Clodagh C.

2015-01-01

Structural studies of viral proteins most often use high-resolution techniques such as X-ray crystallography, nuclear magnetic resonance, single particle negative stain, or cryo-electron microscopy (EM) to reveal atomic interactions of soluble, homogeneous viral proteins or viral protein complexes. Once viral proteins or complexes are separated from their host’s cellular environment, their natural in-situ structure and details of how they interact with other cellular components may be lost. EM has been an invaluable tool in virology since its introduction in the late 1940’s and subsequent application to cells in the 1950’s. EM studies have expanded our knowledge of viral entry, viral replication, alteration of cellular components, and viral lysis. Most of these early studies were focused on conspicuous morphological cellular changes, because classic EM metal stains were designed to highlight classes of cellular structures rather than specific molecular structures. Much later, to identify viral proteins inducing specific structural configurations at the cellular level, immunostaining with a primary antibody followed by colloidal gold secondary antibody was employed to mark the location of specific viral proteins. This technique can suffer from artifacts in cellular ultrastructure due to compromises required to provide access to the immuno-reagents. Immunolocalization methods also require the generation of highly specific antibodies, which may not be available for every viral protein. Here we discuss new methods to visualize viral proteins and structures at high resolutions in-situ using correlated light and electron microscopy (CLEM). We discuss the use of genetically encoded protein fusions that oxidize diaminobenzidine (DAB) into an osmiophilic polymer that can be visualized by EM. Detailed protocols for applying the genetically encoded photo-oxidizing protein MiniSOG to a viral protein, photo-oxidation of the fusion protein to yield DAB polymer staining, and preparation of photo-oxidized samples for TEM and serial block-face scanning EM (SBEM) for large-scale volume EM data acquisition are also presented. As an example, we discuss the recent multi-scale analysis of Adenoviral protein E4-ORF3 that reveals a new type of multi-functional polymer that disrupts multiple cellular proteins. This new capability to visualize unambiguously specific viral protein structures at high resolutions in the native cellular environment is revealing new insights into how they usurp host proteins and functions to drive pathological viral replication. PMID:26066760

Visualizing viral protein structures in cells using genetic probes for correlated light and electron microscopy.

PubMed

Ou, Horng D; Deerinck, Thomas J; Bushong, Eric; Ellisman, Mark H; O'Shea, Clodagh C

2015-11-15

Structural studies of viral proteins most often use high-resolution techniques such as X-ray crystallography, nuclear magnetic resonance, single particle negative stain, or cryo-electron microscopy (EM) to reveal atomic interactions of soluble, homogeneous viral proteins or viral protein complexes. Once viral proteins or complexes are separated from their host's cellular environment, their natural in situ structure and details of how they interact with other cellular components may be lost. EM has been an invaluable tool in virology since its introduction in the late 1940's and subsequent application to cells in the 1950's. EM studies have expanded our knowledge of viral entry, viral replication, alteration of cellular components, and viral lysis. Most of these early studies were focused on conspicuous morphological cellular changes, because classic EM metal stains were designed to highlight classes of cellular structures rather than specific molecular structures. Much later, to identify viral proteins inducing specific structural configurations at the cellular level, immunostaining with a primary antibody followed by colloidal gold secondary antibody was employed to mark the location of specific viral proteins. This technique can suffer from artifacts in cellular ultrastructure due to compromises required to provide access to the immuno-reagents. Immunolocalization methods also require the generation of highly specific antibodies, which may not be available for every viral protein. Here we discuss new methods to visualize viral proteins and structures at high resolutions in situ using correlated light and electron microscopy (CLEM). We discuss the use of genetically encoded protein fusions that oxidize diaminobenzidine (DAB) into an osmiophilic polymer that can be visualized by EM. Detailed protocols for applying the genetically encoded photo-oxidizing protein MiniSOG to a viral protein, photo-oxidation of the fusion protein to yield DAB polymer staining, and preparation of photo-oxidized samples for TEM and serial block-face scanning EM (SBEM) for large-scale volume EM data acquisition are also presented. As an example, we discuss the recent multi-scale analysis of Adenoviral protein E4-ORF3 that reveals a new type of multi-functional polymer that disrupts multiple cellular proteins. This new capability to visualize unambiguously specific viral protein structures at high resolutions in the native cellular environment is revealing new insights into how they usurp host proteins and functions to drive pathological viral replication. Copyright © 2015 Elsevier Inc. All rights reserved.

Modular extracellular sensor architecture for engineering mammalian cell-based devices.

PubMed

Daringer, Nichole M; Dudek, Rachel M; Schwarz, Kelly A; Leonard, Joshua N

2014-12-19

Engineering mammalian cell-based devices that monitor and therapeutically modulate human physiology is a promising and emerging frontier in clinical synthetic biology. However, realizing this vision will require new technologies enabling engineered circuitry to sense and respond to physiologically relevant cues. No existing technology enables an engineered cell to sense exclusively extracellular ligands, including proteins and pathogens, without relying upon native cellular receptors or signal transduction pathways that may be subject to crosstalk with native cellular components. To address this need, we here report a technology we term a Modular Extracellular Sensor Architecture (MESA). This self-contained receptor and signal transduction platform is maximally orthogonal to native cellular processes and comprises independent, tunable protein modules that enable performance optimization and straightforward engineering of novel MESA that recognize novel ligands. We demonstrate ligand-inducible activation of MESA signaling, optimization of receptor performance using design-based approaches, and generation of MESA biosensors that produce outputs in the form of either transcriptional regulation or transcription-independent reconstitution of enzymatic activity. This systematic, quantitative platform characterization provides a framework for engineering MESA to recognize novel ligands and for integrating these sensors into diverse mammalian synthetic biology applications.

Correlation of cellular factors and differential scrapie prion permissiveness in ovine microglia

USDA-ARS?s Scientific Manuscript database

Prion diseases are fatal neurodegenerative disorders by which the native cellular prion protein (PrP-C) is misfolded into an accumulating, disease-associated isoform (PrP-D). To improve the understanding of prion pathogenesis and develop effective treatments, it is essential to elucidate factors con...

Structural Interface Parameters Are Discriminatory in Recognising Near-Native Poses of Protein-Protein Interactions

PubMed Central

Malhotra, Sony; Sankar, Kannan; Sowdhamini, Ramanathan

2014-01-01

Interactions at the molecular level in the cellular environment play a very crucial role in maintaining the physiological functioning of the cell. These molecular interactions exist at varied levels viz. protein-protein interactions, protein-nucleic acid interactions or protein-small molecules interactions. Presently in the field, these interactions and their mechanisms mark intensively studied areas. Molecular interactions can also be studied computationally using the approach named as Molecular Docking. Molecular docking employs search algorithms to predict the possible conformations for interacting partners and then calculates interaction energies. However, docking proposes number of solutions as different docked poses and hence offers a serious challenge to identify the native (or near native) structures from the pool of these docked poses. Here, we propose a rigorous scoring scheme called DockScore which can be used to rank the docked poses and identify the best docked pose out of many as proposed by docking algorithm employed. The scoring identifies the optimal interactions between the two protein partners utilising various features of the putative interface like area, short contacts, conservation, spatial clustering and the presence of positively charged and hydrophobic residues. DockScore was first trained on a set of 30 protein-protein complexes to determine the weights for different parameters. Subsequently, we tested the scoring scheme on 30 different protein-protein complexes and native or near-native structure were assigned the top rank from a pool of docked poses in 26 of the tested cases. We tested the ability of DockScore to discriminate likely dimer interactions that differ substantially within a homologous family and also demonstrate that DOCKSCORE can distinguish correct pose for all 10 recent CAPRI targets. PMID:24498255

Structural interface parameters are discriminatory in recognising near-native poses of protein-protein interactions.

PubMed

Malhotra, Sony; Sankar, Kannan; Sowdhamini, Ramanathan

2014-01-01

Interactions at the molecular level in the cellular environment play a very crucial role in maintaining the physiological functioning of the cell. These molecular interactions exist at varied levels viz. protein-protein interactions, protein-nucleic acid interactions or protein-small molecules interactions. Presently in the field, these interactions and their mechanisms mark intensively studied areas. Molecular interactions can also be studied computationally using the approach named as Molecular Docking. Molecular docking employs search algorithms to predict the possible conformations for interacting partners and then calculates interaction energies. However, docking proposes number of solutions as different docked poses and hence offers a serious challenge to identify the native (or near native) structures from the pool of these docked poses. Here, we propose a rigorous scoring scheme called DockScore which can be used to rank the docked poses and identify the best docked pose out of many as proposed by docking algorithm employed. The scoring identifies the optimal interactions between the two protein partners utilising various features of the putative interface like area, short contacts, conservation, spatial clustering and the presence of positively charged and hydrophobic residues. DockScore was first trained on a set of 30 protein-protein complexes to determine the weights for different parameters. Subsequently, we tested the scoring scheme on 30 different protein-protein complexes and native or near-native structure were assigned the top rank from a pool of docked poses in 26 of the tested cases. We tested the ability of DockScore to discriminate likely dimer interactions that differ substantially within a homologous family and also demonstrate that DOCKSCORE can distinguish correct pose for all 10 recent CAPRI targets.

Stabilizing the Native Trimer of HIV-1 Env by Destabilizing the Heterodimeric Interface of the gp41 Postfusion Six-Helix Bundle

PubMed Central

Kesavardhana, Sannula

2014-01-01

ABSTRACT The HIV-1 envelope glycoprotein (Env) is a trimer of gp120-gp41 heterodimers and is essential for viral entry. The gp41 subunit in native, prefusion trimeric Env exists in a metastable conformation and attains a stable six-helix bundle (6-HB) conformation comprised of a trimer of N-heptad repeat (NHR) and C-heptad repeat (CHR) heterodimers, that drives the fusion of viral and cellular membranes. We attempted to stabilize native Env trimers by incorporation of mutations at the NHR-CHR interface that disrupt the postfusion 6-HB of gp41. The mutations V570D and I573D stabilize native Env of the HIV-1 JRFL strain and occlude nonneutralizing epitopes to a greater extent than the previously identified I559P mutation that is at the interface of the NHR trimers in the 6-HB. The mutations prevent soluble-CD4 (sCD4)-induced gp120 shedding and 6-HB formation. In the context of cell surface-expressed JRFL Env, introduction of a previously reported additional disulfide between residues A501 and T605 perturbs the native conformation, though this effect is partially alleviated by furin coexpression. The data suggest that positions 570 and 573 are surface proximal in native Env and that the NHR homotrimeric coiled coil in native Env terminates before or close to residue 573. Aspartic acid substitutions at these positions stabilize native trimers through destabilization of the postfusion 6-HB conformation. These mutations can be used to stabilize Env in a DNA vaccine format. IMPORTANCE The major protein on the surface of HIV-1 is the envelope (Env) glycoprotein. Env is a trimer of gp120-gp41 heterodimers. gp120 is involved in receptor/coreceptor binding and gp41 in the fusion of viral and cellular membranes. Like many other viral fusion proteins, the gp41 subunit in native trimeric Env exists in a metastable conformation. gp41 readily forms a stable six-helix bundle (6-HB) conformation comprised of a trimer of N-heptad repeat (NHR) and C-heptad repeat (CHR) heterodimers that drives fusion of viral and cellular membranes. While it is expected that native Env is a good immunogen, its metastability results in exposure of immunodominant nonneutralizing epitopes. In the present study, we stabilize native Env trimers by incorporation of a number of different mutations at the NHR-CHR interface that disrupt the postfusion 6-HB of gp41. The stabilized constructs described here can be incorporated into DNA vaccine candidates. PMID:24920800

Fitness landscape transformation through a single amino acid change in the rho terminator.

PubMed

Freddolino, Peter L; Goodarzi, Hani; Tavazoie, Saeed

2012-05-01

Regulatory networks allow organisms to match adaptive behavior to the complex and dynamic contingencies of their native habitats. Upon a sudden transition to a novel environment, the mismatch between the native behavior and the new niche provides selective pressure for adaptive evolution through mutations in elements that control gene expression. In the case of core components of cellular regulation and metabolism, with broad control over diverse biological processes, such mutations may have substantial pleiotropic consequences. Through extensive phenotypic analyses, we have characterized the systems-level consequences of one such mutation (rho*) in the global transcriptional terminator Rho of Escherichia coli. We find that a single amino acid change in Rho results in a massive change in the fitness landscape of the cell, with widely discrepant fitness consequences of identical single locus perturbations in rho* versus rho(WT) backgrounds. Our observations reveal the extent to which a single regulatory mutation can transform the entire fitness landscape of the cell, causing a massive change in the interpretation of individual mutations and altering the evolutionary trajectories which may be accessible to a bacterial population.

High-Fidelity Tissue Engineering of Patient-Specific Auricles for Reconstruction of Pediatric Microtia and Other Auricular Deformities

PubMed Central

Reiffel, Alyssa J.; Kafka, Concepcion; Hernandez, Karina A.; Popa, Samantha; Perez, Justin L.; Zhou, Sherry; Pramanik, Satadru; Brown, Bryan N.; Ryu, Won Seuk; Bonassar, Lawrence J.; Spector, Jason A.

2013-01-01

Introduction Autologous techniques for the reconstruction of pediatric microtia often result in suboptimal aesthetic outcomes and morbidity at the costal cartilage donor site. We therefore sought to combine digital photogrammetry with CAD/CAM techniques to develop collagen type I hydrogel scaffolds and their respective molds that would precisely mimic the normal anatomy of the patient-specific external ear as well as recapitulate the complex biomechanical properties of native auricular elastic cartilage while avoiding the morbidity of traditional autologous reconstructions. Methods Three-dimensional structures of normal pediatric ears were digitized and converted to virtual solids for mold design. Image-based synthetic reconstructions of these ears were fabricated from collagen type I hydrogels. Half were seeded with bovine auricular chondrocytes. Cellular and acellular constructs were implanted subcutaneously in the dorsa of nude rats and harvested after 1 and 3 months. Results Gross inspection revealed that acellular implants had significantly decreased in size by 1 month. Cellular constructs retained their contour/projection from the animals' dorsa, even after 3 months. Post-harvest weight of cellular constructs was significantly greater than that of acellular constructs after 1 and 3 months. Safranin O-staining revealed that cellular constructs demonstrated evidence of a self-assembled perichondrial layer and copious neocartilage deposition. Verhoeff staining of 1 month cellular constructs revealed de novo elastic cartilage deposition, which was even more extensive and robust after 3 months. The equilibrium modulus and hydraulic permeability of cellular constructs were not significantly different from native bovine auricular cartilage after 3 months. Conclusions We have developed high-fidelity, biocompatible, patient-specific tissue-engineered constructs for auricular reconstruction which largely mimic the native auricle both biomechanically and histologically, even after an extended period of implantation. This strategy holds immense potential for durable patient-specific tissue-engineered anatomically proper auricular reconstructions in the future. PMID:23437148

The effects of scaffold architecture and fibrin gel addition on tendon cell phenotype.

PubMed

Pawelec, K M; Wardale, R J; Best, S M; Cameron, R E

2015-01-01

Development of tissue engineering scaffolds relies on careful selection of pore architecture and chemistry of the cellular environment. Repair of skeletal soft tissue, such as tendon, is particularly challenging, since these tissues have a relatively poor healing response. When removed from their native environment, tendon cells (tenocytes) lose their characteristic morphology and the expression of phenotypic markers. To stimulate tendon cells to recreate a healthy extracellular matrix, both architectural cues and fibrin gels have been used in the past, however, their relative effects have not been studied systematically. Within this study, a combination of collagen scaffold architecture, axial and isotropic, and fibrin gel addition was assessed, using ovine tendon-derived cells to determine the optimal strategy for controlling the proliferation and protein expression. Scaffold architecture and fibrin gel addition influenced tendon cell behavior independently in vitro. Addition of fibrin gel within a scaffold doubled cell number and increased matrix production for all architectures studied. However, scaffold architecture dictated the type of matrix produced by cells, regardless of fibrin addition. Axial scaffolds, mimicking native tendon, promoted a mature matrix, with increased tenomodulin, a marker for mature tendon cells, and decreased scleraxis, an early transcription factor for connective tissue. This study demonstrated that both architectural cues and fibrin gel addition alter cell behavior and that the combination of these signals could improve clinical performance of current tissue engineering constructs.

A scalable strategy for high-throughput GFP tagging of endogenous human proteins.

PubMed

Leonetti, Manuel D; Sekine, Sayaka; Kamiyama, Daichi; Weissman, Jonathan S; Huang, Bo

2016-06-21

A central challenge of the postgenomic era is to comprehensively characterize the cellular role of the ∼20,000 proteins encoded in the human genome. To systematically study protein function in a native cellular background, libraries of human cell lines expressing proteins tagged with a functional sequence at their endogenous loci would be very valuable. Here, using electroporation of Cas9 nuclease/single-guide RNA ribonucleoproteins and taking advantage of a split-GFP system, we describe a scalable method for the robust, scarless, and specific tagging of endogenous human genes with GFP. Our approach requires no molecular cloning and allows a large number of cell lines to be processed in parallel. We demonstrate the scalability of our method by targeting 48 human genes and show that the resulting GFP fluorescence correlates with protein expression levels. We next present how our protocols can be easily adapted for the tagging of a given target with GFP repeats, critically enabling the study of low-abundance proteins. Finally, we show that our GFP tagging approach allows the biochemical isolation of native protein complexes for proteomic studies. Taken together, our results pave the way for the large-scale generation of endogenously tagged human cell lines for the proteome-wide analysis of protein localization and interaction networks in a native cellular context.

Proteomic differences between native and tissue-engineered tendon and ligament.

PubMed

Kharaz, Yalda A; Tew, Simon R; Peffers, Mandy; Canty-Laird, Elizabeth G; Comerford, Eithne

2016-05-01

Tendons and ligaments (T/Ls) play key roles in the musculoskeletal system, but they are susceptible to traumatic or age-related rupture, leading to severe morbidity as well as increased susceptibility to degenerative joint diseases such as osteoarthritis. Tissue engineering represents an attractive therapeutic approach to treating T/L injury but it is hampered by our poor understanding of the defining characteristics of the two tissues. The present study aimed to determine differences in the proteomic profile between native T/Ls and tissue engineered (TE) T/L constructs. The canine long digital extensor tendon and anterior cruciate ligament were analyzed along with 3D TE fibrin-based constructs created from their cells. Native tendon and ligament differed in their content of key structural proteins, with the ligament being more abundant in fibrocartilaginous proteins. 3D T/L TE constructs contained less extracellular matrix (ECM) proteins and had a greater proportion of cellular-associated proteins than native tissue, corresponding to their low collagen and high DNA content. Constructs were able to recapitulate native T/L tissue characteristics particularly with regard to ECM proteins. However, 3D T/L TE constructs had similar ECM and cellular protein compositions indicating that cell source may not be an important factor for T/L tissue engineering. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Native aggregation as a cause of origin of temporary cellular structures needed for all forms of cellular activity, signaling and transformations.

PubMed

Matveev, Vladimir V

2010-06-09

According to the hypothesis explored in this paper, native aggregation is genetically controlled (programmed) reversible aggregation that occurs when interacting proteins form new temporary structures through highly specific interactions. It is assumed that Anfinsen's dogma may be extended to protein aggregation: composition and amino acid sequence determine not only the secondary and tertiary structure of single protein, but also the structure of protein aggregates (associates). Cell function is considered as a transition between two states (two states model), the resting state and state of activity (this applies to the cell as a whole and to its individual structures). In the resting state, the key proteins are found in the following inactive forms: natively unfolded and globular. When the cell is activated, secondary structures appear in natively unfolded proteins (including unfolded regions in other proteins), and globular proteins begin to melt and their secondary structures become available for interaction with the secondary structures of other proteins. These temporary secondary structures provide a means for highly specific interactions between proteins. As a result, native aggregation creates temporary structures necessary for cell activity."One of the principal objects of theoretical research in any department of knowledge is to find the point of view from which the subject appears in its greatest simplicity."Josiah Willard Gibbs (1839-1903).

In situ generation of ultrafast transient "acid spikes" in the 10B(n,α)7Li radiolysis of water

NASA Astrophysics Data System (ADS)

Islam, Muhammad Mainul; Kanike, Vanaja; Meesungnoen, Jintana; Lertnaisat, Phantira; Katsumura, Yosuke; Jay-Gerin, Jean-Paul

2018-02-01

Monte Carlo track chemistry simulations of the 10B(n,α)7Li radiolysis of water show that the in situ formation of H3O+ by the two He and Li recoiling ions renders the native track regions temporarily very acidic. For these irradiating ions, the pH remains near 0 at times less than ∼100 ps after which the system gradually returns to neutral pH at ∼0.1 ms. These 'acid spikes' have never been invoked in water or in a cellular environment exposed to densely ionizing radiations. The question of their implications in boron neutron capture therapy and, more generally, in hadrontherapy, is discussed briefly.

Direct tissue analysis by matrix-assisted laser desorption ionization mass spectrometry: application to kidney biology.

PubMed

Herring, Kristen D; Oppenheimer, Stacey R; Caprioli, Richard M

2007-11-01

Direct tissue analysis using matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) provides in situ molecular analysis of a wide variety of biological molecules including xenobiotics. This technology allows measurement of these species in their native biological environment without the use of target-specific reagents such as antibodies. It can be used to profile discrete cellular regions and obtain region-specific images, providing information on the relative abundance and spatial distribution of proteins, peptides, lipids, and drugs. In this article, we report the sample preparation, MS data acquisition and analysis, and protein identification methodologies used in our laboratory for profiling/imaging MS and how this has been applied to kidney disease and toxicity.

Peptide-Based Technologies to Alter Adenoviral Vector Tropism: Ways and Means for Systemic Treatment of Cancer

PubMed Central

Reetz, Julia; Herchenröder, Ottmar; Pützer, Brigitte M.

2014-01-01

Due to the fundamental progress in elucidating the molecular mechanisms of human diseases and the arrival of the post-genomic era, increasing numbers of therapeutic genes and cellular targets are available for gene therapy. Meanwhile, the most important challenge is to develop gene delivery vectors with high efficiency through target cell selectivity, in particular under in situ conditions. The most widely used vector system to transduce cells is based on adenovirus (Ad). Recent endeavors in the development of selective Ad vectors that target cells or tissues of interest and spare the alteration of all others have focused on the modification of the virus broad natural tropism. A popular way of Ad targeting is achieved by directing the vector towards distinct cellular receptors. Redirecting can be accomplished by linking custom-made peptides with specific affinity to cellular surface proteins via genetic integration, chemical coupling or bridging with dual-specific adapter molecules. Ideally, targeted vectors are incapable of entering cells via their native receptors. Such altered vectors offer new opportunities to delineate functional genomics in a natural environment and may enable efficient systemic therapeutic approaches. This review provides a summary of current state-of-the-art techniques to specifically target adenovirus-based gene delivery vectors. PMID:24699364

Cellular immune response to β2-glycoprotein-I valine/leucine247 phenotypes in Mexican patients with primary antiphospholipid syndrome.

PubMed

Núñez-Álvarez, Carlos A; Hernández-Ramírez, Diego F; Martinez-Castillo, Araceli; Pascual Ramos, Virginia; Cabiedes, Javier; Ortega, Alicia; Cabral, Antonio R

2017-02-01

Homozygote genotype V 247 of the β 2 -glycoprotein-I (β 2 GP-I) gene has been associated with anti-β 2 GP-I and thrombosis in patients with primary anti-phospholipid syndrome APS (PAPS). However, the cellular immune response to β 2 GP-I 247 has been little studied. To evaluate the immune cellular proliferation in response to native and non-native β 2 GP-I 247 valine/leucine phenotype from Mexican patients with PAPS. We studied 10 patients with PAPS and 10 healthy control subjects (HC). The polymorphism at position 247 of the β 2 GP-I gene was determined by PCR-RFLP and the corresponding β 2 GP-I protein was subsequently purified from normal human plasma by affinity chromatography. PBMC purified from patients and controls were stimulated with β 2 GP-I under native and in non native (reduced) conditions. We also determined the anti-β 2 GP-I production in vitro by B cell clones (EBV) generated in cocultures experiments. Differential Scanning Calorimetry (DSC) was studied to determine the structural differences between the β 2 GP-I 247 valine/leucine isoforms. Cytokine profile (IL-2, IL-4, IL-6, TNFα, INFγ) was evaluated in culture supernatants. PAPS and healthy control PBMCs had a higher proliferative response when stimulated with β 2 GP-I under reduced cultures conditions compared to non-denatured conditions. PBMCs response from PAPS patients was higher. We observed more cell proliferation in response to β 2 GP-I 247 valine/leucine or valine isoforms in non-native conditions. In contrast, this response was not significant against β 2 GP-I 247 leucine. These findings were T CD4 + -dependent. Similar results were obtained with B cell clones derived from PAPS patients, which showed more pronounced proliferation in non native conditions and higher against β 2 GP-I 247 valine. No differences were found in anti-β 2 GP-I production, but high levels of IL-6 in vitro were identified. The structural analysis of both β 2 GP-I 247 isoforms by DSC showed a major conformational change due to a single mutation in the β 2 GP-I variants. PAPS PBMCs had a higher cellular response against β 2 GP-I 247 in non-native culture conditions preferentially to the β 2 GP-I 247 valine phenotype. This effect is T CD4 + dependent and appears to be driven by tertiary structural changes adopted by β 2 GP-I 247 polymorphism. Copyright © 2016 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

Climate modifies response of non-native and native species richness to nutrient enrichment

USDA-ARS?s Scientific Manuscript database

Ecosystem eutrophication often increases domination by non-natives and causes displacement of native taxa. However, variation in environmental conditions may affect the outcome of interactions between native and non-native taxa in environments where nutrient supply is elevated. We examined the int...

Multi-Element Bioimaging of Arabidopsis thaliana Roots.

PubMed

Persson, Daniel Pergament; Chen, Anle; Aarts, Mark G M; Salt, David E; Schjoerring, Jan K; Husted, Søren

2016-10-01

Better understanding of root function is central for the development of plants with more efficient nutrient uptake and translocation. We here present a method for multielement bioimaging at the cellular level in roots of the genetic model system Arabidopsis (Arabidopsis thaliana). Using conventional protocols for microscopy, we observed that diffusible ions such as potassium and sodium were lost during sample dehydration. Thus, we developed a protocol that preserves ions in their native, cellular environment. Briefly, fresh roots are encapsulated in paraffin, cryo-sectioned, and freeze dried. Samples are finally analyzed by laser ablation-inductively coupled plasma-mass spectrometry, utilizing a specially designed internal standard procedure. The method can be further developed to maintain the native composition of proteins, enzymes, RNA, and DNA, making it attractive in combination with other omics techniques. To demonstrate the potential of the method, we analyzed a mutant of Arabidopsis unable to synthesize the metal chelator nicotianamine. The mutant accumulated substantially more zinc and manganese than the wild type in the tissues surrounding the vascular cylinder. For iron, the images looked completely different, with iron bound mainly in the epidermis of the wild-type plants but confined to the cortical cell walls of the mutant. The method offers the power of inductively coupled plasma-mass spectrometry to be fully employed, thereby providing a basis for detailed studies of ion transport in roots. Being applicable to Arabidopsis, the molecular and genetic approaches available in this system can now be fully exploited in order to gain a better mechanistic understanding of these processes. © 2016 American Society of Plant Biologists. All Rights Reserved.

Multi-Element Bioimaging of Arabidopsis thaliana Roots1[OPEN

PubMed Central

Salt, David E.

2016-01-01

Better understanding of root function is central for the development of plants with more efficient nutrient uptake and translocation. We here present a method for multielement bioimaging at the cellular level in roots of the genetic model system Arabidopsis (Arabidopsis thaliana). Using conventional protocols for microscopy, we observed that diffusible ions such as potassium and sodium were lost during sample dehydration. Thus, we developed a protocol that preserves ions in their native, cellular environment. Briefly, fresh roots are encapsulated in paraffin, cryo-sectioned, and freeze dried. Samples are finally analyzed by laser ablation-inductively coupled plasma-mass spectrometry, utilizing a specially designed internal standard procedure. The method can be further developed to maintain the native composition of proteins, enzymes, RNA, and DNA, making it attractive in combination with other omics techniques. To demonstrate the potential of the method, we analyzed a mutant of Arabidopsis unable to synthesize the metal chelator nicotianamine. The mutant accumulated substantially more zinc and manganese than the wild type in the tissues surrounding the vascular cylinder. For iron, the images looked completely different, with iron bound mainly in the epidermis of the wild-type plants but confined to the cortical cell walls of the mutant. The method offers the power of inductively coupled plasma-mass spectrometry to be fully employed, thereby providing a basis for detailed studies of ion transport in roots. Being applicable to Arabidopsis, the molecular and genetic approaches available in this system can now be fully exploited in order to gain a better mechanistic understanding of these processes. PMID:27566167

Correlative Microscopy of Vitreous Sections Provides Insights into BAR-Domain Organization In Situ.

PubMed

Bharat, Tanmay A M; Hoffmann, Patrick C; Kukulski, Wanda

2018-04-10

Electron microscopy imaging of macromolecular complexes in their native cellular context is limited by the inherent difficulty to acquire high-resolution tomographic data from thick cells and to specifically identify elusive structures within crowded cellular environments. Here, we combined cryo-fluorescence microscopy with electron cryo-tomography of vitreous sections into a coherent correlative microscopy workflow, ideal for detection and structural analysis of elusive protein assemblies in situ. We used this workflow to address an open question on BAR-domain coating of yeast plasma membrane compartments known as eisosomes. BAR domains can sense or induce membrane curvature, and form scaffold-like membrane coats in vitro. Our results demonstrate that in cells, the BAR protein Pil1 localizes to eisosomes of varying membrane curvature. Sub-tomogram analysis revealed a dense protein coat on curved eisosomes, which was not present on shallow eisosomes, indicating that while BAR domains can assemble at shallow membranes in vivo, scaffold formation is tightly coupled to curvature generation. Copyright © 2018 MRC Laboratory of Molecular Biology. Published by Elsevier Ltd.. All rights reserved.

Sequence context and crosslinking mechanism affect the efficiency of in vivo capture of a protein-protein interaction

PubMed Central

Lancia, Jody K.; Nwokoye, Adaora; Dugan, Amanda; Joiner, Cassandra; Pricer, Rachel; Mapp, Anna K.

2014-01-01

Protein-protein interactions (PPIs) are essential for implementing cellular processes and thus methods for the discovery and study of PPIs are highly desirable. An emerging method for capturing PPIs in their native cellular environment is in vivo covalent chemical capture, a method that uses nonsense suppression to site specifically incorporate photoactivable unnatural amino acids in living cells. However, in one study we found that this method did not capture a PPI for which there was abundant functional evidence, a complex formed between the transcriptional activator Gal4 and its repressor protein Gal80. Here we describe the factors that influence the success of covalent chemical capture and show that the innate reactivity of the two unnatural amino acids utilized, (p-benzoylphenylalanine (pBpa) and p-azidophenylalanine (pAzpa)), plays a profound role in the capture of Gal80 by Gal4. Based upon these data, guidelines are outlined for the successful use of in vivo photo-crosslinking to capture novel PPIs and to characterize the interfaces. PMID:24037947

Cell interactions in bone tissue engineering.

PubMed

Pirraco, R P; Marques, A P; Reis, R L

2010-01-01

Bone fractures, where the innate regenerative bone response is compromised, represent between 4 and 8 hundred thousands of the total fracture cases, just in the United States. Bone tissue engineering (TE) brought the notion that, in cases such as those, it was preferable to boost the healing process of bone tissue instead of just adding artificial parts that could never properly replace the native tissue. However, despite the hype, bone TE so far could not live up to its promises and new bottom-up approaches are needed. The study of the cellular interactions between the cells relevant for bone biology can be of essential importance to that. In living bone, cells are in a context where communication with adjacent cells is almost permanent. Many fundamental works have been addressing these communications nonetheless, in a bone TE approach, the 3D perspective, being part of the microenvironment of a bone cell, is as crucial. Works combining the study of cell-to-cell interactions in a 3D environment are not as many as expected. Therefore, the bone TE field should not only gain knowledge from the field of fundamental Biology but also contribute for further understanding the biology of bone. In this review, a summary of the main works in the field of bone TE, aiming at studying cellular interactions in a 3D environment, and how they contributed towards the development of a functional engineered bone tissue, is presented.

Investigating molecular crowding within nuclear pores using polarization-PALM

PubMed Central

Fu, Guo; Tu, Li-Chun; Zilman, Anton

2017-01-01

The key component of the nuclear pore complex (NPC) controlling permeability, selectivity, and the speed of nucleocytoplasmic transport is an assembly of natively unfolded polypeptides, which contain phenylalanine-glycine (FG) binding sites for nuclear transport receptors. The architecture and dynamics of the FG-network have been refractory to characterization due to the paucity of experimental methods able to probe the mobility and density of the FG-polypeptides and embedded macromolecules within intact NPCs. Combining fluorescence polarization, super-resolution microscopy, and mathematical analyses, we examined the rotational mobility of fluorescent probes at various locations within the FG-network under different conditions. We demonstrate that polarization PALM (p-PALM) provides a rich source of information about low rotational mobilities that are inaccessible with bulk fluorescence anisotropy approaches, and anticipate that p-PALM is well-suited to explore numerous crowded cellular environments. In total, our findings indicate that the NPC’s internal organization consists of multiple dynamic environments with different local properties. PMID:28949296

Cytoplasmically Retargeted HSV1-tk/GFP Reporter Gene Mutants for Optimization of Noninvasive Molecular-Genetic Imaging

PubMed Central

Ponomarev, Vladimir; Doubrovin, Michael; Serganova, Inna; Beresten, Tatiana; Vider, Jelena; Shavrin, Aleksander; Ageyeva, Ludmila; Balatoni, Julius; Blasberg, Ronald; Tjuvajev, Juri Gelovani

2003-01-01

Abstract To optimize the sensitivity of imaging HSV1-tk/GFP reporter gene expression, a series of HSV1-tk/GFP mutants was developed with altered nuclear localization and better cellular enzymatic activity, compared to that of the native HSV1-tk/GFP fusion protein (HSV1-tk/GFP). Several modifications of HSV1-tk/GFP reporter gene were performed, including targeted inactivating mutations in the nuclear localization signal (NLS), the addition of a nuclear export signal (NES), a combination of both mutation types, and a truncation of the first 135 bp of the native hsv1-tk coding sequence containing a “cryptic” testicular promoter and the NLS. A recombinant HSV1-tk/GFP protein and a highly sensitive sandwich enzyme-linked immunosorbent assay for HSV1-tk/GFP were developed to quantitate the amount of reporter gene product in different assays to allow normalization of the data. These different mutations resulted in various degrees of nuclear clearance, predominant cytoplasmic distribution, and increased total cellular enzymatic activity of the HSV1-tk/GFP mutants, compared to native HSV1-tk/GFP when expressed at the same levels. This appears to be the result of improvedmetabolic bioavailability of cytoplasmically retargeted mutant HSV1-tk/GFP enzymes for reaction with the radiolabeled probe (e.g., FIAU). The analysis of enzymatic properties of different HSV1-tk/GFP mutants using FIAU as a substrate revealed no significant differences from that of the native HSV1-tk/GFP. Improved total cellular enzymatic activity of cytoplasmically retargeted HSV1-tk/GFP mutants observed in vitro was confirmed by noninvasive imaging of transduced subcutaneous tumor xenografts bearing these reporters using [131I]FIAU and a γ-camera. PMID:12869307

Vive la résistance: genome-wide selection against introduced alleles in invasive hybrid zones

USGS Publications Warehouse

Kovach, Ryan P.; Hand, Brian K.; Hohenlohe, Paul A.; Cosart, Ted F.; Boyer, Matthew C.; Neville, Helen H.; Muhlfeld, Clint C.; Amish, Stephen J.; Carim, Kellie; Narum, Shawn R.; Lowe, Winsor H.; Allendorf, Fred W.; Luikart, Gordon

2016-01-01

Evolutionary and ecological consequences of hybridization between native and invasive species are notoriously complicated because patterns of selection acting on non-native alleles can vary throughout the genome and across environments. Rapid advances in genomics now make it feasible to assess locus-specific and genome-wide patterns of natural selection acting on invasive introgression within and among natural populations occupying diverse environments. We quantified genome-wide patterns of admixture across multiple independent hybrid zones of native westslope cutthroat trout and invasive rainbow trout, the world's most widely introduced fish, by genotyping 339 individuals from 21 populations using 9380 species-diagnostic loci. A significantly greater proportion of the genome appeared to be under selection favouring native cutthroat trout (rather than rainbow trout), and this pattern was pervasive across the genome (detected on most chromosomes). Furthermore, selection against invasive alleles was consistent across populations and environments, even in those where rainbow trout were predicted to have a selective advantage (warm environments). These data corroborate field studies showing that hybrids between these species have lower fitness than the native taxa, and show that these fitness differences are due to selection favouring many native genes distributed widely throughout the genome.

Bilingual Infants Demonstrate Perceptual Flexibility in Phoneme Discrimination but Perceptual Constraint in Face Discrimination

PubMed Central

Singh, Leher; Loh, Darrell; Xiao, Naiqi G.

2017-01-01

Perceptual narrowing is a highly significant development associated with the first year of life. It conventionally refers to an orientation toward nativeness whereby infant's perceptual sensitivities begin to align with the phonetic properties of their native environment. Nativeness effects, such as perceptual narrowing, have been observed in several domains, most notably, in face discrimination within other-race faces and speech discrimination of non-native phonemes. Thus, far, nativeness effects in the face and speech perception have been theoretically linked, but have mostly been investigated independently. An important caveat to nativeness effects is that diversifying experiences, such as bilingualism or multiracial exposure, can lead to a reduction or postponement in attunement to the native environment. The present study was designed to investigate whether bilingualism influences nativeness effects in phonetic and face perception. Eleven-month-old monolingual and bilingual infants were tested on their abilities to discriminate native and non-native speech contrasts as well as own-race and other-race face contrasts. While monolingual infants demonstrated nativeness effects in face and speech perception, bilingual infants demonstrated nativeness effects in the face perception but demonstrated flexibility in speech perception. Results support domain-specific effects of bilingual experience on nativeness effects. PMID:28955278

Bone scaffolds with homogeneous and discrete gradient mechanical properties.

PubMed

Jelen, C; Mattei, G; Montemurro, F; De Maria, C; Mattioli-Belmonte, M; Vozzi, G

2013-01-01

Bone TE uses a scaffold either to induce bone formation from surrounding tissue or to act as a carrier or template for implanted bone cells or other agents. We prepared different bone tissue constructs based on collagen, gelatin and hydroxyapatite using genipin as cross-linking agent. The fabricated construct did not present a release neither of collagen neither of genipin over its toxic level in the surrounding aqueous environment. Each scaffold has been mechanically characterized with compression, swelling and creep tests, and their respective viscoelastic mechanical models were derived. Mechanical characterization showed a practically elastic behavior of all samples and that compressive elastic modulus basically increases as content of HA increases, and it is strongly dependent on porosity and water content. Moreover, by considering that gradients in cellular and extracellular architecture as well as in mechanical properties are readily apparent in native tissues, we developed discrete functionally graded scaffolds (discrete FGSs) in order to mimic the graded structure of bone tissue. These new structures were mechanically characterized showing a marked anisotropy as the native bone tissue. Results obtained have shown FGSs could represent valid bone substitutes. Copyright © 2012 Elsevier B.V. All rights reserved.

3D Cell Printing of Functional Skeletal Muscle Constructs Using Skeletal Muscle-Derived Bioink.

PubMed

Choi, Yeong-Jin; Kim, Taek Gyoung; Jeong, Jonghyeon; Yi, Hee-Gyeong; Park, Ji Won; Hwang, Woonbong; Cho, Dong-Woo

2016-10-01

Engineered skeletal muscle tissues that mimic the structure and function of native muscle have been considered as an alternative strategy for the treatment of various muscular diseases and injuries. Here, it is demonstrated that 3D cell-printing of decellularized skeletal muscle extracellular matrix (mdECM)-based bioink facilitates the fabrication of functional skeletal muscle constructs. The cellular alignment and the shape of the tissue constructs are controlled by 3D cell-printing technology. mdECM bioink provides the 3D cell-printed muscle constructs with a myogenic environment that supports high viability and contractility as well as myotube formation, differentiation, and maturation. More interestingly, the preservation of agrin is confirmed in the mdECM, and significant increases in the formation of acetylcholine receptor clusters are exhibited in the 3D cell-printed muscle constructs. In conclusion, mdECM bioink and 3D cell-printing technology facilitate the mimicking of both the structural and functional properties of native muscle and hold great promise for producing clinically relevant engineered muscle for the treatment of muscular injuries. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

FLANAGAN,J.M.; BEWLEY,M.C.

It is generally accepted that the information necessary to specify the native, functional, three-dimensional structure of a protein is encoded entirely within its amino acid sequence; however, efficient reversible folding and unfolding is observed only with a subset of small single-domain proteins. Refolding experiments often lead to the formation of kinetically-trapped, misfolded species that aggregate, even in dilute solution. In the cellular environment, the barriers to efficient protein folding and maintenance of native structure are even larger due to the nature of this process. First, nascent polypeptides must fold in an extremely crowded environment where the concentration of macromolecules approachesmore » 300-400 mg/mL and on average, each ribosome is within its own diameter of another ribosome (1-3). These conditions of severe molecular crowding, coupled with high concentrations of nascent polypeptide chains, favor nonspecific aggregation over productive folding (3). Second, folding of newly-translated polypeptides occurs in the context of their vehtorial synthesis process. Amino acids are added to a growing nascent chain at the rate of -5 residues per set, which means that for a 300 residue protein its N-terminus will be exposed to the cytosol {approx}1 min before its C-terminus and be free to begin the folding process. However, because protein folding is highly cooperative, the nascent polypeptide cannot reach its native state until a complete folding domain (50-250 residues) has emerged from the ribosome. Thus, for a single-domain protein, the final steps in folding are only completed post-translationally since {approx}40 residues of a nascent chain are sequestered within the exit channel of the ribosome and are not available for folding (4). A direct consequence of this limitation in cellular folding is that during translation incomplete domains will exist in partially-folded states that tend to expose hydrophobic residues that are prone to aggregation and/or misfolding. Thus it is not surprising that, in cells, the protein folding process is error prone and organisms have evolved ''editing'' or quality control (QC) systems to assist in the folding, maintenance and, when necessary, selective removal of damaged proteins. In fact, there is growing evidence that failure of these QC-systems contributes to a number of disease states (5-8). This chapter describes our current understanding of the nature and mechanisms of the protein quality control systems in the cytosol of bacteria. Parallel systems are exploited in the cytosol and mitochondria of eukaryotes to prevent the accumulation of misfolded proteins.« less

Environmentally induced development costs underlie fitness tradeoffs.

PubMed

Walter, Greg M; Wilkinson, Melanie J; Aguirre, J David; Blows, Mark W; Ortiz-Barrientos, Daniel

2018-06-01

Local adaptation can lead to genotype-by-environment interactions, which can create fitness tradeoffs in alternative environments, and govern the distribution of biodiversity across geographic landscapes. Exploring the ecological circumstances that promote the evolution of fitness tradeoffs requires identifying how natural selection operates and during which ontogenetic stages natural selection is strongest. When organisms disperse to areas outside their natural range, tradeoffs might emerge when organisms struggle to reach key life history stages, or alternatively, die shortly after reaching life history stages if there are greater risks of mortality associated with costs to developing in novel environments. We used multiple populations from four ecotypes of an Australian native wildflower (Senecio pinnatifolius) in reciprocal transplants to explore how fitness tradeoffs arise across ontogeny. We then assessed whether the survival probability for plants from native and foreign populations was contingent on reaching key developmental stages. We found that fitness tradeoffs emerged as ontogeny progressed when native plants were more successful than foreign plants at reaching seedling establishment and maturity. Native and foreign plants that failed to reach seedling establishment died at the same rate, but plants from foreign populations died quicker than native plants after reaching seedling establishment, and died quicker regardless of whether they reached sexual maturity or not. Development rates were similar for native and foreign populations, but changed depending on the environment. Together, our results suggest that natural selection for environment-specific traits early in life history created tradeoffs between contrasting environments. Plants from foreign populations were either unable to develop to seedling establishment, or they suffered increased mortality as a consequence of reaching seedling establishment. The observation of tradeoffs together with environmentally dependent changes in development rate suggest that foreign environments induce organisms to develop at a rate different from their native habitat, incurring consequences for lifetime fitness and population divergence. © 2018 by the Ecological Society of America.

Non-native salmonids affect amphibian occupancy at multiple spatial scales

Treesearch

David S. Pilliod; Blake R. Hossack; Peter F. Bahls; Evelyn L. Bull; Paul Stephen Corn; Grant Hokit; Bryce A. Maxell; James C. Munger; Aimee Wyrick

2010-01-01

The introduction of non-native species into aquatic environments has been linked with local extinctions and altered distributions of native species. We investigated the effect of non-native salmonids on the occupancy of two native amphibians, the long-toed salamander (Ambystoma macrodactylum) and Columbia spotted frog (Rana luteiventris), across three spatial scales:...

Differential modulation of host plant delta13C and delta18O by native and nonnative arbuscular mycorrhizal fungi in a semiarid environment.

PubMed

Querejeta, J I; Allen, M F; Caravaca, F; Roldán, A

2006-01-01

Native, drought-adapted arbuscular mycorrhizal fungi (AMF) often improve host-plant performance to a greater extent than nonnative AMF in dry environments. However, little is known about the physiological basis for this differential plant response. Seedlings of Olea europaea and Rhamnus lycioides were inoculated with either a mixture of eight native Glomus species or with the nonnative Glomus claroideum before field transplanting in a semiarid area. Inoculation with native AMF produced the greatest improvement in nutrient and water status as well as in long-term growth for both Olea and Rhamnus. Foliar delta18O measurements indicated that native AMF enhanced stomatal conductance to a greater extent than nonnative AMF in Olea and Rhamnus.delta13C data showed that intrinsic water-use efficiency in Olea was differentially stimulated by native AMF compared with nonnative AMF. Our results suggest that modulation of leaf gas exchange by native, drought-adapted AMF is critical to the long-term performance of host plants in semiarid environments. delta18O can provide a time-integrated measure of the effect of mycorrhizal infection on host-plant water relations.

Invasive alien plants benefit more from clonal integration in heterogeneous environments than natives.

PubMed

Wang, Yong-Jian; Müller-Schärer, Heinz; van Kleunen, Mark; Cai, Ai-Ming; Zhang, Ping; Yan, Rong; Dong, Bi-Cheng; Yu, Fei-Hai

2017-12-01

What confers invasive alien plants a competitive advantage over native plants remains open to debate. Many of the world's worst invasive alien plants are clonal and able to share resources within clones (clonal integration), particularly in heterogeneous environments. Here, we tested the hypothesis that clonal integration benefits invasive clonal plants more than natives and thus confers invasives a competitive advantage. We selected five congeneric and naturally co-occurring pairs of invasive alien and native clonal plants in China, and grew pairs of connected and disconnected ramets under heterogeneous light, soil nutrient and water conditions that are commonly encountered by alien plants during their invasion into new areas. Clonal integration increased biomass of all plants in all three heterogeneous resource environments. However, invasive plants benefited more from clonal integration than natives. Consequently, invasive plants produced more biomass than natives. Our results indicate that clonal integration may confer invasive alien clonal plants a competitive advantage over natives. Therefore, differences in the ability of clonal integration could potentially explain, at least partly, the invasion success of alien clonal plants in areas where resources are heterogeneously distributed. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Responses of Plant Proteins to Heavy Metal Stress—A Review

PubMed Central

Hasan, Md. Kamrul; Cheng, Yuan; Kanwar, Mukesh K.; Chu, Xian-Yao; Ahammed, Golam J.; Qi, Zhen-Yu

2017-01-01

Plants respond to environmental pollutants such as heavy metal(s) by triggering the expression of genes that encode proteins involved in stress response. Toxic metal ions profoundly affect the cellular protein homeostasis by interfering with the folding process and aggregation of nascent or non-native proteins leading to decreased cell viability. However, plants possess a range of ubiquitous cellular surveillance systems that enable them to efficiently detoxify heavy metals toward enhanced tolerance to metal stress. As proteins constitute the major workhorses of living cells, the chelation of metal ions in cytosol with phytochelatins and metallothioneins followed by compartmentalization of metals in the vacuoles as well as the repair of stress-damaged proteins or removal and degradation of proteins that fail to achieve their native conformations are critical for plant tolerance to heavy metal stress. In this review, we provide a broad overview of recent advances in cellular protein research with regards to heavy metal tolerance in plants. We also discuss how plants maintain functional and healthy proteomes for survival under such capricious surroundings. PMID:28928754

Differences in beliefs and home environments regarding energy balance behaviors according to parental education and ethnicity among schoolchildren in Europe: the ENERGY cross sectional study.

PubMed

Brug, Johannes; Uijtdewilligen, Léonie; van Stralen, Maartje M; Singh, Amika S; ChinAPaw, Mai J M; De Bourdeaudhuij, Ilse; Lien, Nanna; Bere, Elling; Maes, Lea; Fernández-Alvira, Juan M; Jan, Nataša; Kovacs, Eva; Dössegger, Alain; Manios, Yannis; te Velde, Saskia J

2014-06-17

To explore differences in personal and home environmental factors that are regarded as determinants of energy balance-related behaviors (EBRBs) according to parental education and ethnic background among 10-12 year old schoolchildren across Europe. A school-based survey among 10-12 year olds was conducted in eight countries across Europe. A range of personal and home environment variables relevant for soft drink consumption, daily breakfast, sport participation and TV time was assessed by means of child report. Personal factors included attitude, health beliefs, and preference/liking. Home environment factors included parental subjective norm, modeling, support, practices and home availability. Children were classified based on parental education (i.e., low vs. high) and ethnic background (i.e., native vs. non-native). Data from 6018 children originating from 83 schools were included in the analyses. Multilevel logistic regression analyses showed that the majority of the factors tested -and especially home environment variables- were more favorable among children from higher educated parents and from native ethnicity. None of the personal and home environment factors was found to be more favorable among children from lower educated parents or non-native ethnicity. The present study indicates that schoolchildren from lower educated and non-native parents across Europe have EBRB-related beliefs and are exposed to home environments that are less favorable for engagement in healthy EBRBs.

Cellular Electron Cryotomography: Toward Structural Biology In Situ.

PubMed

Oikonomou, Catherine M; Jensen, Grant J

2017-06-20

Electron cryotomography (ECT) provides three-dimensional views of macromolecular complexes inside cells in a native frozen-hydrated state. Over the last two decades, ECT has revealed the ultrastructure of cells in unprecedented detail. It has also allowed us to visualize the structures of macromolecular machines in their native context inside intact cells. In many cases, such machines cannot be purified intact for in vitro study. In other cases, the function of a structure is lost outside the cell, so that the mechanism can be understood only by observation in situ. In this review, we describe the technique and its history and provide examples of its power when applied to cell biology. We also discuss the integration of ECT with other techniques, including lower-resolution fluorescence imaging and higher-resolution atomic structure determination, to cover the full scale of cellular processes.

Mobilizing and Empowering Native American Youth through Service, the Environment and Heritage.

ERIC Educational Resources Information Center

Kast, Sherry

1994-01-01

Describes activities of various youth councils of the United National Indian Tribal Youth (UNITY) network. The activities include developing projects in the areas of alcohol abuse education, community service, Native American heritage, and the environment. (HTH)

Thermal physiology of native cool-climate, and non-native warm-climate Pumpkinseed sunfish raised in a common environment.

PubMed

Rooke, Anna C; Burness, Gary; Fox, Michael G

2017-02-01

Contemporary evolution of thermal physiology has the potential to help limit the physiological stress associated with rapidly changing thermal environments; however it is unclear if wild populations can respond quickly enough for such changes to be effective. We used native Canadian Pumpkinseed (Lepomis gibbosus) sunfish, and non-native Pumpkinseed introduced into the milder climate of Spain ~100 years ago, to assess genetic differences in thermal physiology in response to the warmer non-native climate. We compared temperature performance reaction norms of two Canadian and two Spanish Pumpkinseed populations born and raised within a common environment. We found that Canadian Pumpkinseed had higher routine metabolic rates when measured at seasonally high temperatures (15°C in winter, 30°C in summer), and that Spanish Pumpkinseed had higher critical thermal maxima when acclimated to 30°C in the summer. Growth rates were not significantly different among populations, however Canadian Pumpkinseed tended to have faster growth at the warmest temperatures measured (32°C). The observed differences in physiology among Canadian and Spanish populations at the warmest acclimation temperatures are consistent with the introduced populations being better suited to the warmer non-native climate than native populations. The observed differences could be the result of either founder effects, genetic drift, and/or contemporary adaptive evolution in the warmer non-native climate. Copyright © 2016 Elsevier Ltd. All rights reserved.

Photoactivatable protein labeling by singlet oxygen mediated reactions.

PubMed

To, Tsz-Leung; Medzihradszky, Katalin F; Burlingame, Alma L; DeGrado, William F; Jo, Hyunil; Shu, Xiaokun

2016-07-15

Protein-protein interactions regulate many biological processes. Identification of interacting proteins is thus an important step toward molecular understanding of cell signaling. The aim of this study was to investigate the use of photo-generated singlet oxygen and a small molecule for proximity labeling of interacting proteins in cellular environment. The protein of interest (POI) was fused with a small singlet oxygen photosensitizer (miniSOG), which generates singlet oxygen ((1)O2) upon irradiation. The locally generated singlet oxygen then activated a biotin-conjugated thiol molecule to form a covalent bond with the proteins nearby. The labeled proteins can then be separated and subsequently identified by mass spectrometry. To demonstrate the applicability of this labeling technology, we fused the miniSOG to Skp2, an F-box protein of the SCF ubiquitin ligase, and expressed the fusion protein in mammalian cells and identified that the surface cysteine of its interacting partner Skp1 was labeled by the biotin-thiol molecule. This photoactivatable protein labeling method may find important applications including identification of weak and transient protein-protein interactions in the native cellular context, as well as spatial and temporal control of protein labeling. Copyright © 2016 Elsevier Ltd. All rights reserved.

Visualizing protein partnerships in living cells and organisms.

PubMed

Lowder, Melissa A; Appelbaum, Jacob S; Hobert, Elissa M; Schepartz, Alanna

2011-12-01

In recent years, scientists have expanded their focus from cataloging genes to characterizing the multiple states of their translated products. One anticipated result is a dynamic map of the protein association networks and activities that occur within the cellular environment. While in vitro-derived network maps can illustrate which of a multitude of possible protein-protein associations could exist, they supply a falsely static picture lacking the subtleties of subcellular location (where) or cellular state (when). Generating protein association network maps that are informed by both subcellular location and cell state requires novel approaches that accurately characterize the state of protein associations in living cells and provide precise spatiotemporal resolution. In this review, we highlight recent advances in visualizing protein associations and networks under increasingly native conditions. These advances include second generation protein complementation assays (PCAs), chemical and photo-crosslinking techniques, and proximity-induced ligation approaches. The advances described focus on background reduction, signal optimization, rapid and reversible reporter assembly, decreased cytotoxicity, and minimal functional perturbation. Key breakthroughs have addressed many challenges and should expand the repertoire of tools useful for generating maps of protein interactions resolved in both time and space. Copyright © 2011 Elsevier Ltd. All rights reserved.

The Role of Tourism and Recreation in the Spread of Non-Native Species: A Systematic Review and Meta-Analysis.

PubMed

Anderson, Lucy G; Rocliffe, Steve; Haddaway, Neal R; Dunn, Alison M

2015-01-01

Managing the pathways by which non-native species are introduced and spread is considered the most effective way of preventing species invasions. Tourism and outdoor recreation involve the frequent congregation of people, vehicles and vessels from geographically diverse areas. They are therefore perceived to be major pathways for the movement of non-native species, and ones that will become increasingly important with the continued growth of these sectors. However, a global assessment of the relationship between tourism activities and the introduction of non-native species-particularly in freshwater and marine environments-is lacking. We conducted a systematic review and meta-analysis to determine the impact of tourism and outdoor recreation on non-native species in terrestrial, marine and freshwater environments. Our results provide quantitative evidence that the abundance and richness of non-native species are significantly higher in sites where tourist activities take place than in control sites. The pattern was consistent across terrestrial, freshwater and marine environments; across a variety of vectors (e.g. horses, hikers, yachts); and across a range of taxonomic groups. These results highlight the need for widespread biosecurity interventions to prevent the inadvertent introduction of invasive non-native species (INNS) as the tourism and outdoor recreation sectors grow.

Superresolution intrinsic fluorescence imaging of chromatin utilizing native, unmodified nucleic acids for contrast

PubMed Central

Dong, Biqin; Almassalha, Luay M.; Stypula-Cyrus, Yolanda; Urban, Ben E.; Chandler, John E.; Nguyen, The-Quyen; Sun, Cheng; Zhang, Hao F.; Backman, Vadim

2016-01-01

Visualizing the nanoscale intracellular structures formed by nucleic acids, such as chromatin, in nonperturbed, structurally and dynamically complex cellular systems, will help expand our understanding of biological processes and open the next frontier for biological discovery. Traditional superresolution techniques to visualize subdiffractional macromolecular structures formed by nucleic acids require exogenous labels that may perturb cell function and change the very molecular processes they intend to study, especially at the extremely high label densities required for superresolution. However, despite tremendous interest and demonstrated need, label-free optical superresolution imaging of nucleotide topology under native nonperturbing conditions has never been possible. Here we investigate a photoswitching process of native nucleotides and present the demonstration of subdiffraction-resolution imaging of cellular structures using intrinsic contrast from unmodified DNA based on the principle of single-molecule photon localization microscopy (PLM). Using DNA-PLM, we achieved nanoscopic imaging of interphase nuclei and mitotic chromosomes, allowing a quantitative analysis of the DNA occupancy level and a subdiffractional analysis of the chromosomal organization. This study may pave a new way for label-free superresolution nanoscopic imaging of macromolecular structures with nucleotide topologies and could contribute to the development of new DNA-based contrast agents for superresolution imaging. PMID:27535934

Modelling biological invasions: species traits, species interactions, and habitat heterogeneity.

PubMed

Cannas, Sergio A; Marco, Diana E; Páez, Sergio A

2003-05-01

In this paper we explore the integration of different factors to understand, predict and control ecological invasions, through a general cellular automaton model especially developed. The model includes life history traits of several species in a modular structure interacting multiple cellular automata. We performed simulations using field values corresponding to the exotic Gleditsia triacanthos and native co-dominant trees in a montane area. Presence of G. triacanthos juvenile bank was a determinant condition for invasion success. Main parameters influencing invasion velocity were mean seed dispersal distance and minimum reproductive age. Seed production had a small influence on the invasion velocity. Velocities predicted by the model agreed well with estimations from field data. Values of population density predicted matched field values closely. The modular structure of the model, the explicit interaction between the invader and the native species, and the simplicity of parameters and transition rules are novel features of the model.

Native Geoscience: Pathways to Knowledge

NASA Astrophysics Data System (ADS)

Bolman, J. R.; Seielstad, G.

2006-12-01

We are living in a definite time of change. Distinct changes are being experienced in our most sacred and natural environments. This is especially true on Native lands. Native people have lived for millennia in distinct and unique ways. The knowledge of balancing the needs of people with the needs of our natural environments is paramount in all tribal societies. This inherent accumulated knowledge has become the foundation on which to build a "blended" contemporary understanding of western science. The Dakota's and Northern California have embraced the critical need of understanding successful tribal strategies to engage educational systems (K-12 and higher education), to bring to prominence the professional development opportunities forged through working with tribal peoples and ensure the continued growth of Native earth and environmental scientists The presentation will highlight: 1) past and present philosophies on building and maintaining Native/Tribal students in earth and environmental sciences; 2) successful educational programs/activities in PreK-Ph.D. systems; 3) current Native leadership development in earth and environmental sciences; and 4) forward thinking for creating proaction collaborations addressing sustainable environmental, educational and social infrastructures for all people. Humboldt State University (HSU) and the University of North Dakota's Northern Great Plains Center for People and the Environment and the Upper Midwest Aerospace Consortium (UMAC) have been recognized nationally for their partnerships with Native communities. Unique collaborations are emerging "bridging" Native people across geographic areas in developing educational/research experiences which integrate the distinctive earth/environmental knowledge of tribal people. The presentation will highlight currently funded projects and initiatives as well as success stories of emerging Native earth system students and scientists.

Liquid scanning transmission electron microscopy: imaging protein complexes in their native environment in whole eukaryotic cells.

PubMed

Peckys, Diana B; de Jonge, Niels

2014-04-01

Scanning transmission electron microscopy (STEM) of specimens in liquid, so-called Liquid STEM, is capable of imaging the individual subunits of macromolecular complexes in whole eukaryotic cells in liquid. This paper discusses this new microscopy modality within the context of state-of-the-art microscopy of cells. The principle of operation and equations for the resolution are described. The obtained images are different from those acquired with standard transmission electron microscopy showing the cellular ultrastructure. Instead, contrast is obtained on specific labels. Images can be recorded in two ways, either via STEM at 200 keV electron beam energy using a microfluidic chamber enclosing the cells, or via environmental scanning electron microscopy at 30 keV of cells in a wet environment. The first series of experiments involved the epidermal growth factor receptor labeled with gold nanoparticles. The labels were imaged in whole fixed cells with nanometer resolution. Since the cells can be kept alive in the microfluidic chamber, it is also feasible to detect the labels in unfixed, live cells. The rapid sample preparation and imaging allows studies of multiple whole cells.

40 CFR 255.33 - Inclusion of Federal facilities and Native American Reservations.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 26 2013-07-01 2013-07-01 false Inclusion of Federal facilities and Native American Reservations. 255.33 Section 255.33 Protection of Environment ENVIRONMENTAL PROTECTION... Responsibilities of Identified Agencies and Relationship to Other Programs § 255.33 Inclusion of Federal facilities...

40 CFR 255.33 - Inclusion of Federal facilities and Native American Reservations.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 26 2012-07-01 2011-07-01 true Inclusion of Federal facilities and Native American Reservations. 255.33 Section 255.33 Protection of Environment ENVIRONMENTAL PROTECTION... Responsibilities of Identified Agencies and Relationship to Other Programs § 255.33 Inclusion of Federal facilities...

40 CFR 255.33 - Inclusion of Federal facilities and Native American Reservations.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 25 2014-07-01 2014-07-01 false Inclusion of Federal facilities and Native American Reservations. 255.33 Section 255.33 Protection of Environment ENVIRONMENTAL PROTECTION... Responsibilities of Identified Agencies and Relationship to Other Programs § 255.33 Inclusion of Federal facilities...

40 CFR 255.33 - Inclusion of Federal facilities and Native American Reservations.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 24 2010-07-01 2010-07-01 false Inclusion of Federal facilities and Native American Reservations. 255.33 Section 255.33 Protection of Environment ENVIRONMENTAL PROTECTION... Responsibilities of Identified Agencies and Relationship to Other Programs § 255.33 Inclusion of Federal facilities...

40 CFR 255.33 - Inclusion of Federal facilities and Native American Reservations.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 25 2011-07-01 2011-07-01 false Inclusion of Federal facilities and Native American Reservations. 255.33 Section 255.33 Protection of Environment ENVIRONMENTAL PROTECTION... Responsibilities of Identified Agencies and Relationship to Other Programs § 255.33 Inclusion of Federal facilities...

3D Printing Variable Stiffness Foams Using Viscous Thread Instability

NASA Astrophysics Data System (ADS)

Lipton, Jeffrey I.; Lipson, Hod

2016-08-01

Additive manufacturing of cellular structures has numerous applications ranging from fabrication of biological scaffolds and medical implants, to mechanical weight reduction and control over mechanical properties. Various additive manufacturing processes have been used to produce open regular cellular structures limited only by the resolution of the printer. These efforts have focused on printing explicitly designed cells or explicitly planning offsets between strands. Here we describe a technique for producing cellular structures implicitly by inducing viscous thread instability when extruding material. This process allows us to produce complex cellular structures at a scale that is finer than the native resolution of the printer. We demonstrate tunable effective elastic modulus and density that span two orders of magnitude. Fine grained cellular structures allow for fabrication of foams for use in a wide range of fields ranging from bioengineering, to robotics to food printing.

Deterred but not preferred: Predation by native whelk Reishia clavigera on invasive bivalves.

PubMed

Astudillo, Juan C; Bonebrake, Timothy C; Leung, Kenneth M Y

2018-01-01

This study tested the potential bio-control role of the common native predatory whelk Reishia clavigera on the invasive bivalves Xenostrobus securis and Mytilopsis sallei and the native Brachidontes variabilis in Hong Kong. Predation experiments were conducted in the laboratory under salinity levels of 22‰ and 32‰, as well as under field conditions. The results indicate that the invasive bivalves are more vulnerable to predation than the native bivalve in environments with high salinity, whereas environments with moderately low salinity (22‰) may reduce predation. Because R. clavigera did not show clear prey preference, the low survival of the invasive species might be due to a lack of effective anti-predatory defenses under experimental conditions. These findings could explain the high abundance of the invasive bivalves in disturbed environments in Hong Kong where predation appears to be lower.

Redox State of Cytochromes in Frozen Yeast Cells Probed by Resonance Raman Spectroscopy.

PubMed

Okotrub, Konstantin A; Surovtsev, Nikolay V

2015-12-01

Cryopreservation is a well-established technique used for the long-term storage of biological materials whose biological activity is effectively stopped under low temperatures (suspended animation). Since most biological methods do not work in a low-temperature frozen environment, the mechanism and details of the depression of cellular activity in the frozen state remain largely uncharacterized. In this work, we propose, to our knowledge, a new approach to study the downregulation of the redox activity of cytochromes b and c in freezing yeast cells in a contactless, label-free manner. Our approach is based on cytochrome photobleaching effects observed in the resonance Raman spectra of live cells. Photoinduced and native redox reactions that contributed to the photobleaching rate were studied over a wide temperature range (from -173 to +25 °C). We found that ice formation influences both the rate of cytochrome redox reactions and the balance between the reduced and oxidized cytochromes. We demonstrate that the temperature dependence of native redox reaction rates can be well described by the thermal activation law with an apparent energy of 32.5 kJ/mol, showing that the redox reaction rate is ∼10(15) times slower at liquid nitrogen temperature than at room temperature. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Intercellular Variation in Signaling through the TGF-β Pathway and Its Relation to Cell Density and Cell Cycle Phase*

PubMed Central

Zieba, Agata; Pardali, Katerina; Söderberg, Ola; Lindbom, Lena; Nyström, Erik; Moustakas, Aristidis; Heldin, Carl-Henrik; Landegren, Ulf

2012-01-01

Fundamental open questions in signal transduction remain concerning the sequence and distribution of molecular signaling events among individual cells. In this work, we have characterized the intercellular variability of transforming growth factor β-induced Smad interactions, providing essential information about TGF-β signaling and its dependence on the density of cell populations and the cell cycle phase. By employing the recently developed in situ proximity ligation assay, we investigated the dynamics of interactions and modifications of Smad proteins and their partners under native and physiological conditions. We analyzed the kinetics of assembly of Smad complexes and the influence of cellular environment and relation to mitosis. We report rapid kinetics of formation of Smad complexes, including native Smad2-Smad3-Smad4 trimeric complexes, in a manner influenced by the rate of proteasomal degradation of these proteins, and we found a striking cell to cell variation of signaling complexes. The single-cell analysis of TGF-β signaling in genetically unmodified cells revealed previously unknown aspects of regulation of this pathway, and it provided a basis for analysis of these signaling events to diagnose pathological perturbations in patient samples and to evaluate their susceptibility to drug treatment. PMID:22442258

Constitutively expressing cell lines that secrete a truncated bovine herpes virus-1 glycoprotein (gpI) stimulate T-lymphocyte responsiveness.

PubMed

Leary, T P; Gao, Y; Splitter, G A

1992-07-01

The desire to obtain authentically glycosylated viral protein products in sufficient quantity for immunological study has led to the use of eucaryotic expression vectors for protein production. An additional advantage is that these protein products can be studied individually in the absence of their native viral environment. We have cloned a complementary DNA (cDNA) encoding bovine herpes virus-1 (BHV-1) glycoprotein 1 (gpI) into the eucaryotic expression vector, pZipNeo SVX1. Since this protein is normally embedded within the membrane of BHV-1 infected cells, we removed sequences encoding the transmembrane domain of the native protein. After transfection of the plasmid construct into the canine osteosarcoma cell line, D17, or Madin-Darby bovine kidney (MDBK) cells, a truncated BHV-1 (gpI) was secreted into the culture medium as demonstrated by radioimmunoprecipitation and SDS-PAGE. Both a CD4+ T-lymphocyte line specific for BHV-1 and freshly isolated T lymphocytes could recognize and respond to the secreted recombinant gpI. Further, recombinant gpI could elicit both antibody and cellular responses in cattle when used as an immunogen. Having established constitutively glycoprotein producing cell lines, future studies in vaccine evaluation of gpI will be facilitated.

Matrix composition and mechanics of decellularized lung scaffolds.

PubMed

Petersen, Thomas H; Calle, Elizabeth A; Colehour, Maegen B; Niklason, Laura E

2012-01-01

The utility of decellularized native tissues for tissue engineering has been widely demonstrated. Here, we examine the production of decellularized lung scaffolds from native rodent lung using two different techniques, principally defined by use of either the detergent 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS) or sodium dodecyl sulfate (SDS). All viable cellular material is removed, including at least 99% of DNA. Histochemical staining and mechanical testing indicate that collagen and elastin are retained in the decellularized matrices with CHAPS-based decellularization, while SDS-based decellularization leads to loss of collagen and decline in mechanical strength. Quantitative assays confirm that most collagen is retained with CHAPS treatment but that about 80% of collagen is lost with SDS treatment. In contrast, for both detergent methods, at least 60% of elastin content is lost along with about 95% of native proteoglycan content. Mechanical testing of the decellularized scaffolds indicates that they are mechanically similar to native lung using CHAPS decellularization, including retained tensile strength and elastic behavior, demonstrating the importance of collagen and elastin in lung mechanics. With SDS decellularization, the mechanical integrity of scaffolds is significantly diminished with some loss of elastic function as well. Finally, a simple theoretical model of peripheral lung matrix mechanics is consonant with our experimental findings. This work demonstrates the feasibility of producing a decellularized lung scaffold that can be used to study lung matrix biology and mechanics, independent of the effects of cellular components. Copyright © 2011 S. Karger AG, Basel.

How Native American Success and Leadership Is Cultivated at the Corporate Level: A Native American Employee Perspective.

ERIC Educational Resources Information Center

One Feather, Sandra

2003-01-01

A Chippewa-Cree engineer helps educate Native American college students on how to adjust to the corporate environment and become successful employees and leaders. Issues include differences between Native and corporate cultures, impact of cultural differences on group dynamics, business etiquette, and the importance of workplace mentors. Corporate…

A tool for multi-scale modelling of the renal nephron

PubMed Central

Nickerson, David P.; Terkildsen, Jonna R.; Hamilton, Kirk L.; Hunter, Peter J.

2011-01-01

We present the development of a tool, which provides users with the ability to visualize and interact with a comprehensive description of a multi-scale model of the renal nephron. A one-dimensional anatomical model of the nephron has been created and is used for visualization and modelling of tubule transport in various nephron anatomical segments. Mathematical models of nephron segments are embedded in the one-dimensional model. At the cellular level, these segment models use models encoded in CellML to describe cellular and subcellular transport kinetics. A web-based presentation environment has been developed that allows the user to visualize and navigate through the multi-scale nephron model, including simulation results, at the different spatial scales encompassed by the model description. The Zinc extension to Firefox is used to provide an interactive three-dimensional view of the tubule model and the native Firefox rendering of scalable vector graphics is used to present schematic diagrams for cellular and subcellular scale models. The model viewer is embedded in a web page that dynamically presents content based on user input. For example, when viewing the whole nephron model, the user might be presented with information on the various embedded segment models as they select them in the three-dimensional model view. Alternatively, the user chooses to focus the model viewer on a cellular model located in a particular nephron segment in order to view the various membrane transport proteins. Selecting a specific protein may then present the user with a description of the mathematical model governing the behaviour of that protein—including the mathematical model itself and various simulation experiments used to validate the model against the literature. PMID:22670210

Digital Native and Digital Immigrant Use of Scholarly Network for Doctoral Learners

ERIC Educational Resources Information Center

Berman, Ronald; Hassell, Deliesha

2014-01-01

The Doctoral Community Network (DC) is a learner driven, scholarly community designed to help online doctoral learners successfully complete their dissertation and program of study. While digital natives grew up in an environment immersed in technology, digital immigrants adapted to this environment through their ability to learn and adjust to…

Native America: American Indian Geoscientists & Earth System Science Leaders

NASA Astrophysics Data System (ADS)

Bolman, J. R.

2011-12-01

We are living in a definite time of change. Distinct changes are being experienced in our most sacred and natural environments. This is especially true on Native lands across the Americas. Native people have lived for millennia in distinct and unique ways. The knowledge of balancing the needs of people with the needs of our natural environments is paramount in all Tribal societies. These changes have accelerated the momentum to ensure the future of American Indian Geoscientists and Earth Systems Science Leaders. The presentation will bring to prominence the unique recruitment and mentoring necessary to achieve success that emerged through working with Tribal people. The presentation will highlight: 1) past and present philosophies on recruitment and mentoring of Native/Tribal students in geoscience and earth systems science; 2) current Native leadership and research development; 3) unique collaborations "bridging" Native people across geographic areas (International) in developing educational/research experiences which integrate the distinctive geoscience and earth systems science knowledge of Tribal peoples throughout the Americas. The presentation will highlight currently funded projects and initiatives as well as success stories of emerging Native geoscientists and earth systems science leaders.

A COTS-Based Replacement Strategy for Aging Avionics Computers

DTIC Science & Technology

2001-12-01

Communication Control Unit. A COTS-Based Replacement Strategy for Aging Avionics Computers COTS Microprocessor Real Time Operating System New Native Code...Native Code Objec ts Native Code Thread Real - Time Operating System Legacy Function x Virtual Component Environment Context Switch Thunk Add-in Replace

3D Printing Variable Stiffness Foams Using Viscous Thread Instability

PubMed Central

Lipton, Jeffrey I.; Lipson, Hod

2016-01-01

Additive manufacturing of cellular structures has numerous applications ranging from fabrication of biological scaffolds and medical implants, to mechanical weight reduction and control over mechanical properties. Various additive manufacturing processes have been used to produce open regular cellular structures limited only by the resolution of the printer. These efforts have focused on printing explicitly designed cells or explicitly planning offsets between strands. Here we describe a technique for producing cellular structures implicitly by inducing viscous thread instability when extruding material. This process allows us to produce complex cellular structures at a scale that is finer than the native resolution of the printer. We demonstrate tunable effective elastic modulus and density that span two orders of magnitude. Fine grained cellular structures allow for fabrication of foams for use in a wide range of fields ranging from bioengineering, to robotics to food printing. PMID:27503148

Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA

NASA Astrophysics Data System (ADS)

Lin, Chenxiang; Jungmann, Ralf; Leifer, Andrew M.; Li, Chao; Levner, Daniel; Church, George M.; Shih, William M.; Yin, Peng

2012-10-01

The identification and differentiation of a large number of distinct molecular species with high temporal and spatial resolution is a major challenge in biomedical science. Fluorescence microscopy is a powerful tool, but its multiplexing ability is limited by the number of spectrally distinguishable fluorophores. Here, we used (deoxy)ribonucleic acid (DNA)-origami technology to construct submicrometre nanorods that act as fluorescent barcodes. We demonstrate that spatial control over the positioning of fluorophores on the surface of a stiff DNA nanorod can produce 216 distinct barcodes that can be decoded unambiguously using epifluorescence or total internal reflection fluorescence microscopy. Barcodes with higher spatial information density were demonstrated via the construction of super-resolution barcodes with features spaced by ˜40 nm. One species of the barcodes was used to tag yeast surface receptors, which suggests their potential applications as in situ imaging probes for diverse biomolecular and cellular entities in their native environments.

Capturing extracellular matrix properties in vitro: Microengineering materials to decipher cell and tissue level processes.

PubMed

Abdeen, Amr A; Lee, Junmin; Kilian, Kristopher A

2016-05-01

Rapid advances in biology have led to the establishment of new fields with tremendous translational potential including regenerative medicine and immunoengineering. One commonality to these fields is the need to extract cells for manipulation in vitro; however, results obtained in laboratory cell culture will often differ widely from observations made in vivo. To more closely emulate native cell biology in the laboratory, designer engineered environments have proved a successful methodology to decipher the properties of the extracellular matrix that govern cellular decision making. Here, we present an overview of matrix properties that affect cell behavior, strategies for recapitulating important parameters in vitro, and examples of how these properties can affect cell and tissue level processes, with emphasis on leveraging these tools for immunoengineering. © 2016 by the Society for Experimental Biology and Medicine.

Sub-micrometer Geometrically Encoded Fluorescent Barcodes Self-Assembled from DNA

PubMed Central

Lin, Chenxiang; Jungmann, Ralf; Leifer, Andrew M.; Li, Chao; Levner, Daniel; Church, George M.; Shih, William M.; Yin, Peng

2012-01-01

The identification and differentiation of a large number of distinct molecular species with high temporal and spatial resolution is a major challenge in biomedical science. Fluorescence microscopy is a powerful tool, but its multiplexing ability is limited by the number of spectrally distinguishable fluorophores. Here we use DNA-origami technology to construct sub-micrometer nanorods that act as fluorescent barcodes. We demonstrate that spatial control over the positioning of fluorophores on the surface of a stiff DNA nanorod can produce 216 distinct barcodes that can be unambiguously decoded using epifluorescence or total internal reflection fluorescence (TIRF) microscopy. Barcodes with higher spatial information density were demonstrated via the construction of super-resolution barcodes with features spaced by ~40 nm. One species of the barcodes was used to tag yeast surface receptors, suggesting their potential applications as in situ imaging probes for diverse biomolecular and cellular entities in their native environments. PMID:23000997

Assay Methods for ACS Activity and ACS Phosphorylation by MAP Kinases In Vitro and In Vivo.

PubMed

Han, Xiaomin; Li, Guojing; Zhang, Shuqun

2017-01-01

Ethylene, a gaseous phytohormone, has profound effects on plant growth, development, and adaptation to the environment. Ethylene-regulated processes begin with the induction of ethylene biosynthesis. There are two key steps in ethylene biosynthesis. The first is the biosynthesis of 1-aminocyclopropane-1-carboxylic acid (ACC) from S-Adenosyl-Methionine (SAM), a common precursor in many metabolic pathways, which is catalyzed by ACC synthase (ACS). The second is the oxidative cleavage of ACC to form ethylene under the action of ACC oxidase (ACO). ACC biosynthesis is the committing and generally the rate-limiting step in ethylene biosynthesis. As a result, characterizing the cellular ACS activity and understanding its regulation are important. In this chapter, we detail the methods used to measure, (1) the enzymatic activity of both recombinant and native ACS proteins, and (2) the phosphorylation of ACS protein by mitogen-activated protein kinases (MAPKs) in vivo and in vitro.

Complex, multi-scale small intestinal topography replicated in cellular growth substrates fabricated via chemical vapor deposition of Parylene C.

PubMed

Koppes, Abigail N; Kamath, Megha; Pfluger, Courtney A; Burkey, Daniel D; Dokmeci, Mehmet; Wang, Lin; Carrier, Rebecca L

2016-08-22

Native small intestine possesses distinct multi-scale structures (e.g., crypts, villi) not included in traditional 2D intestinal culture models for drug delivery and regenerative medicine. The known impact of structure on cell function motivates exploration of the influence of intestinal topography on the phenotype of cultured epithelial cells, but the irregular, macro- to submicron-scale features of native intestine are challenging to precisely replicate in cellular growth substrates. Herein, we utilized chemical vapor deposition of Parylene C on decellularized porcine small intestine to create polymeric intestinal replicas containing biomimetic irregular, multi-scale structures. These replicas were used as molds for polydimethylsiloxane (PDMS) growth substrates with macro to submicron intestinal topographical features. Resultant PDMS replicas exhibit multiscale resolution including macro- to micro-scale folds, crypt and villus structures, and submicron-scale features of the underlying basement membrane. After 10 d of human epithelial colorectal cell culture on PDMS substrates, the inclusion of biomimetic topographical features enhanced alkaline phosphatase expression 2.3-fold compared to flat controls, suggesting biomimetic topography is important in induced epithelial differentiation. This work presents a facile, inexpensive method for precisely replicating complex hierarchal features of native tissue, towards a new model for regenerative medicine and drug delivery for intestinal disorders and diseases.

Status of native stream fishes within selected protected areas of Niobrara River in western Nebraska

USGS Publications Warehouse

Spurgeon, Jonathan J.; Stasiak, Richard H.; Cunningham, George R.; Pope, Kevin L.; Pegg, Mark A.

2014-01-01

Lotic systems within the Great Plains are characterized by highly fluctuating conditions through both space and time. Fishes inhabiting these systems have adopted specific life-history strategies to survive in such environments; however, anthropogenic disturbance to prairie streams has resulted in declines and extirpation of many native stream fishes. Terrestrial protected areas (i.e., parks and reserves) are designated to support native flora and fauna and, it is assumed, to provide protection to native fishes. We assessed the presence and relative abundance of stream fish populations within protected areas along the Niobrara River in western Nebraska based on data collected during 1979, 1989, 2008, and 2011. The spatial extent of protection, landscape changes resulting in degraded physiochemical parameters, and introduced species may reduce the effectiveness of these terrestrial protected areas in protecting native fishes in Great Plains stream environments.

A case study of cultural educational opportunities for Native students: The scientific storyteller

NASA Astrophysics Data System (ADS)

Valdez, Shelly Ann

2002-09-01

This case study examines cultural educational opportunities for Native Alaskan students in Native Alaskan community schools. The study looks at three components of a larger initiative of systemic educational reform efforts for rural Alaskan communities: Native science fairs, summer science camps and involvement of elders. The study focuses on six Native Alaskan students from one Native Alaskan rural village in northern Alaska. The six students ranged from seventh, ninth and eleventh grades. Additionally twenty-one teachers, five Native Alaskan elders and four Alaskan Rural Systemic Initiative staff were interviewed as a part of this study. With interviews, observations, surveys, analysis of science and mathematics achievement scores, this case study will explore the effectiveness of including the science of Native Alaskan culture in the learning environment of rural Alaskan community schools. The outcomes of this study indicate that the self-esteem and attitudes of Native Alaskan students changed positively in relationship to pride in culture, honor of elders, interest in language maintenance and concern for inclusion of Native ways of knowing in school activities as a result of the cultural-rich experiences included in the learning environment. There were no significant results that indicated these types of cultural-rich experiences impacted positive gains in science and mathematics achievement scores of Native Alaskan students. At the end of the study several suggestions are made to improve and consider continued research in this area. It is hoped that this study will provide input to the continued dialogue on Indian Education.

Native American Student Perceptions of the Cultural Environment and Factors for Academic Success at the University of South Dakota

ERIC Educational Resources Information Center

Grignon, Charles M.

2009-01-01

Considering the high retention rates for Native American students in 2009 and 2008 in the two semesters at the University of South Dakota, there is a need to know the Native student perceptions of factors for their academic success. Native professors and administrators would benefit to know this information to continue to make improvements in…

Differences in Competitive Ability between Plants from Nonnative and Native Populations of a Tropical Invader Relates to Adaptive Responses in Abiotic and Biotic Environments

PubMed Central

Liao, Zhi-Yong; Zhang, Ru; Barclay, Gregor F.; Feng, Yu-Long

2013-01-01

The evolution of competitive ability of invasive plant species is generally studied in the context of adaptive responses to novel biotic environments (enemy release) in introduced ranges. However, invasive plants may also respond to novel abiotic environments. Here we studied differences in competitive ability between Chromolaena odorata plants of populations from nonnative versus native ranges, considering biogeographical differences in both biotic and abiotic environments. An intraspecific competition experiment was conducted at two nutrient levels in a common garden. In both low and high nutrient treatments, C. odorata plants from nonnative ranges showed consistently lower root to shoot ratios than did plants from native ranges grown in both monoculture and competition. In the low nutrient treatment, C. odorata plants from nonnative ranges showed significantly lower competitive ability (competition-driven decreases in plant height and biomass were more), which was associated with their lower root to shoot ratios and higher total leaf phenolic content (defense trait). In the high nutrient treatment, C. odorata plants from nonnative ranges showed lower leaf toughness and cellulosic contents (defense traits) but similar competitive ability compared with plants from native ranges, which was also associated with their lower root to shoot ratios. Our results indicate that genetically based shifts in biomass allocation (responses to abiotic environments) also influence competitive abilities of invasive plants, and provide a first potential mechanism for the interaction between range and environment (environment-dependent difference between ranges). PMID:23977140

Interaction of human low density lipoprotein and apolipoprotein B with ternary lipid microemulsion. Physical and functional properties.

PubMed

Chun, P W; Brumbaugh, E E; Shiremann, R B

1986-12-31

Based on data from sedimentation velocity experiments, electrophoresis, electron microscopy, cellular uptake studies, scanning molecular sieve chromatography using a quasi-three-dimensional data display and flow performance liquid chromatography (FPLC), models for the interaction of human serum low density lipoprotein (LDL) and of apolipoprotein B (apo B) with a ternary lipid microemulsion (ME) are proposed. The initial step in the interaction of LDL (Stokes radius 110 A) with the ternary microemulsion (Stokes radius 270 A) appears to be attachment of the LDL to emulsion particles. This attachment is followed by a very slow fusion into particles having a radius of approx. 280 A. Sonication of this mixture yields large aggregates. Electron micrographs of deoxycholate-solubilized apo B indicate an arrangement of apo B resembling strings of beads. During incubation, these particles also attach to the ternary microemulsion particles and, upon sonication, spherical particles result which resemble native LDL particles in size. Scanning chromatography corroborates the electron microscopy results. By appropriate choice of display angles in a quasi-three-dimensional display of the scanning data (corrected for gel apparent absorbance) taken at equal time intervals during passage of a sample through the column, changes in molecular radius of less than 10 A can be detected visually. Such a display gives a quantitative estimate of 101 +/- 2 A for these particles (compared to 110 A for native LDL). The LDL-ME particles and apo B-ME particles compete efficiently with native LDL for cellular binding and uptake. Cellular association studies indicate that both LDL- and apo B-ME particles are effective vehicles for lipid delivery into cells.

Native American Recipes for the Classroom.

ERIC Educational Resources Information Center

Harvey, Karen D., Comp.

This collection of recipes is intended to assist teachers in using food in the classroom to enhance the study of Native American people. Several concepts are identified to guide teachers in developing instructional units centering around food as a means of understanding the Native American culture: (1) the impact of physical environment and…

Distance Measurement on an Endogenous Membrane Transporter in E. coli Cells and Native Membranes Using EPR Spectroscopy.

PubMed

Joseph, Benesh; Sikora, Arthur; Bordignon, Enrica; Jeschke, Gunnar; Cafiso, David S; Prisner, Thomas F

2015-05-18

Membrane proteins may be influenced by the environment, and they may be unstable in detergents or fail to crystallize. As a result, approaches to characterize structures in a native environment are highly desirable. Here, we report a novel general strategy for precise distance measurements on outer membrane proteins in whole Escherichia coli cells and isolated outer membranes. The cobalamin transporter BtuB was overexpressed and spin-labeled in whole cells and outer membranes and interspin distances were measured to a spin-labeled cobalamin using pulse EPR spectroscopy. A comparative analysis of the data reveals a similar interspin distance between whole cells, outer membranes, and synthetic vesicles. This approach provides an elegant way to study conformational changes or protein-protein/ligand interactions at surface-exposed sites of membrane protein complexes in whole cells and native membranes, and provides a method to validate outer membrane protein structures in their native environment. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Contactless Stimulation and Control of Biomimetic Nanotubes by Calcium Ion Gradients.

PubMed

Kirejev, Vladimir; Ali Doosti, Baharan; Shaali, Mehrnaz; Jeffries, Gavin D M; Lobovkina, Tatsiana

2018-04-17

Membrane tubular structures are important communication pathways between cells and cellular compartments. Studying these structures in their native environment is challenging, due to the complexity of membranes and varying chemical conditions within and outside of the cells. This work demonstrates that a calcium ion gradient, applied to a synthetic lipid nanotube, triggers lipid flow directed toward the application site, resulting in the formation of a bulge aggregate. This bulge can be translated in a contactless manner by moving a calcium ion source along the lipid nanotube. Furthermore, entrapment of polystyrene nanobeads within the bulge does not tamper the bulge movement and allows transporting of the nanoparticle cargo along the lipid nanotube. In addition to the synthetic lipid nanotubes, the response of cell plasma membrane tethers to local calcium ion stimulation is investigated. The directed membrane transport in these tethers is observed, but with slower kinetics in comparison to the synthetic lipid nanotubes. The findings of this work demonstrate a novel and contactless mode of transport in lipid nanotubes, guided by local exposure to calcium ions. The observed lipid nanotube behavior can advance the current understanding of the cell membrane tubular structures, which are constantly reshaped during dynamic cellular processes. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Understanding FRET as a Research Tool for Cellular Studies

PubMed Central

Shrestha, Dilip; Jenei, Attila; Nagy, Péter; Vereb, György; Szöllősi, János

2015-01-01

Communication of molecular species through dynamic association and/or dissociation at various cellular sites governs biological functions. Understanding these physiological processes require delineation of molecular events occurring at the level of individual complexes in a living cell. Among the few non-invasive approaches with nanometer resolution are methods based on Förster Resonance Energy Transfer (FRET). FRET is effective at a distance of 1–10 nm which is equivalent to the size of macromolecules, thus providing an unprecedented level of detail on molecular interactions. The emergence of fluorescent proteins and SNAP- and CLIP- tag proteins provided FRET with the capability to monitor changes in a molecular complex in real-time making it possible to establish the functional significance of the studied molecules in a native environment. Now, FRET is widely used in biological sciences, including the field of proteomics, signal transduction, diagnostics and drug development to address questions almost unimaginable with biochemical methods and conventional microscopies. However, the underlying physics of FRET often scares biologists. Therefore, in this review, our goal is to introduce FRET to non-physicists in a lucid manner. We will also discuss our contributions to various FRET methodologies based on microscopy and flow cytometry, while describing its application for determining the molecular heterogeneity of the plasma membrane in various cell types. PMID:25815593

Electrospun Fibers for Recruitment and Differentiation of Stem Cells in Regenerative Medicine.

PubMed

Sankar, Sharanya; Sharma, Chandra S; Rath, Subha N; Ramakrishna, Seeram

2017-12-01

Electrospinning is a popular technique used to mimic the natural sub-micron features of the native tissue. The ultra-fine fibers provide a favorable extracellular matrix-like environment for regulation of cellular functions. This article summarizes and reviews the current advances in electrospun fiber application and focuses on the novel strategies applied for tissue regeneration and repair. It explores the different factors affecting the attachment and proliferation of mesenchymal stem cells (MSCs) on the electrospun substrates. The influence of different features of electrospun fibers in the differentiation of MSCs into specific lineages (bone, cartilage, tendon/ligament, and nerves) has been elaborated. In addition, the different techniques to mimic the hierarchical features of tissues and its effect on cellular functions are reviewed. Additionally, the new developments like three-dimensional (3D) electrospinning, 3D spheroid double strategy and the comparative analysis of dynamic and static culture on electrospun scaffolds are discussed. With the intricate understanding of the interaction between the cells and the electrospun fiber matrix we can aim to combine the newer strategies to overcome the existing challenges and improve the potential application of electrospun fibers in the field of tissue regeneration and repair. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

3D membrane segmentation and quantification of intact thick cells using cryo soft X-ray transmission microscopy: A pilot study

PubMed Central

Klementieva, Oxana; Werner, Stephan; Guttmann, Peter; Pratsch, Christoph; Cladera, Josep

2017-01-01

Structural analysis of biological membranes is important for understanding cell and sub-cellular organelle function as well as their interaction with the surrounding environment. Imaging of whole cells in three dimension at high spatial resolution remains a significant challenge, particularly for thick cells. Cryo-transmission soft X-ray microscopy (cryo-TXM) has recently gained popularity to image, in 3D, intact thick cells (∼10μm) with details of sub-cellular architecture and organization in near-native state. This paper reports a new tool to segment and quantify structural changes of biological membranes in 3D from cryo-TXM images by tracking an initial 2D contour along the third axis of the microscope, through a multi-scale ridge detection followed by an active contours-based model, with a subsequent refinement along the other two axes. A quantitative metric that assesses the grayscale profiles perpendicular to the membrane surfaces is introduced and shown to be linearly related to the membrane thickness. Our methodology has been validated on synthetic phantoms using realistic microscope properties and structure dimensions, as well as on real cryo-TXM data. Results demonstrate the validity of our algorithms for cryo-TXM data analysis. PMID:28376110

Embryos of non-native anoles are robust to urban thermal environments.

PubMed

Tiatragul, Sarin; Kurniawan, Audeline; Kolbe, Jason J; Warner, Daniel A

2017-04-01

The transformation of natural habitats into urban landscapes dramatically alters thermal environments, which in turn, can impact local biota. Ectothermic organisms that are oviparous are particularly sensitive to these altered environments because their embryos cannot behaviorally thermoregulate and the surrounding environment determines the temperature experienced during development. We studied the effects of urban and forested thermal environments on embryo development and hatchling phenotypes in two non-native lizards (Anolis sagrei and A. cristatellus) in metropolitan Miami, Florida. To determine if embryos from urban and forested sites are adapted to their respective thermal environments, we incubated eggs from each site using temperatures that simulate likely nest conditions in both urban and forested environments. For both species, urban thermal environments accelerated embryonic development, but had no impact on egg survival or any of the phenotypic traits that were measured (e.g., body size, running performance, and locomotor behavior). Our results provide no evidence that embryos from urban and forested sites are adapted to their respective thermal environments. Instead, the lack of any major effects suggest that embryos of both species are physiologically robust with respect to novel environments, which could have facilitated their success in establishing in non-native ranges and in human-modified landscapes. Copyright © 2017 Elsevier Ltd. All rights reserved.

RNA Imaging with Multiplexed Error Robust Fluorescence in situ Hybridization

PubMed Central

Moffitt, Jeffrey R.; Zhuang, Xiaowei

2016-01-01

Quantitative measurements of both the copy number and spatial distribution of large fractions of the transcriptome in single-cells could revolutionize our understanding of a variety of cellular and tissue behaviors in both healthy and diseased states. Single-molecule Fluorescence In Situ Hybridization (smFISH)—an approach where individual RNAs are labeled with fluorescent probes and imaged in their native cellular and tissue context—provides both the copy number and spatial context of RNAs but has been limited in the number of RNA species that can be measured simultaneously. Here we describe Multiplexed Error Robust Fluorescence In Situ Hybridization (MERFISH), a massively parallelized form of smFISH that can image and identify hundreds to thousands of different RNA species simultaneously with high accuracy in individual cells in their native spatial context. We provide detailed protocols on all aspects of MERFISH, including probe design, data collection, and data analysis to allow interested laboratories to perform MERFISH measurements themselves. PMID:27241748

Measurement of Rapid Protein Diffusion in the Cytoplasm by Photo-Converted Intensity Profile Expansion.

PubMed

Gura Sadovsky, Rotem; Brielle, Shlomi; Kaganovich, Daniel; England, Jeremy L

2017-03-14

The fluorescence microscopy methods presently used to characterize protein motion in cells infer protein motion from indirect observables, rather than measuring protein motion directly. Operationalizing these methods requires expertise that can constitute a barrier to their broad utilization. Here, we have developed PIPE (photo-converted intensity profile expansion) to directly measure the motion of tagged proteins and quantify it using an effective diffusion coefficient. PIPE works by pulsing photo-convertible fluorescent proteins, generating a peaked fluorescence signal at the pulsed region, and analyzing the spatial expansion of the signal. We demonstrate PIPE's success in measuring accurate diffusion coefficients in silico and in vitro and compare effective diffusion coefficients of native cellular proteins and free fluorophores in vivo. We apply PIPE to measure diffusion anomality in the cell and use it to distinguish free fluorophores from native cellular proteins. PIPE's direct measurement and ease of use make it appealing for cell biologists. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Regulation of decellularized tissue remodeling via scaffold-mediated lentiviral delivery in anatomically-shaped osteochondral constructs.

PubMed

Rowland, Christopher R; Glass, Katherine A; Ettyreddy, Adarsh R; Gloss, Catherine C; Matthews, Jared R L; Huynh, Nguyen P T; Guilak, Farshid

2018-05-30

Cartilage-derived matrix (CDM) has emerged as a promising scaffold material for tissue engineering of cartilage and bone due to its native chondroinductive capacity and its ability to support endochondral ossification. Because it consists of native tissue, CDM can undergo cellular remodeling, which can promote integration with host tissue and enables it to be degraded and replaced by neotissue over time. However, enzymatic degradation of decellularized tissues can occur unpredictably and may not allow sufficient time for mechanically competent tissue to form, especially in the harsh inflammatory environment of a diseased joint. The goal of the current study was to engineer cartilage and bone constructs with the ability to inhibit aberrant inflammatory processes caused by the cytokine interleukin-1 (IL-1), through scaffold-mediated delivery of lentiviral particles containing a doxycycline-inducible IL-1 receptor antagonist (IL-1Ra) transgene on anatomically-shaped CDM constructs. Additionally, scaffold-mediated lentiviral gene delivery was used to facilitate spatial organization of simultaneous chondrogenic and osteogenic differentiation via site-specific transduction of a single mesenchymal stem cell (MSC) population to overexpress either chondrogenic, transforming growth factor-beta 3 (TGF-β3), or osteogenic, bone morphogenetic protein-2 (BMP-2), transgenes. Controlled induction of IL-1Ra expression protected CDM hemispheres from inflammation-mediated degradation, and supported robust bone and cartilage tissue formation even in the presence of IL-1. In the absence of inflammatory stimuli, controlled cellular remodeling was exploited as a mechanism for fusing concentric CDM hemispheres overexpressing BMP-2 and TGF-β3 into a single bi-layered osteochondral construct. Our findings demonstrate that site-specific delivery of inducible and tunable transgenes confers spatial and temporal control over both CDM scaffold remodeling and neotissue composition. Furthermore, these constructs provide a microphysiological in vitro joint organoid model with site-specific, tunable, and inducible protein delivery systems for examining the spatiotemporal response to pro-anabolic and/or inflammatory signaling across the osteochondral interface. Copyright © 2018 Elsevier Ltd. All rights reserved.

Initial Exploration of a Construct Representing Native Language and Culture (NLC) in Elementary and Middle School Instruction

ERIC Educational Resources Information Center

Van Ryzin, Mark J.; Vincent, Claudia G.; Hoover, Joseph

2016-01-01

Students from American Indian/Alaska Native (AI/AN) backgrounds have typically experienced poor academic and behavioral outcomes. In response, the educational community has recommended that teachers integrate Native Language and Culture (NLC) into instruction to create a welcoming and culturally relevant classroom environment. However, translating…

Phonetic Influences on English and French Listeners' Assimilation of Mandarin Tones to Native Prosodic Categories

ERIC Educational Resources Information Center

So, Connie K.; Best, Catherine T.

2014-01-01

This study examined how native speakers of Australian English and French, nontone languages with different lexical stress properties, perceived Mandarin tones in a sentence environment according to their native sentence intonation categories (i-Categories) in connected speech. Results showed that both English and French speakers categorized…

Employment, psychosocial work environment and well-being among migrant and native physicians in Finnish health care.

PubMed

Aalto, Anna-Mari; Heponiemi, Tarja; Keskimäki, Ilmo; Kuusio, Hannamaria; Hietapakka, Laura; Lämsä, Riikka; Sinervo, Timo; Elovainio, Marko

2014-06-01

Although international migration of physicians is increasing, research information on their adjustment to working in a new country is scarce. This study examined the differences in employment, perceptions of psychosocial work environment and well-being between migrant and native physicians in Finland. A cross-sectional survey was sent to a random sample of physicians in Finland (N = 7000) and additionally to all foreign-born physicians licensed to practice in Finland (N = 1292). The final response rates were 56% (n = 3646) among native Finns and 43% (n = 553) among foreign-born physicians. Migrant physicians worked more often in primary care and on-call services and less often in leadership positions than native Finns. They more often experienced lack of professional support and lower work-related well-being compared with native Finns. Those migrant physicians who had lived for a shorter time in Finland perceived less stress related to electronic patient records systems and higher organizational justice compared with native physicians or those foreign physicians who had migrated earlier. Foreign-born physicians are more often employed in the primary care sector, where there are most difficulties in recruiting from the native workforce in Finland. Attention should be paid to enhancing equitable career opportunities and well-being among foreign-born physicians working in Finnish health care. Although migrant physicians are relatively well adjusted to Finnish health care in terms of perceptions of psychosocial work environment, their lower well-being calls for attention. © The Author 2014. Published by Oxford University Press on behalf of the European Public Health Association. All rights reserved.

Light energy partitioning, photosynthetic efficiency and biomass allocation in invasive Prunus serotina and native Quercus petraea in relation to light environment, competition and allelopathy.

PubMed

Robakowski, Piotr; Bielinis, Ernest; Sendall, Kerrie

2018-05-01

This study addressed whether competition under different light environments was reflected by changes in leaf absorbed light energy partitioning, photosynthetic efficiency, relative growth rate and biomass allocation in invasive and native competitors. Additionally, a potential allelopathic effect of mulching with invasive Prunus serotina leaves on native Quercus petraea growth and photosynthesis was tested. The effect of light environment on leaf absorbed light energy partitioning and photosynthetic characteristics was more pronounced than the effects of interspecific competition and allelopathy. The quantum yield of PSII of invasive P. serotina increased in the presence of a competitor, indicating a higher plasticity in energy partitioning for the invasive over the native Q. petraea, giving it a competitive advantage. The most striking difference between the two study species was the higher crown-level net CO 2 assimilation rates (A crown ) of P. serotina compared with Q. petraea. At the juvenile life stage, higher relative growth rate and higher biomass allocation to foliage allowed P. serotina to absorb and use light energy for photosynthesis more efficiently than Q. petraea. Species-specific strategies of growth, biomass allocation, light energy partitioning and photosynthetic efficiency varied with the light environment and gave an advantage to the invader over its native competitor in competition for light. However, higher biomass allocation to roots in Q. petraea allows for greater belowground competition for water and nutrients as compared to P. serotina. This niche differentiation may compensate for the lower aboveground competitiveness of the native species and explain its ability to co-occur with the invasive competitor in natural forest settings.

Environmental resources of selected areas of Hawaii: Cultural environment and aesthetic resources

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

Trettin, L.D.; Petrich, C.H.; Saulsbury, J.W.

This report has been prepared to make available and archive the background scientific data and related information collected on the cultural environment and aesthetic resources during the preparation of the environmental impact statement (EIS) for Phases 3 and 4 of the Hawaii Geothermal Project (HGP) as defined by the state of Hawaii in its April 1989 proposal to Congress. The cultural environment in the Geothermal Resource Zone (GRZ) and associated study area consists of Native Hawaiian cultural and religious practices and both Native Hawaiian and non-Native Hawaiian cultural resources. This report consists of three sections: (1) a description of Nativemore » Hawaiian cultural and religious rights, practices, and values; (2) a description of historic, prehistoric, and traditional Native Hawaiian sites; and (3) a description of other (non-native) sites that could be affected by development in the study area. Within each section, the level of descriptive detail varies according to the information currently available. The description of the cultural environment is most specific in its coverage of the Geothermal Resource Subzones in the Puna District of the island of Hawaii and the study area of South Maui. Ethnographic and archaeological reports by Cultural Advocacy Network Developing Options and International Archaeological Research Institute, Inc., respectively, supplement the descriptions of these two areas with new information collected specifically for this study. Less detailed descriptions of additional study areas on Oahu, Maui, Molokai, and the island of Hawaii are based on existing archaeological surveys.« less

Passport, a native Tc1 transposon from flatfish, is functionally active in vertebrate cells

PubMed Central

Clark, Karl J.; Carlson, Daniel F.; Leaver, Michael J.; Foster, Linda K.; Fahrenkrug, Scott C.

2009-01-01

The Tc1/mariner family of DNA transposons is widespread across fungal, plant and animal kingdoms, and thought to contribute to the evolution of their host genomes. To date, an active Tc1 transposon has not been identified within the native genome of a vertebrate. We demonstrate that Passport, a native transposon isolated from a fish (Pleuronectes platessa), is active in a variety of vertebrate cells. In transposition assays, we found that the Passport transposon system improved stable cellular transgenesis by 40-fold, has an apparent preference for insertion into genes, and is subject to overproduction inhibition like other Tc1 elements. Passport represents the first vertebrate Tc1 element described as both natively intact and functionally active, and given its restricted phylogenetic distribution, may be contemporaneously active. The Passport transposon system thus complements the available genetic tools for the manipulation of vertebrate genomes, and may provide a unique system for studying the infiltration of vertebrate genomes by Tc1 elements. PMID:19136468

Passport, a native Tc1 transposon from flatfish, is functionally active in vertebrate cells.

PubMed

Clark, Karl J; Carlson, Daniel F; Leaver, Michael J; Foster, Linda K; Fahrenkrug, Scott C

2009-03-01

The Tc1/mariner family of DNA transposons is widespread across fungal, plant and animal kingdoms, and thought to contribute to the evolution of their host genomes. To date, an active Tc1 transposon has not been identified within the native genome of a vertebrate. We demonstrate that Passport, a native transposon isolated from a fish (Pleuronectes platessa), is active in a variety of vertebrate cells. In transposition assays, we found that the Passport transposon system improved stable cellular transgenesis by 40-fold, has an apparent preference for insertion into genes, and is subject to overproduction inhibition like other Tc1 elements. Passport represents the first vertebrate Tc1 element described as both natively intact and functionally active, and given its restricted phylogenetic distribution, may be contemporaneously active. The Passport transposon system thus complements the available genetic tools for the manipulation of vertebrate genomes, and may provide a unique system for studying the infiltration of vertebrate genomes by Tc1 elements.

A New Method for Preparing Mesenchymal Stem Cells and Labeling with Ferumoxytol for Cell Tracking by MRI.

PubMed

Liu, Li; Tseng, Lanya; Ye, Qing; Wu, Yijen L; Bain, Daniel J; Ho, Chien

2016-05-18

Mesenchymal stem cells (MSCs) are among the major stem cells used for cell therapy and regenerative medicine. In-vivo cell-tracking by magnetic resonance imaging (MRI) is crucial for regenerative medicine, allowing verification that the transplanted cells reach the targeted sites. Cellular MRI combined with superparamagnetic iron-oxide (SPIO) contrast agents is an effective cell-tracking method. Here, we are reporting a new "bio-mimicry" method by making use of the "in-vivo environment" of MSCs to prepare native MSCs, so that (i) the phagocytic activity of cultured MSCs can be recovered and expanded MSCs can be ex-vivo labeled with Ferumoxytol, which is currently the only FDA approved SPIO nanoparticles for human use. Using our new method, 7-day cultured MSCs regain the capability to take up Ferumoxytol and exhibit an intracellular iron concentration of 2.50 ± 0.50 pg/MSC, comparable to that obtained by using Ferumoxytol-heparin-protamine nanocomplex; and (ii) cells can be re-sized to more native size, reducing from 32.0 ± 7.2 μm to 19.5 ± 5.2 μm. Our method can be very useful for expanding MSCs and labeling with Ferumoxytol, without the need for transfection agents and/or electroporation, allowing cell-tracking by MRI in both pre-clinical and clinical studies.

High-throughput Isolation and Characterization of Untagged Membrane Protein Complexes: Outer Membrane Complexes of Desulfovibrio vulgaris

PubMed Central

2012-01-01

Cell membranes represent the “front line” of cellular defense and the interface between a cell and its environment. To determine the range of proteins and protein complexes that are present in the cell membranes of a target organism, we have utilized a “tagless” process for the system-wide isolation and identification of native membrane protein complexes. As an initial subject for study, we have chosen the Gram-negative sulfate-reducing bacterium Desulfovibrio vulgaris. With this tagless methodology, we have identified about two-thirds of the outer membrane- associated proteins anticipated. Approximately three-fourths of these appear to form homomeric complexes. Statistical and machine-learning methods used to analyze data compiled over multiple experiments revealed networks of additional protein–protein interactions providing insight into heteromeric contacts made between proteins across this region of the cell. Taken together, these results establish a D. vulgaris outer membrane protein data set that will be essential for the detection and characterization of environment-driven changes in the outer membrane proteome and in the modeling of stress response pathways. The workflow utilized here should be effective for the global characterization of membrane protein complexes in a wide range of organisms. PMID:23098413

A Model of Successful Adaptation to Online Learning for College-Bound Native American High School Students

ERIC Educational Resources Information Center

Kaler, Collier Butler

2012-01-01

Purpose: The purpose of this paper is to examine the conditions for Native American high school students that result in successful adaptation to an online learning environment. Design/methodology/approach: In total, eight Native American students attending high schools located on Montana Indian reservations, and one urban city, were interviewed.…

The Native American Persistence in Higher Education: A Journey through Story to Identify the Family Support to Native American Graduates

ERIC Educational Resources Information Center

Bisbee, Yolanda J. Guzman

2013-01-01

This Indigenous Framed Research will utilize counter-storytelling through shared collaborator stories provided by Nez Perce Native American Graduates. The methodology is shaped by an Indigenous Framework as this form of research promotes and develops a culturally resonant environment for constructing, analyzing and sharing information. The…

Ethnoecology of Fire: An Experimental Approach in the Ohio Valley

Treesearch

Erin B. Hines; Jan Salick; Elaine Kennedy Sutherland; Todd F. Hutchinson; Steve Sutherland; Steve Sutherland

2000-01-01

Native Americans used fire to manipulate nature and directly benefit their survival. Certain plant species, many of which were useful to Native Americans as sources of food, fiber, dye, medicine, and game browse, are adapted to survive and even thrive in post-burn environments. Evidence suggests that Native Americans intentionally set fires to encourage growth and...

Applications of systems biology towards microbial fuel production.

PubMed

Gowen, Christopher M; Fong, Stephen S

2011-10-01

Harnessing the immense natural diversity of biological functions for economical production of fuel has enormous potential benefits. Inevitably, however, the native capabilities for any given organism must be modified to increase the productivity or efficiency of a biofuel bioprocess. From a broad perspective, the challenge is to sufficiently understand the details of cellular functionality to be able to prospectively predict and modify the cellular function of a microorganism. Recent advances in experimental and computational systems biology approaches can be used to better understand cellular level function and guide future experiments. With pressure to quickly develop viable, renewable biofuel processes a balance must be maintained between obtaining depth of biological knowledge and applying that knowledge. Copyright © 2011 Elsevier Ltd. All rights reserved.

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

Kleiner, J.B.; Amiel, D.; Harwood, F.L.

A rabbit model for anterior cruciate ligament (ACL) reconstruction using autogenous patellar tendon was utilized to study the early events of autograft cellular dynamics. Biochemical, autoradiographic, histological, and vascular injection techniques demonstrated that the native autograft cell population rapidly necroses. This repopulation occurs without a vascular contribution; cells entering the autograft are reliant upon synovial fluid nutrition.

Native Geosciences: Strengthening the Future Through Tribal Traditions

NASA Astrophysics Data System (ADS)

Bolman, J. R.; Quigley, I.; Douville, V.; Hollow Horn Bear, D.

2008-12-01

Native people have lived for millennia in distinct and unique ways in our natural sacred homelands and environments. Tribal cultures are the expression of deep understandings of geosciences shared through oral histories, language and ceremonies. Today, Native people as all people are living in a definite time of change. The developing awareness of "change" brings forth an immense opportunity to expand and elevate Native geosciences knowledge, specifically in the areas of earth, wind, fire and water. At the center of "change" is the need to balance the needs of the people with the needs of the environment. Native tradition and our inherent understanding of what is "sacred above is sacred below" is the foundation for an emerging multi-faceted approach to increasing the representation of Natives in geosciences. The approach is also a pathway to assist in Tribal language revitalization, connection of oral histories and ceremonies as well as building an intergenerational teaching/learning community. Humboldt State University, Sinte Gleska University and South Dakota School of Mines and Technology in partnership with Northern California (Hoopa, Yurok, & Karuk) and Great Plains (Lakota) Tribes have nurtured Native geosciences learning communities connected to Tribal Sacred Sites and natural resources. These sites include the Black Hills (Mato Paha, Mato Tiplia, Hinhan Kaga Paha, Mako Sica etc.), Klamath River (Ishkêesh), and Hoopa Valley (Natinixwe). Native geosciences learning is centered on the themes of earth, wind, fire and water and Native application of remote sensing technologies. Tribal Elders and Native geoscientists work collaboratively providing Native families in-field experiential intergenerational learning opportunities which invite participants to immerse themselves spiritually, intellectually, physically and emotionally in the experiences. Through this immersion and experience Native students and families strengthen the circle of our future Tribal communities and a return to traditional ways of supporting the development of our "story" or purpose for being. The opportunities include residential summer field experiences, interdisciplinary curriculums and development of Tribally-driven Native research experiences. The National Science Foundation, University of North Dakota's Northern Great Plains Center for People and the Environment, Upper Midwest Aerospace Consortium (UMAC), and Tribes have provided funding to support the development of Native geosciences. The presentation will focus on current projects: NSF OEDG "He Sapa Bloketu Woecun; Geosciences at the Heart of Everything That Is", NSF S-STEM "Scientific Leadership Scholars" and the NSF BPC "Coalition of American Indians in Computing". The expressed goal of future initiatives is to connect Tribal communities across the Midwest and West in developing a Native Geosciences Pathway. This pathway supports the identification and support of Tribal students with an interest or "story" connected to geosciences ensuring a future Native geosciences workforce.

Pepsinized cashew proteins are hypoallergenic and immunogenic and provide effective immunotherapy in mice with cashew allergy.

PubMed

Kulis, Mike; Macqueen, Ian; Li, Yifan; Guo, Rishu; Zhong, Xiao-Ping; Burks, A Wesley

2012-09-01

IgE-mediated allergic reactions to cashews and other nuts can trigger life-threatening anaphylaxis. Proactive therapies to decrease reaction severity do not exist. We aimed to determine the efficacy of pepsin-digested cashew proteins used as immunotherapy in a murine model of cashew allergy. Mice were sensitized to cashew and then underwent challenges with digested or native cashew allergens to assess the allergenicity of the protein preparations. Using native or pepsinized cashew proteins, mice underwent oral or intraperitoneal sensitization protocols to determine the immunogenic properties of the protein preparations. Finally, cashew-sensitized mice underwent an immunotherapy protocol with native or pepsinized cashew proteins and subsequent provocation challenges. Pepsinized cashew proteins elicited weaker allergic reactions than native cashew proteins but importantly retained the ability to stimulate cellular proliferation and cytokine production. Mice sensitized with pepsinized proteins reacted on challenge with native allergens, demonstrating that pepsinized allergens retain immunogenicity in vivo. Immunotherapy with pepsinized cashew allergens significantly decreased allergic symptoms and body temperature decrease relative to placebo after challenge with native and pepsinized proteins. Immunologic changes were comparable after immunotherapy with native or pepsinized allergens: T(H)2-type cytokine secretion from splenocytes was decreased, whereas specific IgG(1) and IgG(2a) levels were increased. Pepsinized cashew proteins are effective in treating cashew allergy in mice and appear to work through the same mechanisms as native protein immunotherapy. Copyright © 2012 American Academy of Allergy, Asthma & Immunology. Published by Mosby, Inc. All rights reserved.

The role thermal physiology plays in species invasion

PubMed Central

Kelley, Amanda L.

2014-01-01

The characterization of physiological phenotypes that may play a part in the establishment of non-native species can broaden our understanding about the ecology of species invasion. Here, an assessment was carried out by comparing the responses of invasive and native species to thermal stress. The goal was to identify physiological patterns that facilitate invasion success and to investigate whether these traits are widespread among invasive ectotherms. Four hypotheses were generated and tested using a review of the literature to determine whether they could be supported across taxonomically diverse invasive organisms. The four hypotheses are as follows: (i) broad geographical temperature tolerances (thermal width) confer a higher upper thermal tolerance threshold for invasive rather than native species; (ii) the upper thermal extreme experienced in nature is more highly correlated with upper thermal tolerance threshold for invasive vs. native animals; (iii) protein chaperone expression—a cellular mechanism that underlies an organism's thermal tolerance threshold—is greater in invasive organisms than in native ones; and (iv) acclimation to higher temperatures can promote a greater range of thermal tolerance for invasive compared with native species. Each hypothesis was supported by a meta-analysis of the invasive/thermal physiology literature, providing further evidence that physiology plays a substantial role in the establishment of invasive ectotherms. PMID:27293666

CN-GELFrEE - Clear Native Gel-eluted Liquid Fraction Entrapment Electrophoresis

PubMed Central

Skinner, Owen S.; Do Vale, Luis H. F.; Catherman, Adam D.; Havugimana, Pierre C.; Valle de Sousa, Marcelo; Domont, Gilberto B.; Kelleher, Neil L.; Compton, Philip D.

2016-01-01

Protein complexes perform an array of crucial cellular functions. Elucidating their non-covalent interactions and dynamics is paramount for understanding the role of complexes in biological systems. While the direct characterization of biomolecular assemblies has become increasingly important in recent years, native fractionation techniques that are compatible with downstream analysis techniques, including mass spectrometry, are necessary to further expand these studies. Nevertheless, the field lacks a high-throughput, wide-range, high-recovery separation method for native protein assemblies. Here, we present clear native gel-eluted liquid fraction entrapment electrophoresis (CN-GELFrEE), which is a novel separation modality for non-covalent protein assemblies. CN-GELFrEE separation performance was demonstrated by fractionating complexes extracted from mouse heart. Fractions were collected over 2 hr and displayed discrete bands ranging from ~30 to 500 kDa. A consistent pattern of increasing molecular weight bandwidths was observed, each ranging ~100 kDa. Further, subsequent reanalysis of native fractions via SDS-PAGE showed molecular-weight shifts consistent with the denaturation of protein complexes. Therefore, CN-GELFrEE was proved to offer the ability to perform high-resolution and high-recovery native separations on protein complexes from a large molecular weight range, providing fractions that are compatible with downstream protein analyses. PMID:26967310

Balancing Uplink and Downlink under Asymmetric Traffic Environments Using Distributed Receive Antennas

NASA Astrophysics Data System (ADS)

Sohn, Illsoo; Lee, Byong Ok; Lee, Kwang Bok

Recently, multimedia services are increasing with the widespread use of various wireless applications such as web browsers, real-time video, and interactive games, which results in traffic asymmetry between the uplink and downlink. Hence, time division duplex (TDD) systems which provide advantages in efficient bandwidth utilization under asymmetric traffic environments have become one of the most important issues in future mobile cellular systems. It is known that two types of intercell interference, referred to as crossed-slot interference, additionally arise in TDD systems; the performances of the uplink and downlink transmissions are degraded by BS-to-BS crossed-slot interference and MS-to-MS crossed-slot interference, respectively. The resulting performance unbalance between the uplink and downlink makes network deployment severely inefficient. Previous works have proposed intelligent time slot allocation algorithms to mitigate the crossed-slot interference problem. However, they require centralized control, which causes large signaling overhead in the network. In this paper, we propose to change the shape of the cellular structure itself. The conventional cellular structure is easily transformed into the proposed cellular structure with distributed receive antennas (DRAs). We set up statistical Markov chain traffic model and analyze the bit error performances of the conventional cellular structure and proposed cellular structure under asymmetric traffic environments. Numerical results show that the uplink and downlink performances of the proposed cellular structure become balanced with the proper number of DRAs and thus the proposed cellular structure is notably cost-effective in network deployment compared to the conventional cellular structure. As a result, extending the conventional cellular structure into the proposed cellular structure with DRAs is a remarkably cost-effective solution to support asymmetric traffic environments in future mobile cellular systems.

The Role of Tourism and Recreation in the Spread of Non-Native Species: A Systematic Review and Meta-Analysis

PubMed Central

Anderson, Lucy G.; Rocliffe, Steve; Haddaway, Neal R.; Dunn, Alison M.

2015-01-01

Managing the pathways by which non-native species are introduced and spread is considered the most effective way of preventing species invasions. Tourism and outdoor recreation involve the frequent congregation of people, vehicles and vessels from geographically diverse areas. They are therefore perceived to be major pathways for the movement of non-native species, and ones that will become increasingly important with the continued growth of these sectors. However, a global assessment of the relationship between tourism activities and the introduction of non-native species–particularly in freshwater and marine environments–is lacking. We conducted a systematic review and meta-analysis to determine the impact of tourism and outdoor recreation on non-native species in terrestrial, marine and freshwater environments. Our results provide quantitative evidence that the abundance and richness of non-native species are significantly higher in sites where tourist activities take place than in control sites. The pattern was consistent across terrestrial, freshwater and marine environments; across a variety of vectors (e.g. horses, hikers, yachts); and across a range of taxonomic groups. These results highlight the need for widespread biosecurity interventions to prevent the inadvertent introduction of invasive non-native species (INNS) as the tourism and outdoor recreation sectors grow. PMID:26485300

Smooth muscle cell seeding of decellularized scaffolds: the importance of bioreactor preconditioning to development of a more native architecture for tissue-engineered blood vessels.

PubMed

Yazdani, Saami K; Watts, Benjamin; Machingal, Masood; Jarajapu, Yagna P R; Van Dyke, Mark E; Christ, George J

2009-04-01

Vascular smooth muscle cells (VSMCs) impart important functional characteristics in the native artery and, therefore, should logically be incorporated in the development of tissue-engineered blood vessels. However, the native architecture and low porosity of naturally derived biomaterials (i.e., decellularized vessels) have impeded efforts to seed and incorporate a VSMC layer in tissue-engineered blood vessels. To this end, the goal of this study was to develop improved methods for seeding, proliferation, and maturation of VSMCs on decellularized porcine carotid arteries. Decellularized vessels were prepared in the absence and presence of the adventitial layer, and statically seeded with a pipette containing a suspension of rat aortic VSMCs. After cell seeding, recellularized engineered vessels were placed in a custom bioreactor system for 1-2 weeks to enhance cellular proliferation, alignment, and maturation. Initial attachment of VSMCs was dramatically enhanced by removing the adventitial layer of the decellularized porcine artery. Moreover, cyclic bioreactor conditioning (i.e., flow and pressure) resulted in increased VSMC proliferation and accelerated formation of a muscularized medial layer in the absence of the adventitial layer during the first week of preconditioning. Fura-2-based digital imaging microscopy revealed marked and reproducible depolarization-induced calcium mobilization after bioreactor preconditioning in the absence, but not in the presence, of the adventitia. The major finding of this investigation is that bioreactor preconditioning accelerates the formation of a significant muscular layer on decellularized scaffolds, in particular on adventitia-denuded scaffolds. Further, the VSMC layer of bioreactor-preconditioned vessels was capable of mobilizing calcium in response to cellular depolarization. These findings represent an important first step toward the development of tissue-engineered vascular grafts that more closely mimic native vasculature.

Spatial reconstruction of single-cell gene expression

PubMed Central

Satija, Rahul; Farrell, Jeffrey A.; Gennert, David; Schier, Alexander F.; Regev, Aviv

2015-01-01

Spatial localization is a key determinant of cellular fate and behavior, but spatial RNA assays traditionally rely on staining for a limited number of RNA species. In contrast, single-cell RNA-seq allows for deep profiling of cellular gene expression, but established methods separate cells from their native spatial context. Here we present Seurat, a computational strategy to infer cellular localization by integrating single-cell RNA-seq data with in situ RNA patterns. We applied Seurat to spatially map 851 single cells from dissociated zebrafish (Danio rerio) embryos, inferring a transcriptome-wide map of spatial patterning. We confirmed Seurat’s accuracy using several experimental approaches, and used it to identify a set of archetypal expression patterns and spatial markers. Additionally, Seurat correctly localizes rare subpopulations, accurately mapping both spatially restricted and scattered groups. Seurat will be applicable to mapping cellular localization within complex patterned tissues in diverse systems. PMID:25867923

Cellular therapy in bone-tendon interface regeneration

PubMed Central

Rothrauff, Benjamin B; Tuan, Rocky S

2014-01-01

The intrasynovial bone-tendon interface is a gradual transition from soft tissue to bone, with two intervening zones of uncalcified and calcified fibrocartilage. Following injury, the native anatomy is not restored, resulting in inferior mechanical properties and an increased risk of re-injury. Recent in vivo studies provide evidence of improved healing when surgical repair of the bone-tendon interface is augmented with cells capable of undergoing chondrogenesis. In particular, cellular therapy in bone-tendon healing can promote fibrocartilage formation and associated improvements in mechanical properties. Despite these promising results in animal models, cellular therapy in human patients remains largely unexplored. This review highlights the development and structure-function relationship of normal bone-tendon insertions. The natural healing response to injury is discussed, with subsequent review of recent research on cellular approaches for improved healing. Finally, opportunities for translating in vivo findings into clinical practice are identified. PMID:24326955

Cellular water distribution, transport, and its investigation methods for plant-based food material.

PubMed

Khan, Md Imran H; Karim, M A

2017-09-01

Heterogeneous and hygroscopic characteristics of plant-based food material make it complex in structure, and therefore water distribution in its different cellular environments is very complex. There are three different cellular environments, namely the intercellular environment, the intracellular environment, and the cell wall environment inside the food structure. According to the bonding strength, intracellular water is defined as loosely bound water, cell wall water is categorized as strongly bound water, and intercellular water is known as free water (FW). During food drying, optimization of the heat and mass transfer process is crucial for the energy efficiency of the process and the quality of the product. For optimizing heat and mass transfer during food processing, understanding these three types of waters (strongly bound, loosely bound, and free water) in plant-based food material is essential. However, there are few studies that investigate cellular level water distribution and transport. As there is no direct method for determining the cellular level water distributions, various indirect methods have been applied to investigate the cellular level water distribution, and there is, as yet, no consensus on the appropriate method for measuring cellular level water in plant-based food material. Therefore, the main aim of this paper is to present a comprehensive review on the available methods to investigate the cellular level water, the characteristics of water at different cellular levels and its transport mechanism during drying. The effect of bound water transport on quality of food product is also discussed. This review article presents a comparative study of different methods that can be applied to investigate cellular water such as nuclear magnetic resonance (NMR), bioelectric impedance analysis (BIA), differential scanning calorimetry (DSC), and dilatometry. The article closes with a discussion of current challenges to investigating cellular water. Copyright © 2017 Elsevier Ltd. All rights reserved.

Native Geosciences: Pathways to Traditional Knowledge in Modern Research and Education

NASA Astrophysics Data System (ADS)

Bolman, J. R.

2010-12-01

Native people have lived for millennia in distinct and unique ways in our natural sacred homelands and environments. Tribal cultures are the expression of deep understandings of geosciences shared through oral histories, language, traditional practices and ceremonies. Today, Native people as all people are living in a definite time of change. The developing awareness of "change" brings forth an immense opportunity to expand, elevate and incorporate Traditional Native geosciences knowledge into modern research and education to expand understandings for all learners. At the center of "change" is the need to balance the needs of the people with the needs of the environment. Native traditions and our inherent understanding of what is "sacred above is sacred below" is the foundation for a multi-faceted approach for increasing the representation of Natives in geosciences. The approach is centered on the incorporation of traditional knowledge into modern research/education. The approach is also a pathway to assist in Tribal language revitalization, connection of oral histories and ceremonies to place and building an intergenerational teaching/learning community. Humboldt State University, Sinte Gleska University and Tribes in Northern California (Hoopa, Yurok, & Karuk) and Great Plains (Lakota) Tribes have nurtured Native geosciences learning and research communities connected to Tribal Sacred Sites and natural resources. Native geoscience learning is centered on the themes of earth, wind, fire and water and the Native application of remote sensing technologies. Tribal Elders and Native geoscientists work collaboratively providing Native families in-field experiential intergenerational learning opportunities which invite participants to immerse themselves spiritually, intellectually, physically and emotionally in the experiences. Through this immersion and experience Native students and families strengthen the circle of our future Tribal communities and a return to traditional ways of supporting the development of our "story" or purpose for being. The opportunities include residential summer field experiences, interdisciplinary curriculums and development of Tribally-driven Native research/education experiences.

High water-use efficiency and growth contribute to success of non-native Erodium cicutarium in a Sonoran Desert winter annual community.

PubMed

Kimball, Sarah; Gremer, Jennifer R; Barron-Gafford, Greg A; Angert, Amy L; Huxman, Travis E; Venable, D Lawrence

2014-01-01

The success of non-native, invasive species may be due to release from natural enemies, superior competitive abilities, or both. In the Sonoran Desert, Erodium cicutarium has increased in abundance over the last 30 years. While native species in this flora exhibit a strong among-species trade-off between relative growth rate and water-use efficiency, E. cicutarium seems to have a higher relative growth rate for its water-use efficiency value relative to the pattern across native species. This novel trait combination could provide the non-native species with a competitive advantage in this water-limited environment. To test the hypothesis that E. cicutarium is able to achieve high growth rates due to release from native herbivores, we compared the effects of herbivory on E. cicutarium and its native congener, Erodium texanum. We also compared these two species across a range of environmental conditions, both in a common garden and in two distinct seasons in the field, using growth analysis, isotopic compositions and leaf-level gas exchange. Additionally, we compared the competitive abilities of the two Erodium species in a greenhouse experiment. We found no evidence of herbivory to either species. Physiological measurements in a common environment revealed that E. cicutarium was able to achieve high growth rates while simultaneously controlling leaf-level water loss. Non-native E. cicutarium responded to favourable conditions in the field with greater specific leaf area and leaf area ratio than native E. texanum. The non-native Erodium was a stronger competitor than its native congener in a greenhouse competition experiment. The ability to maintain relatively higher values of water-use efficiency:relative growth rate in comparison to the native flora may be what enables E. cictarium to outcompete native species in both wet and dry years, resulting in an increase in abundance in the highly variable Sonoran Desert.

Significant Impact of Environment Regarding Eligibility of Native American and Alaskan Native Students for ESEA Title VII Regulations.

ERIC Educational Resources Information Center

Travis, Michael

Early Russian religious and educational influences on the 20 various Alaskan Native languages are described, followed by those of American origin in schools and religious groups after the American purchase in 1867, all of which show the development of diglossia and language shifts. The present dual educational system, which includes state schools…

Teacher Training Institute for Native American Bilingual/Bicultural Education. Phase I (S.U.N.Y. Brockport, Summer, 1978).

ERIC Educational Resources Information Center

New York State Education Dept., Albany. Office of Cultural Education.

A two week teacher training institute for Native American bilingual/bicultural education was held in the summer of 1978 at Brockport State University of New York. Educational Programs for bilingual and bicultural learning environments for Native American students had been hampered by insufficient teachers and teacher trainers and the use of…

An Investigation of Native and Nonnative English Speakers' Levels of Written Syntactic Complexity in Asynchronous Online Discussions

ERIC Educational Resources Information Center

Mancilla, Rae L.; Polat, Nihat; Akcay, Ahmet O.

2017-01-01

This manuscript reports on a corpus-based comparison of native and nonnative graduate students' language production in an asynchronous learning environment. Using 486 discussion board postings from a five-year period (2009-2013), we analyzed the extent to which native and nonnative university students' writing differed in 10 measures of syntactic…

Non-native plant invasion along elevation and canopy closure gradients in a Middle Rocky Mountain ecosystem

Treesearch

Joshua P. Averett; Bruce McCune; Catherine G. Parks; Bridgett J. Naylor; Tim DelCurto; Ricardo Mata-Gonz??lez; RunGuo Zang

2016-01-01

Mountain environments are currently among the ecosystems least invaded by non-native species; however, mountains are increasingly under threat of non-native plant invasion. The slow pace of exotic plant invasions in mountain ecosystems is likely due to a combination of low anthropogenic disturbances, low propagule supply, and extreme/steep environmental gradients. The...

Socioeconomic Status, Parental Investments, and the Cognitive and Behavioral Outcomes of Low-Income Children from Immigrant and Native Households

ERIC Educational Resources Information Center

Mistry, R.S.; Biesanz, J.C.; Chien, N.; Howes, C.; Benner, A.D.

2008-01-01

The current study examines the effects of socioeconomic status (SES) on preschool children's cognitive and behavioral outcomes and if these relations are mediated by the quality of children's home environment and moderated by family nativity status. Data come from 1459 low-income families (n=257 and 1202 immigrant and native families,…

Socio spatial adaptation as a resilience form of native unplanned settlement in confrontation with new planned settlement development pressure (case study: enclave native settlement in Serpong, Tangerang)

NASA Astrophysics Data System (ADS)

Ischak, Mohammad; Setioko, Bambang; Nurgandarum, Dedes

2017-12-01

Urban growth refers to expansion of a metropolitan into sub urban areas as the surrounding environment, with no exception of Jakarta city due to limited availability and high price of land within the city. The city of Jakarta, as a metropolitan, carries of expansion in its surrounding environment including Tangerang. Privat developers may an important role in this urban growth through their large scale of new settlement development project. The formation of establishment of enclave native unplanned sub urban settlement scattered within planned new settlement in Tangerang is to be an consequence of Jakarta urban growth. This fenomena could be comprehended as a form of resilience native settlement in confrontation with the new planned settlement pressure. The aim of this research, presented in this paper is to understand the socio-spatial concept of those enclave native settlement as an adaptation form to the new planned settlement pressure. Through descriptive qualitative research method, with indepth interview as a main research instrument, this research could depict or uncover the facts that there are various form of socio-spatial adaptation as the main theme of resilience native suburban settlement formation.

Maynard Participation in Alaska Forum on the Environment Panel Discussion on Increasing Input to the US National Climate Assessment (NCA) and the Intergovernmental Panel on Climate Change (IPCC) Processes from Alaska, with Emphasis on Indigenous Peoples Issues

NASA Technical Reports Server (NTRS)

Maynard, Nancy G.

2012-01-01

Dr. Nancy Maynard was invited by the Alaska Forum on the Environment to participate in a Panel Discussion to discuss (1) background about what the US NCA and International IPCC assessments are, (2) the impact the assessments have on policy-making, (3) the process for participation in both assessments, (4) how we can increase participation by Indigenous Peoples such as Native Americans and Alaska Natives, (5) How we can increase historical and current impacts input from Native communities through stories, oral history, "grey" literature, etc. The session will be chaired by Dr. Bull Bennett, a cochair of the US NCA's chapter on "Native and Tribal Lands and Resources" and Dr. Maynard is the other co-chair of that chapter and they will discuss the latest activities under the NCA process relevant to Native Americans and Alaska Natives. Dr. Maynard is also a Lead Author of the "Polar Regions" chapter of the IPCC WG2 (5th Assessment) and she will describes some of the latest approaches by the IPCC to entrain more Indigenous peoples into the IPCC process.

Aggregation of model amyloid insulin protein in crowding environments and under ac-electric fields

NASA Astrophysics Data System (ADS)

Zheng, Zhongli; Jing, Benxin; Murray, Brian; Sorci, Mirco; Belfort, Georges; Zhu, Y.

2013-03-01

In vitro experiments have been widely used to characterize the misfolding/unfolding pathway characteristic of amylodogenic proteins. Conversion from natively folded amyloidogenic proteins to oligomers via nucleation is the accepted path to fibril formation upon heating over a certain lag time period. In this work, we investigate the effect of crowing environment and external electric fields on the pathway and kinetics of insulin, a well-established amyloid model protein by single fluorescence spectroscopy and imaging. With added co-solutes, such as glycerol and polyvinylpyrrolidone (PVP), to mimic the cellular crowding environments, we have observed that the lag time can be significantly prolonged. The lag time increases with increasing co-solute concentration, yet showing little dependence on solution viscosity. Conversely, applied ac-electric fields can considerably shorten the lag timewhen a critical ac-voltage is exceeded. The strong dependence of lag time on ac-frequency over a narrow range of 500 Hz-5 kHz indicates the effect of ac-electroosmosis on the diffusion controlled process of insulin nucleation. Yet, no conformational structure is detected with insulin under applied ac-fields, suggesting the equivalence of ac-polarization to the conventional thermal activation process for insulin aggregation. These finding suggest that at least the aggregation kinetics of insulin can be altered by local solution condition or external stimuli, which gives new insight to the treatment of amyloid related diseases.

Invasive Acer negundo outperforms native species in non-limiting resource environments due to its higher phenotypic plasticity

PubMed Central

2011-01-01

Background To identify the determinants of invasiveness, comparisons of traits of invasive and native species are commonly performed. Invasiveness is generally linked to higher values of reproductive, physiological and growth-related traits of the invasives relative to the natives in the introduced range. Phenotypic plasticity of these traits has also been cited to increase the success of invasive species but has been little studied in invasive tree species. In a greenhouse experiment, we compared ecophysiological traits between an invasive species to Europe, Acer negundo, and early- and late-successional co-occurring native species, under different light, nutrient availability and disturbance regimes. We also compared species of the same species groups in situ, in riparian forests. Results Under non-limiting resources, A. negundo seedlings showed higher growth rates than the native species. However, A. negundo displayed equivalent or lower photosynthetic capacities and nitrogen content per unit leaf area compared to the native species; these findings were observed both on the seedlings in the greenhouse experiment and on adult trees in situ. These physiological traits were mostly conservative along the different light, nutrient and disturbance environments. Overall, under non-limiting light and nutrient conditions, specific leaf area and total leaf area of A. negundo were substantially larger. The invasive species presented a higher plasticity in allocation to foliage and therefore in growth with increasing nutrient and light availability relative to the native species. Conclusions The higher level of plasticity of the invasive species in foliage allocation in response to light and nutrient availability induced a better growth in non-limiting resource environments. These results give us more elements on the invasiveness of A. negundo and suggest that such behaviour could explain the ability of A. negundo to outperform native tree species, contributes to its spread in European resource-rich riparian forests and impedes its establishment under closed-canopy hardwood forests. PMID:22115342

Bacterial Reaction Centers Purified with Styrene Maleic Acid Copolymer Retain Native Membrane Functional Properties and Display Enhanced Stability**

PubMed Central

Swainsbury, David J K; Scheidelaar, Stefan; van Grondelle, Rienk; Killian, J Antoinette; Jones, Michael R

2014-01-01

Integral membrane proteins often present daunting challenges for biophysical characterization, a fundamental issue being how to select a surfactant that will optimally preserve the individual structure and functional properties of a given membrane protein. Bacterial reaction centers offer a rare opportunity to compare the properties of an integral membrane protein in different artificial lipid/surfactant environments with those in the native bilayer. Here, we demonstrate that reaction centers purified using a styrene maleic acid copolymer remain associated with a complement of native lipids and do not display the modified functional properties that typically result from detergent solubilization. Direct comparisons show that reaction centers are more stable in this copolymer/lipid environment than in a detergent micelle or even in the native membrane, suggesting a promising new route to exploitation of such photovoltaic integral membrane proteins in device applications. PMID:25212490

Effects of a detergent micelle environment on P-glycoprotein (ABCB1)-ligand interactions

PubMed Central

Shukla, Suneet; Abel, Biebele; Chufan, Eduardo E.; Ambudkar, Suresh V.

2017-01-01

P-glycoprotein (P-gp) is a multidrug transporter that uses energy from ATP hydrolysis to export many structurally dissimilar hydrophobic and amphipathic compounds, including anticancer drugs from cells. Several structural studies on purified P-gp have been reported, but only limited and sometimes conflicting information is available on ligand interactions with the isolated transporter in a dodecyl-maltoside detergent environment. In this report we compared the biochemical properties of P-gp in native membranes, detergent micelles, and when reconstituted in artificial membranes. We found that the modulators zosuquidar, tariquidar, and elacridar stimulated the ATPase activity of purified human or mouse P-gp in a detergent micelle environment. In contrast, these drugs inhibited ATPase activity in native membranes or in proteoliposomes, with IC50 values in the 10–40 nm range. Similarly, a 30–150-fold decrease in the apparent affinity for verapamil and cyclic peptide inhibitor QZ59-SSS was observed in detergent micelles compared with native or artificial membranes. Together, these findings demonstrate that the high-affinity site is inaccessible because of either a conformational change or binding of detergent at the binding site in a detergent micelle environment. The ligands bind to a low-affinity site, resulting in altered modulation of P-gp ATPase activity. We, therefore, recommend studying structural and functional aspects of ligand interactions with purified P-gp and other ATP-binding cassette transporters that transport amphipathic or hydrophobic substrates in a detergent-free native or artificial membrane environment. PMID:28283574

Relationships between the health of Alaska Native communities and our environment -- phase 1, exploring and communicating

USGS Publications Warehouse

Smith, Durelle

2013-01-01

Alaska Natives depend on local natural resources for nutritional and, for many, spiritual health. As a result, public health in Alaska is strongly influenced by the relationship between people and their surrounding physical, chemical, and biological environments. Alaska is vast with diverse wildlife and plant communities that are valued as subsistence foods (fig. 1). These resources are supported by equally diverse ecosystems and their underpinning landforms and geologies. The U.S. Geological Survey (USGS) is attempting to integrate physical, chemical, and biological information to better describe current (2013) environments and project scenarios for the future. Integrating ecological data into the public health dialogue is challenging for the more than 280 rural communities of Alaska. This fact sheet reviews a recent USGS effort, the Geographic Information System (GIS) Native Health Project, to better incorporate scientific information into such dialogue.

Antiprion activity of DB772 and related monothiophene-and furan-based analogs in a persistently infected ovine microglia culture system

USDA-ARS?s Scientific Manuscript database

The transmissible spongiform encephalopathies are fatal neurodegenerative disorders characterized by the misfolding of the native cellular prion protein (PrP-C) into the accumulating, disease-associated isoform (PrP-Sc). Despite extensive research into the inhibition of prion accumulation, no effect...

Non-lethal effects of an invasive species in the marine environment: the importance of early life-history stages.

PubMed

Rius, Marc; Turon, Xavier; Marshall, Dustin J

2009-04-01

Studies examining the effects of invasive species have focussed traditionally on the direct/lethal effects of the invasive on the native community but there is a growing recognition that invasive species may also have non-lethal effects. In terrestrial systems, non-lethal effects of invasive species can disrupt early life-history phases (such as fertilisation, dispersal and subsequent establishment) of native species, but in the marine environment most studies focus on adult rather than early life-history stages. Here, we examine the potential for an introduced sessile marine invertebrate (Styela plicata) to exert both lethal and non-lethal effects on a native species (Microcosmus squamiger) across multiple early life-history stages. We determined whether sperm from the invasive species interfered with the fertilisation of eggs from the native species and found no effect. However, we did find strong effects of the invasive species on the post-fertilisation performance of the native species. The invasive species inhibited the settlement of native larvae and, in the field, the presence of the invasive species was associated with a ten-fold increase in the post-settlement mortality of the native species, as well as an initial reduction of growth in the native. Our results suggest that larvae of the native species avoid settling near the invasive species due to reduced post-settlement survival in its presence. Overall, we found that invasive species can have complex and pervasive effects (both lethal and non-lethal) across the early life-history stages of the native species, which are likely to result in its displacement and to facilitate further invasion.

UV Screening in Native and Non-native Plant Species in the Tropical Alpine: Implications for Climate Change-Driven Migration of Species to Higher Elevations.

PubMed

Barnes, Paul W; Ryel, Ronald J; Flint, Stephan D

2017-01-01

Ongoing changes in Earth's climate are shifting the elevation ranges of many plant species with non-native species often experiencing greater expansion into higher elevations than native species. These climate change-induced shifts in distributions inevitably expose plants to novel biotic and abiotic environments, including altered solar ultraviolet (UV)-B (280-315 nm) radiation regimes. Do the greater migration potentials of non-native species into higher elevations imply that they have more effective UV-protective mechanisms than native species? In this study, we surveyed leaf epidermal UV-A transmittance (T UV A ) in a diversity of plant species representing different growth forms to test whether native and non-native species growing above 2800 m elevation on Mauna Kea, Hawaii differed in their UV screening capabilities. We further compared the degree to which T UV A varied along an elevation gradient in the native shrub Vaccinium reticulatum and the introduced forb Verbascum thapsus to evaluate whether these species differed in their abilities to adjust their levels of UV screening in response to elevation changes in UV-B. For plants growing in the Mauna Kea alpine/upper subalpine, we found that adaxial T UV A , measured with a UVA-PAM fluorometer, varied significantly among species but did not differ between native (mean = 6.0%; n = 8) and non-native (mean = 5.8%; n = 11) species. When data were pooled across native and non-native taxa, we also found no significant effect of growth form on T UV A , though woody plants (shrubs and trees) were represented solely by native species whereas herbaceous growth forms (grasses and forbs) were dominated by non-native species. Along an elevation gradient spanning 2600-3800 m, T UV A was variable (mean range = 6.0-11.2%) and strongly correlated with elevation and relative biologically effective UV-B in the exotic V. thapsus ; however, T UV A was consistently low (3%) and did not vary with elevation in the native V. reticulatum . Results indicate that high levels of UV protection occur in both native and non-native species in this high UV-B tropical alpine environment, and that flexibility in UV screening is a mechanism employed by some, but not all species to cope with varying solar UV-B exposures along elevation gradients.

UV Screening in Native and Non-native Plant Species in the Tropical Alpine: Implications for Climate Change-Driven Migration of Species to Higher Elevations

PubMed Central

Barnes, Paul W.; Ryel, Ronald J.; Flint, Stephan D.

2017-01-01

Ongoing changes in Earth’s climate are shifting the elevation ranges of many plant species with non-native species often experiencing greater expansion into higher elevations than native species. These climate change-induced shifts in distributions inevitably expose plants to novel biotic and abiotic environments, including altered solar ultraviolet (UV)-B (280–315 nm) radiation regimes. Do the greater migration potentials of non-native species into higher elevations imply that they have more effective UV-protective mechanisms than native species? In this study, we surveyed leaf epidermal UV-A transmittance (TUV A) in a diversity of plant species representing different growth forms to test whether native and non-native species growing above 2800 m elevation on Mauna Kea, Hawaii differed in their UV screening capabilities. We further compared the degree to which TUV A varied along an elevation gradient in the native shrub Vaccinium reticulatum and the introduced forb Verbascum thapsus to evaluate whether these species differed in their abilities to adjust their levels of UV screening in response to elevation changes in UV-B. For plants growing in the Mauna Kea alpine/upper subalpine, we found that adaxial TUV A, measured with a UVA-PAM fluorometer, varied significantly among species but did not differ between native (mean = 6.0%; n = 8) and non-native (mean = 5.8%; n = 11) species. When data were pooled across native and non-native taxa, we also found no significant effect of growth form on TUV A, though woody plants (shrubs and trees) were represented solely by native species whereas herbaceous growth forms (grasses and forbs) were dominated by non-native species. Along an elevation gradient spanning 2600–3800 m, TUV A was variable (mean range = 6.0–11.2%) and strongly correlated with elevation and relative biologically effective UV-B in the exotic V. thapsus; however, TUV A was consistently low (3%) and did not vary with elevation in the native V. reticulatum. Results indicate that high levels of UV protection occur in both native and non-native species in this high UV-B tropical alpine environment, and that flexibility in UV screening is a mechanism employed by some, but not all species to cope with varying solar UV-B exposures along elevation gradients. PMID:28878792

Fluid flow in the osteocyte mechanical environment: a fluid-structure interaction approach.

PubMed

Verbruggen, Stefaan W; Vaughan, Ted J; McNamara, Laoise M

2014-01-01

Osteocytes are believed to be the primary sensor of mechanical stimuli in bone, which orchestrate osteoblasts and osteoclasts to adapt bone structure and composition to meet physiological loading demands. Experimental studies to quantify the mechanical environment surrounding bone cells are challenging, and as such, computational and theoretical approaches have modelled either the solid or fluid environment of osteocytes to predict how these cells are stimulated in vivo. Osteocytes are an elastic cellular structure that deforms in response to the external fluid flow imposed by mechanical loading. This represents a most challenging multi-physics problem in which fluid and solid domains interact, and as such, no previous study has accounted for this complex behaviour. The objective of this study is to employ fluid-structure interaction (FSI) modelling to investigate the complex mechanical environment of osteocytes in vivo. Fluorescent staining of osteocytes was performed in order to visualise their native environment and develop geometrically accurate models of the osteocyte in vivo. By simulating loading levels representative of vigorous physiological activity ([Formula: see text] compression and 300 Pa pressure gradient), we predict average interstitial fluid velocities [Formula: see text] and average maximum shear stresses [Formula: see text] surrounding osteocytes in vivo. Interestingly, these values occur in the canaliculi around the osteocyte cell processes and are within the range of stimuli known to stimulate osteogenic responses by osteoblastic cells in vitro. Significantly our results suggest that the greatest mechanical stimulation of the osteocyte occurs in the cell processes, which, cell culture studies have indicated, is the most mechanosensitive area of the cell. These are the first computational FSI models to simulate the complex multi-physics mechanical environment of osteocyte in vivo and provide a deeper understanding of bone mechanobiology.

In Situ Target Engagement Studies in Adherent Cells.

PubMed

Axelsson, Hanna; Almqvist, Helena; Otrocka, Magdalena; Vallin, Michaela; Lundqvist, Sara; Hansson, Pia; Karlsson, Ulla; Lundbäck, Thomas; Seashore-Ludlow, Brinton

2018-04-20

A prerequisite for successful drugs is effective binding of the desired target protein in the complex environment of a living system. Drug-target engagement has typically been difficult to monitor in physiologically relevant models, and with current methods, especially, while maintaining spatial information. One recent technique for quantifying drug-target engagement is the cellular thermal shift assay (CETSA), in which ligand-induced protein stabilization is measured after a heat challenge. Here, we describe a CETSA protocol in live A431 cells for p38α (MAPK14), where remaining soluble protein is detected in situ, using high-content imaging in 384-well, microtiter plates. We validate this assay concept using a number of known p38α inhibitors and further demonstrate the potential of this technology for chemical probe and drug discovery purposes by performing a small pilot screen for novel p38α binders. Importantly, this protocol creates a workflow that is amenable to adherent cells in their native state and yields spatially resolved target engagement information measurable at the single-cell level.

Sorption Capacity Measurement of Chlorella Vulgaris and Scenedesmus Acutus to Remove Chromium from Tannery Waste Water

NASA Astrophysics Data System (ADS)

Ardila, Liliana; Godoy, Rubén; Montenegro, Luis

2017-08-01

Tanning process is a polluting activity due to the release of toxic agents into the environment. One of the most important of those toxic chemicals is chromium. Different alternatives have been proposed for the removal of this metal from tanning waste water which include the optimization of the productive processes, physicochemical and biochemical waste water treatment. In this study, the biological adsorption process of trivalent chromium was carried out in synthetic water and tannery waste water through two types of native green microalgae, called Chlorella vulgaris and Scenedesmus acutus in Free State and immobilized in PVA state. This, considering that cellular wall of microalgae has functional groups like amines and carboxyl that might bind with trivalent chromium. Statistical significance of variables as pH temperature, chromium and algae concentrations was evaluated just like bio sorption capacity of different types of water and kind of bioadsorbent was calculated to determine if this process is a competitive solution comparing to other heavy metal removal processes.

Next-generation RNA-based fluorescent biosensors enable anaerobic detection of cyclic di-GMP

PubMed Central

Wang, Xin C.; Wilson, Stephen C.; Hammond, Ming C.

2016-01-01

Bacteria occupy a diverse set of environmental niches with differing oxygen availability. Anaerobic environments such as mammalian digestive tracts and industrial reactors harbor an abundance of both obligate and facultative anaerobes, many of which play significant roles in human health and biomanufacturing. Studying bacterial function under partial or fully anaerobic conditions, however, is challenging given the paucity of suitable live-cell imaging tools. Here, we introduce a series of RNA-based fluorescent biosensors that respond selectively to cyclic di-GMP, an intracellular bacterial second messenger that controls cellular motility and biofilm formation. We demonstrate the utility of these biosensors in vivo under both aerobic and anaerobic conditions, and we show that biosensor expression does not interfere with the native motility phenotype. Together, our results attest to the effectiveness and versatility of RNA-based fluorescent biosensors, priming further development and application of these and other analogous sensors to study host–microbial and microbial–microbial interactions through small molecule signals. PMID:27382070

Nanoscale visualization and characterization of Myxococcus xanthus cells with atomic force microscopy

PubMed Central

Pelling, Andrew E.; Li, Yinuo; Shi, Wenyuan; Gimzewski, James K.

2005-01-01

Multicellular microbial communities are the predominant form of existence for microorganisms in nature. As one of the most primitive social organisms, Myxococcus xanthus has been an ideal model bacterium for studying intercellular interaction and multicellular organization. Through previous genetic and EM studies, various extracellular appendages and matrix components have been found to be involved in the social behavior of M. xanthus, but none of them was directly visualized and analyzed under native conditions. Here, we used atomic force microscopy (AFM) imaging and in vivo force spectroscopy to characterize these cellular structures under native conditions. AFM imaging revealed morphological details on the extracellular ultrastructures at an unprecedented resolution, and in vivo force spectroscopy of live cells in fluid allowed us to nanomechanically characterize extracellular polymeric substances. The findings provide the basis for AFM as a useful tool for investigating microbial-surface ultrastructures and nanomechanical properties under native conditions. PMID:15840722

Cell-to-cell communication and cellular environment alter the somatostatin status of delta cells

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

Kelly, Catriona, E-mail: catriona.kelly@qub.ac.uk; Flatt, Peter R.; McClenaghan, Neville H.

2010-08-20

Research highlights: {yields} TGP52 cells display enhanced functionality in pseudoislet form. {yields} Somatostatin content was reduced, but secretion increased in high glucose conditions. {yields} Cellular interactions and environment alter the somatostatin status of TGP52 cells. -- Abstract: Introduction: Somatostatin, released from pancreatic delta cells, is a potent paracrine inhibitor of insulin and glucagon secretion. Islet cellular interactions and glucose homeostasis are essential to maintain normal patterns of insulin secretion. However, the importance of cell-to-cell communication and cellular environment in the regulation of somatostatin release remains unclear. Methods: This study employed the somatostatin-secreting TGP52 cell line maintained in DMEM:F12 (17.5 mMmore » glucose) or DMEM (25 mM glucose) culture media. The effect of pseudoislet formation and culture medium on somatostatin content and release in response to a variety of stimuli was measured by somatostatin EIA. In addition, the effect of pseudoislet formation on cellular viability (MTT and LDH assays) and proliferation (BrdU ELISA) was determined. Results: TGP52 cells readily formed pseudoislets and showed enhanced functionality in three-dimensional form with increased E-cadherin expression irrespective of the culture environment used. However, culture in DMEM decreased cellular somatostatin content (P < 0.01) and increased somatostatin secretion in response to a variety of stimuli including arginine, calcium and PMA (P < 0.001) when compared with cells grown in DMEM:F12. Configuration of TGP52 cells as pseudoislets reduced the proliferative rate and increased cellular cytotoxicity irrespective of culture medium used. Conclusions: Somatostatin secretion is greatly facilitated by cell-to-cell interactions and E-cadherin expression. Cellular environment and extracellular glucose also significantly influence the function of delta cells.« less

The Role of Auxiliary Subunits for the Functional Diversity of Voltage-Gated Calcium Channels

PubMed Central

Campiglio, Marta; Flucher, Bernhard E

2015-01-01

Voltage-gated calcium channels (VGCCs) represent the sole mechanism to convert membrane depolarization into cellular functions like secretion, contraction, or gene regulation. VGCCs consist of a pore-forming α1 subunit and several auxiliary channel subunits. These subunits come in multiple isoforms and splice-variants giving rise to a stunning molecular diversity of possible subunit combinations. It is generally believed that specific auxiliary subunits differentially regulate the channels and thereby contribute to the great functional diversity of VGCCs. If auxiliary subunits can associate and dissociate from pre-existing channel complexes, this would allow dynamic regulation of channel properties. However, most auxiliary subunits modulate current properties very similarly, and proof that any cellular calcium channel function is indeed modulated by the physiological exchange of auxiliary subunits is still lacking. In this review we summarize available information supporting a differential modulation of calcium channel functions by exchange of auxiliary subunits, as well as experimental evidence in support of alternative functions of the auxiliary subunits. At the heart of the discussion is the concept that, in their native environment, VGCCs function in the context of macromolecular signaling complexes and that the auxiliary subunits help to orchestrate the diverse protein–protein interactions found in these calcium channel signalosomes. Thus, in addition to a putative differential modulation of current properties, differential subcellular targeting properties and differential protein–protein interactions of the auxiliary subunits may explain the need for their vast molecular diversity. J. Cell. Physiol. 999: 00–00, 2015. © 2015 The Authors. Journal of Cellular Physiology Published by Wiley Periodicals, Inc. J. Cell. Physiol. 230: 2019–2031, 2015. © 2015 Wiley Periodicals, Inc. PMID:25820299

Pharmacokinetic studies and anticancer activity of curcumin-loaded nanostructured lipid carriers.

PubMed

Wang, Fengling; Chen, Jin; Dai, Wenting; He, Zhengmin; Zhai, Dandan; Chen, Weidong

2017-09-01

In order to investigate the potential of nanostructured lipid carriers for efficient and targeted delivery of curcumin, the pharmacokinetic parameters of curcumin-loaded nanostructured lipid carriers (Cur-NLC) were evaluated in rats after a single intraperitoneal dose of Cur-NLC. In addition, the anticancer activity of Cur-NLC against human lung adenocarcinoma A549 cells was verified by a cellular uptake study, and a cytotoxicity and apoptosis assay. Bioavailability of Cur-NLC was better than that of native curcumin (p > 0.01), as seen from the area under the plasma concentration-time curve (AUC), maximum plasma concentration (Cmax), mean residence time (MRT) and total plasma clearance (CLz/F). Cur-NLC has a more obvious lung-targeting property in comparison with native curcumin. Cur-NLC showed higher anticancer activity in vitro against A549 cells than native curcumin (IC50 value of 5.66 vs. 9.81 mg L-1, respectively). Meanwhile, Cur-NLC treated A549 cells showed a higher apoptosis rate compared to that of native curcumin. These results indicate that NLC is a promising system for the delivery of curcumin in the treatment of lung adenocarcinoma.

Transgenic banana plants overexpressing a native plasma membrane aquaporin MusaPIP1;2 display high tolerance levels to different abiotic stresses.

PubMed

Sreedharan, Shareena; Shekhawat, Upendra K S; Ganapathi, Thumballi R

2013-10-01

Water transport across cellular membranes is regulated by a family of water channel proteins known as aquaporins (AQPs). As most abiotic stresses like suboptimal temperatures, drought or salinity result in cellular dehydration, it is imperative to study the cause-effect relationship between AQPs and the cellular consequences of abiotic stress stimuli. Although plant cells have a high isoform diversity of AQPs, the individual and integrated roles of individual AQPs in optimal and suboptimal physiological conditions remain unclear. Herein, we have identified a plasma membrane intrinsic protein gene (MusaPIP1;2) from banana and characterized it by overexpression in transgenic banana plants. Cellular localization assay performed using MusaPIP1;2::GFP fusion protein indicated that MusaPIP1;2 translocated to plasma membrane in transformed banana cells. Transgenic banana plants overexpressing MusaPIP1;2 constitutively displayed better abiotic stress survival characteristics. The transgenic lines had lower malondialdehyde levels, elevated proline and relative water content and higher photosynthetic efficiency as compared to equivalent controls under different abiotic stress conditions. Greenhouse-maintained hardened transgenic plants showed faster recovery towards normal growth and development after cessation of abiotic stress stimuli, thereby underlining the importance of these plants in actual environmental conditions wherein the stress stimuli is often transient but severe. Further, transgenic plants where the overexpression of MusaPIP1;2 was made conditional by tagging it with a stress-inducible native dehydrin promoter also showed similar stress tolerance characteristics in in vitro and in vivo assays. Plants developed in this study could potentially enable banana cultivation in areas where adverse environmental conditions hitherto preclude commercial banana cultivation. © 2013 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Non-native and native organisms moving into high elevation and high latitude ecosystems in an era of climate change: new challenges for ecology and conservation

USGS Publications Warehouse

Pauchard, Aníbal; Albihn, Ann; Alexander, Jake; Burgess, Treena; Daehler, Curt; Essl, Franz; Evengard, Birgitta; Greenwood, Greg; Haider, Sylvia; Lenoir, Jonathan; McDougall, K.; Milbau, Ann; Muths, Erin L.; Nunez, Martin; Pellissier, Lois; Rabitsch, Wolfgang; Rew, Lisa; Robertson, Mark; Sanders, Nathan; Kueffer, Christoph

2016-01-01

Cold environments at high elevation and high latitude are often viewed as resistant to biological invasions. However, climate warming, land use change and associated increased connectivity all increase the risk of biological invasions in these environments. Here we present a summary of the key discussions of the workshop ‘Biosecurity in Mountains and Northern Ecosystems: Current Status and Future Challenges’ (Flen, Sweden, 1–3 June 2015). The aims of the workshop were to (1) increase awareness about the growing importance of species expansion—both non-native and native—at high elevation and high latitude with climate change, (2) review existing knowledge about invasion risks in these areas, and (3) encourage more research on how species will move and interact in cold environments, the consequences for biodiversity, and animal and human health and wellbeing. The diversity of potential and actual invaders reported at the workshop and the likely interactions between them create major challenges for managers of cold environments. However, since these cold environments have experienced fewer invasions when compared with many warmer, more populated environments, prevention has a real chance of success, especially if it is coupled with prioritisation schemes for targeting invaders likely to have greatest impact. Communication and co-operation between cold environment regions will facilitate rapid response, and maximise the use of limited research and management resources.

Native American Indian Successes in Natural Resources, Science and Engineering: PreK through Ph.D.

NASA Astrophysics Data System (ADS)

Bolman, J. R.

2005-12-01

We are living in a definite time of change. Distinct changes are being experienced in our most sacred and natural environments. This is especially true on Native lands. Native people have lived for millennia in distinct and unique ways. The knowledge of balancing the needs of people with the needs of our natural environments is paramount in all tribal societies. This inherent knowledge has become the foundation on which to build a "blended" contemporary understanding of western science. The Dakota's and Northern California have recognized the critical need in understanding successful tribal strategies to engage educational systems (K-12 and higher education), to bring to prominence the professional development opportunities forged through working with tribal peoples and ensure the growth of Native people in STEM (Science, Technology, Engineering and Mathematics) professions. The presentation will highlight: 1) current philosophies on building a STEM Native workforce; 2) successful educational programs/activities in PreK-Ph.D. systems; 3) current Native professionals, their research and tribal applicability; and 4) forwarding thinking for creating sustainable environmental and social infrastructures for all people. South Dakota School of Mines and Technology (SDSM&T) and Humboldt State University (HSU) have been recognized nationally for their partnerships with Native communities. SDSM&T has set record numbers for graduating Native students in science and engineering. SDSM&T had 27 graduates in five years (2000-2005) and hosted more than 1000+ Native students for programs and activities. Humboldt State University is the only university in the CSU system with a program focusing specifically on Natives in natural resources, science and engineering as well as a Native American Studies degree. Both universities have designed programs to meet current needs and address challenging issues in Earth, Wind, Fire and Water. The programs are funded through NASA, NSF, NIH and others.

A systematic review on in vitro 3D bone metastases models: A new horizon to recapitulate the native clinical scenario?

PubMed

Salamanna, Francesca; Contartese, Deyanira; Maglio, Melania; Fini, Milena

2016-07-12

While the skeleton is not the only organ where metastasis can occur, it is one of the preferred sites, with a significant impact in patients' quality of life. With the aim of delineating the cellular and molecular mechanisms of bone metastasis, numerous studies have been employed to identify any contributing factors that trigger cancer progression. One of the major limitations of studying cancer-bone metastasis is the multifaceted nature of the native bone environment and the lack of reliable, simple, and not expensive models that strictly mimic the biological processes occurring in vivo allowing a correct translation of results. Currently, with the growing acceptance of in vitro models as effective tools for studying cancer biology, three-dimensional (3D) models have emerged as a compromise between two-dimensional cultures of isolated cancer cells and the complexity of human cancer xenografts in immunocompromised animal hosts. This descriptive systematic literature review summarizes the current status of advanced and alternative 3D in vitro bone metastases models. We have also reviewed the strategies employed by researchers to set-up these models with special reference to recent promising developments trying to better replicate the complexity and heterogeneity of a human metastasis in situ, with an outlook at their use in medicine. All these aspects will greatly contribute to the existing knowledge on bone metastases, providing a specific link to clinical scenarios and thus making 3D in vitro bone metastasis models an attractive tool for multidisciplinary experts.

The Rhinovirus Subviral A-Particle Exposes 3′-Terminal Sequences of Its Genomic RNA

PubMed Central

Harutyunyan, Shushan; Kowalski, Heinrich

2014-01-01

ABSTRACT Enteroviruses, which represent a large genus within the family Picornaviridae, undergo important conformational modifications during infection of the host cell. Once internalized by receptor-mediated endocytosis, receptor binding and/or the acidic endosomal environment triggers the native virion to expand and convert into the subviral (altered) A-particle. The A-particle is lacking the internal capsid protein VP4 and exposes N-terminal amphipathic sequences of VP1, allowing for its direct interaction with a lipid bilayer. The genomic single-stranded (+)RNA then exits through a hole close to a 2-fold axis of icosahedral symmetry and passes through a pore in the endosomal membrane into the cytosol, leaving behind the empty shell. We demonstrate that in vitro acidification of a prototype of the minor receptor group of common cold viruses, human rhinovirus A2 (HRV-A2), also results in egress of the poly(A) tail of the RNA from the A-particle, along with adjacent nucleotides totaling ∼700 bases. However, even after hours of incubation at pH 5.2, 5′-proximal sequences remain inside the capsid. In contrast, the entire RNA genome is released within minutes of exposure to the acidic endosomal environment in vivo. This finding suggests that the exposed 3′-poly(A) tail facilitates the positioning of the RNA exit site onto the putative channel in the lipid bilayer, thereby preventing the egress of viral RNA into the endosomal lumen, where it may be degraded. IMPORTANCE For host cell infection, a virus transfers its genome from within the protective capsid into the cytosol; this requires modifications of the viral shell. In common cold viruses, exit of the RNA genome is prepared by the acidic environment in endosomes converting the native virion into the subviral A-particle. We demonstrate that acidification in vitro results in RNA exit starting from the 3′-terminal poly(A). However, the process halts as soon as about 700 bases have left the viral shell. Conversely, inside the cell, RNA egress completes in about 2 min. This suggests the existence of cellular uncoating facilitators. PMID:24672023

Freezing/Thawing without Cryoprotectant Damages Native but not Decellularized Porcine Renal Tissue

PubMed Central

Poornejad, Nafiseh; Frost, Timothy S; Scott, Daniel R; Elton, Brinden B; Reynolds, Paul R; Roeder, Beverly L; Cook, Alonzo D

2015-01-01

abstract Whole organ decellularization of porcine renal tissue and recellularization with a patient's own cells would potentially overcome immunorejection, which is one of the most significant problems with allogeneic kidney transplantation. However, there are obstacles to achieving this goal, including preservation of the decellularized extracellular matrix (ECM), identifying the proper cell types, and repopulating the ECM before transplantation. Freezing biological tissue is the best option to avoid spoilage; however, it may damage the structure of the tissue or disrupt cellular membranes through ice crystal formation. Cryoprotectants have been used to repress ice formation during freezing, although cell toxicity can still occur. The effect of freezing/thawing on native (n = 10) and decellularized (n = 10) whole porcine kidneys was studied without using cryoprotectants. Results showed that the elastic modulus of native kidneys was reduced by a factor of 22 (P < 0.0001) by freezing/thawing or decellularization, while the elastic modulus for decellularized ECM was essentially unchanged by the freezing/thawing process (p = 0.0636). Arterial pressure, representative of structural integrity, was also reduced by a factor of 52 (P < 0.0001) after freezing/thawing for native kidneys, compared to a factor of 43 (P < 0.0001) for decellularization and a factor of 4 (P < 0.0001) for freezing/thawing decellularized structures. Both freezing/thawing and decellularization reduced stiffness, but the reductions were not additive. Investigation of the microstructure of frozen/thawed native and decellularized renal tissues showed increased porosity due to cell removal and ice crystal formation. Orcein and Sirius staining showed partial damage to elastic and collagen fibers after freezing/thawing. It was concluded that cellular damage and removal was more responsible for reducing stiffness than fibril destruction. Cell viability and growth were demonstrated on decellularized frozen/thawed and non-frozen samples using human renal cortical tubular epithelial (RCTE) cells over 12 d. No adverse effect on the ability to recellularize after freezing/thawing was observed. It is recommended that porcine kidneys be frozen prior to decellularization to prevent contamination, and after decellularization to prevent protein denaturation. Cryoprotectants may still be necessary, however, during storage and transportation after recellularization. PMID:25730294

Proteomic differences between native and tissue‐engineered tendon and ligament

PubMed Central

Tew, Simon R.; Peffers, Mandy; Canty‐Laird, Elizabeth G.; Comerford, Eithne

2016-01-01

Tendons and ligaments (T/Ls) play key roles in the musculoskeletal system, but they are susceptible to traumatic or age‐related rupture, leading to severe morbidity as well as increased susceptibility to degenerative joint diseases such as osteoarthritis. Tissue engineering represents an attractive therapeutic approach to treating T/L injury but it is hampered by our poor understanding of the defining characteristics of the two tissues. The present study aimed to determine differences in the proteomic profile between native T/Ls and tissue engineered (TE) T/L constructs. The canine long digital extensor tendon and anterior cruciate ligament were analyzed along with 3D TE fibrin‐based constructs created from their cells. Native tendon and ligament differed in their content of key structural proteins, with the ligament being more abundant in fibrocartilaginous proteins. 3D T/L TE constructs contained less extracellular matrix (ECM) proteins and had a greater proportion of cellular‐associated proteins than native tissue, corresponding to their low collagen and high DNA content. Constructs were able to recapitulate native T/L tissue characteristics particularly with regard to ECM proteins. However, 3D T/L TE constructs had similar ECM and cellular protein compositions indicating that cell source may not be an important factor for T/L tissue engineering. PMID:27080496

Effect of gangliosides in the autoimmune response induced by liposome-associated antigens.

PubMed

Correa, S G; Rivero, V E; Yranzo-Volonté, N; Romero-Piffiguer, M; Ferro, M E; Riera, C M

1993-01-01

A model of autoimmunity to rat male accessory glands (RAG) was recently developed by intraperitoneal administration of three doses of native RAG associated with liposomes. In this work we analysed the effects of gangliosides in the cellular response to RAG when they were intraperitoneally administrated prior to the second dose of liposome-associated RAG. Results show that the ganglioside treatment could modify an established DTH response. Also, gangliosides markedly reduced the number of Ia antigen-positive peritoneal exudated cells (PEC). However, they modified neither the processing of liposomes through PEC nor their viability. Moreover, we obtained cellular response by transferring PEC from immunized donors into naive receptors.

Native and Nonnative Speakers' Pragmatic Interpretations of English Texts.

ERIC Educational Resources Information Center

Hinkel, Eli

1994-01-01

Considering the complicating effect of cultural differences in writing conventions, this study examines discourse tradition as influenced by Confucian/Taoist precepts and those of U.S. academic environments, the latter requiring rational argumentation, justification, and proof. Pedagogical implications of native-speaker and nonnative-speaker…

Climate modifies response of non-native and native species richness to nutrient enrichment.

PubMed

Flores-Moreno, Habacuc; Reich, Peter B; Lind, Eric M; Sullivan, Lauren L; Seabloom, Eric W; Yahdjian, Laura; MacDougall, Andrew S; Reichmann, Lara G; Alberti, Juan; Báez, Selene; Bakker, Jonathan D; Cadotte, Marc W; Caldeira, Maria C; Chaneton, Enrique J; D'Antonio, Carla M; Fay, Philip A; Firn, Jennifer; Hagenah, Nicole; Harpole, W Stanley; Iribarne, Oscar; Kirkman, Kevin P; Knops, Johannes M H; La Pierre, Kimberly J; Laungani, Ramesh; Leakey, Andrew D B; McCulley, Rebecca L; Moore, Joslin L; Pascual, Jesus; Borer, Elizabeth T

2016-05-19

Ecosystem eutrophication often increases domination by non-natives and causes displacement of native taxa. However, variation in environmental conditions may affect the outcome of interactions between native and non-native taxa in environments where nutrient supply is elevated. We examined the interactive effects of eutrophication, climate variability and climate average conditions on the success of native and non-native plant species using experimental nutrient manipulations replicated at 32 grassland sites on four continents. We hypothesized that effects of nutrient addition would be greatest where climate was stable and benign, owing to reduced niche partitioning. We found that the abundance of non-native species increased with nutrient addition independent of climate; however, nutrient addition increased non-native species richness and decreased native species richness, with these effects dampened in warmer or wetter sites. Eutrophication also altered the time scale in which grassland invasion responded to climate, decreasing the importance of long-term climate and increasing that of annual climate. Thus, climatic conditions mediate the responses of native and non-native flora to nutrient enrichment. Our results suggest that the negative effect of nutrient addition on native abundance is decoupled from its effect on richness, and reduces the time scale of the links between climate and compositional change. © 2016 The Author(s).

Climate modifies response of non-native and native species richness to nutrient enrichment

PubMed Central

Flores-Moreno, Habacuc; Reich, Peter B.; Lind, Eric M.; Sullivan, Lauren L.; Seabloom, Eric W.; Yahdjian, Laura; MacDougall, Andrew S.; Reichmann, Lara G.; Alberti, Juan; Báez, Selene; Bakker, Jonathan D.; Cadotte, Marc W.; Caldeira, Maria C.; Chaneton, Enrique J.; D'Antonio, Carla M.; Fay, Philip A.; Firn, Jennifer; Hagenah, Nicole; Harpole, W. Stanley; Iribarne, Oscar; Kirkman, Kevin P.; Knops, Johannes M. H.; La Pierre, Kimberly J.; Laungani, Ramesh; Leakey, Andrew D. B.; McCulley, Rebecca L.; Moore, Joslin L.; Pascual, Jesus; Borer, Elizabeth T.

2016-01-01

Ecosystem eutrophication often increases domination by non-natives and causes displacement of native taxa. However, variation in environmental conditions may affect the outcome of interactions between native and non-native taxa in environments where nutrient supply is elevated. We examined the interactive effects of eutrophication, climate variability and climate average conditions on the success of native and non-native plant species using experimental nutrient manipulations replicated at 32 grassland sites on four continents. We hypothesized that effects of nutrient addition would be greatest where climate was stable and benign, owing to reduced niche partitioning. We found that the abundance of non-native species increased with nutrient addition independent of climate; however, nutrient addition increased non-native species richness and decreased native species richness, with these effects dampened in warmer or wetter sites. Eutrophication also altered the time scale in which grassland invasion responded to climate, decreasing the importance of long-term climate and increasing that of annual climate. Thus, climatic conditions mediate the responses of native and non-native flora to nutrient enrichment. Our results suggest that the negative effect of nutrient addition on native abundance is decoupled from its effect on richness, and reduces the time scale of the links between climate and compositional change. PMID:27114575

Structural differences between native Hen egg white lysozyme and its fibrils under different environmental conditions

NASA Astrophysics Data System (ADS)

Bhattacharya, Susmita; Ghosh, Sudeshna; Dasgupta, Swagata; Roy, Anushree

2013-10-01

The difference in molecular structure of native HEWL and its fibrils, grown at a pH value near physiological pH 7.4 and at a pH value just above the pI, 10.7 in presence and absence of Cu(II) ions, is discussed. We focus on differences between the molecular structure of the native protein and fibrils using principal component analysis of their Raman spectra. The overlap areas of the scores of each species are used to quantify the difference in the structure of the native HEWL and fibrils in different environments. The overall molecular structures are significantly different for fibrils grown at two pH values. However, in presence of Cu(II) ions, the fibrils have similarities in their molecular structures at these pH environments. Spectral variation within each species, as obtained from the standard deviations of the scores in PCA plots, reveals the variability in the structure within a particular species.

Lateral diffusion and signaling of receptor for advanced glycation end-products (RAGE): a receptor involved in chronic inflammation.

PubMed

Syed, Aleem; Zhu, Qiaochu; Smith, Emily A

2018-01-01

Membrane diffusion is one of the key mechanisms in the cellular function of receptors. The signaling of receptors for advanced glycation end-products (RAGE) has been extensively studied in the context of several pathological conditions, however, very little is known about RAGE diffusion. To fill this gap, RAGE lateral diffusion is probed in native, cholesterol-depleted, and cytoskeleton-altered cellular conditions. In native GM07373 cellular conditions, RAGE has a 90% mobile fraction and an average diffusion coefficient of 0.3 μm 2 /s. When depolymerization of the actin cytoskeleton is inhibited with the small molecule jasplakinolide (Jsp), the RAGE mobile fraction and diffusion coefficient decrease by 22 and 37%, respectively. In contrast, depolymerizing the filamentous actin cytoskeleton using the small molecule cytochalasin D (CD) does not alter the RAGE diffusion properties. There is a 70 and 50% decrease in phosphorylation of extracellular signal-regulated kinase (p-ERK) when the actin cytoskeleton is disrupted by CD or Jsp, respectively, in RAGE-expressing GM07373 cells. Disrupting the actin cytoskeleton in GM07373 cells that do not express detectable amounts of RAGE results in no change in p-ERK. Cholesterol depletion results in no statistically significant change in the diffusion properties of RAGE or p-ERK. This work presents a strong link between the actin cytoskeleton and RAGE diffusion and downstream signaling, and serves to further our understanding of the factors influencing RAGE lateral diffusion.

Risky Business: Do Native Rodents Use Habitat and Odor Cues to Manage Predation Risk in Australian Deserts?

PubMed Central

Spencer, Emma E.; Crowther, Mathew S.; Dickman, Christopher R.

2014-01-01

In open, arid environments with limited shelter there may be strong selection on small prey species to develop behaviors that facilitate predator avoidance. Here, we predicted that rodents should avoid predator odor and open habitats to reduce their probability of encounter with potential predators, and tested our predictions using a native Australian desert rodent, the spinifex hopping-mouse (Notomys alexis). We tested the foraging and movement responses of N. alexis to non-native predator (fox and cat) odor, in sheltered and open macro- and microhabitats. Rodents did not respond to predator odor, perhaps reflecting the inconsistent selection pressure that is imposed on prey species in the desert environment due to the transience of predator-presence. However, they foraged primarily in the open and moved preferentially across open sand. The results suggest that N. alexis relies on escape rather than avoidance behavior when managing predation risk, with its bipedal movement probably allowing it to exploit open environments most effectively. PMID:24587396

Risky business: do native rodents use habitat and odor cues to manage predation risk in Australian deserts?

PubMed

Spencer, Emma E; Crowther, Mathew S; Dickman, Christopher R

2014-01-01

In open, arid environments with limited shelter there may be strong selection on small prey species to develop behaviors that facilitate predator avoidance. Here, we predicted that rodents should avoid predator odor and open habitats to reduce their probability of encounter with potential predators, and tested our predictions using a native Australian desert rodent, the spinifex hopping-mouse (Notomys alexis). We tested the foraging and movement responses of N. alexis to non-native predator (fox and cat) odor, in sheltered and open macro- and microhabitats. Rodents did not respond to predator odor, perhaps reflecting the inconsistent selection pressure that is imposed on prey species in the desert environment due to the transience of predator-presence. However, they foraged primarily in the open and moved preferentially across open sand. The results suggest that N. alexis relies on escape rather than avoidance behavior when managing predation risk, with its bipedal movement probably allowing it to exploit open environments most effectively.

Analysis of Proteins, Protein Complexes, and Organellar Proteomes Using Sheathless Capillary Zone Electrophoresis - Native Mass Spectrometry

NASA Astrophysics Data System (ADS)

Belov, Arseniy M.; Viner, Rosa; Santos, Marcia R.; Horn, David M.; Bern, Marshall; Karger, Barry L.; Ivanov, Alexander R.

2017-12-01

Native mass spectrometry (MS) is a rapidly advancing field in the analysis of proteins, protein complexes, and macromolecular species of various types. The majority of native MS experiments reported to-date has been conducted using direct infusion of purified analytes into a mass spectrometer. In this study, capillary zone electrophoresis (CZE) was coupled online to Orbitrap mass spectrometers using a commercial sheathless interface to enable high-performance separation, identification, and structural characterization of limited amounts of purified proteins and protein complexes, the latter with preserved non-covalent associations under native conditions. The performance of both bare-fused silica and polyacrylamide-coated capillaries was assessed using mixtures of protein standards known to form non-covalent protein-protein and protein-ligand complexes. High-efficiency separation of native complexes is demonstrated using both capillary types, while the polyacrylamide neutral-coated capillary showed better reproducibility and higher efficiency for more complex samples. The platform was then evaluated for the determination of monoclonal antibody aggregation and for analysis of proteomes of limited complexity using a ribosomal isolate from E. coli. Native CZE-MS, using accurate single stage and tandem-MS measurements, enabled identification of proteoforms and non-covalent complexes at femtomole levels. This study demonstrates that native CZE-MS can serve as an orthogonal and complementary technique to conventional native MS methodologies with the advantages of low sample consumption, minimal sample processing and losses, and high throughput and sensitivity. This study presents a novel platform for analysis of ribosomes and other macromolecular complexes and organelles, with the potential for discovery of novel structural features defining cellular phenotypes (e.g., specialized ribosomes). [Figure not available: see fulltext.

Native Hydrophobic Binding Interactions at the Transition State for Association between the TAZ1 Domain of CBP and the Disordered TAD-STAT2 Are Not a Requirement.

PubMed

Lindström, Ida; Dogan, Jakob

2017-08-15

A significant fraction of the eukaryotic proteome consists of proteins that are either partially or completely disordered under native-like conditions. Intrinsically disordered proteins (IDPs) are common in protein-protein interactions and are involved in numerous cellular processes. Although many proteins have been identified as disordered, much less is known about the binding mechanisms of the coupled binding and folding reactions involving IDPs. Here we have analyzed the rate-limiting transition state for binding between the TAZ1 domain of CREB binding protein and the intrinsically disordered transactivation domain of STAT2 (TAD-STAT2) by site-directed mutagenesis and kinetic experiments (Φ-value analysis) and found that the native protein-protein binding interface is not formed at the transition state for binding. Instead, native hydrophobic binding interactions form late, after the rate-limiting barrier has been crossed. The association rate constant in the absence of electrostatic enhancement was determined to be rather high. This is consistent with the Φ-value analysis, which showed that there are few or no obligatory native contacts. Also, linear free energy relationships clearly demonstrate that native interactions are cooperatively formed, a scenario that has usually been observed for proteins that fold according to the so-called nucleation-condensation mechanism. Thus, native hydrophobic binding interactions at the rate-limiting transition state for association between TAD-STAT2 and TAZ1 are not a requirement, which is generally in agreement with previous findings on other IDP systems and might be a common mechanism for IDPs.

Growth, biomass allocation and photosynthesis of invasive and native Hawaiian rainforest species.

PubMed

Pattison, R R; Goldstein, G; Ares, A

1998-12-01

Growth, biomass allocation, and photosynthetic characteristics of seedlings of five invasive non-indigenous and four native species grown under different light regimes were studied to help explain the success of invasive species in Hawaiian rainforests. Plants were grown under three greenhouse light levels representative of those found in the center and edge of gaps and in the understory of Hawaiian rainforests, and under an additional treatment with unaltered shade. Relative growth rates (RGRs) of invasive species grown in sun and partial shade were significantly higher than those for native species, averaging 0.25 and 0.17 g g -1 week -1 , respectively, while native species averaged only 0.09 and 0.06 g g -1 week -1 , respectively. The RGR of invasive species under the shade treatment was 40% higher than that of native species. Leaf area ratios (LARs) of sun and partial-shade-grown invasive and native species were similar but the LAR of invasive species in the shade was, on average, 20% higher than that of native species. There were no differences between invasive and native species in biomass allocation to shoots and roots, or in leaf mass per area across light environments. Light-saturated photosynthetic rates (Pmax) were higher for invasive species than for native species in all light treatments. Pmax of invasive species grown in the sun treatment, for example, ranged from 5.5 to 11.9 μmol m -2 s -1 as compared with 3.0-4.5 μmol m -2 s -1 for native species grown under similar light conditions. The slope of the linear relationship between Pmax and dark respiration was steeper for invasive than for native species, indicating that invasive species assimilate more CO 2 at a lower respiratory cost than native species. These results suggest that the invasive species may have higher growth rates than the native species as a consequence of higher photosynthetic capacities under sun and partial shade, lower dark respiration under all light treatments, and higher LARs when growing under shade conditions. Overall, invasive species appear to be better suited than native species to capturing and utilizing light resources, particularly in high-light environments such as those characterized by relatively high levels of disturbance.

Phytoextraction of heavy metals by potential native plants and their microscopic observation of root growing on stabilised distillery sludge as a prospective tool for in situ phytoremediation of industrial waste.

PubMed

Chandra, Ram; Kumar, Vineet

2017-01-01

The safe disposal of post-methanated distillery sludge (PMDS) in the environment is challenging due to high concentrations of heavy metals along with other complex organic pollutants. The study has revealed that PMDS contained high amounts of Fe (2403), Zn (210), Mn (126), Cu (73.62), Cr (21.825), Pb (16.33) and Ni (13.425 mg kg -1 ) along with melanoidins and other co-pollutants. The phytoextraction pattern in 15 potential native plants growing on sludge showed that the Blumea lacera, Parthenium hysterophorous, Setaria viridis, Chenopodium album, Cannabis sativa, Basella alba, Tricosanthes dioica, Amaranthus spinosus L., Achyranthes sp., Dhatura stramonium, Sacchrum munja and Croton bonplandianum were noted as root accumulator for Fe, Zn and Mn, while S. munja, P. hysterophorous, C. sativa, C. album, T. dioica, D. stramonium, B. lacera, B. alba, Kalanchoe pinnata and Achyranthes sp. were found as shoot accumulator for Fe. In addition, A. spinosus L. was found as shoot accumulator for Zn and Mn. Similarly, all plants found as leaf accumulator for Fe, Zn and Mn except A. spinosus L. and Ricinus communis. Further, the BCF of all tested plants were noted <1, while the TF showed >1. This revealed that metal bioavailability to plant is poor due to strong complexation of heavy metals with organic pollutants. This gives a strong evidence of hyperaccumulation for the tested metals from complex distillery waste. Furthermore, the TEM observations of root of P. hysterophorous, C. sativa, Solanum nigrum and R. communis showed formation of multi-nucleolus, multi-vacuoles and deposition of metal granules in cellular component of roots as a plant adaptation mechanism for phytoextraction of heavy metal-rich polluted site. Hence, these native plants may be used as a tool for in situ phytoremediation and eco-restoration of industrial waste-contaminated site.

Acculturation in Context: The Moderating Effects of Immigrant and Native Peer Orientations on the Acculturation Experiences of Immigrants.

PubMed

Titzmann, Peter F; Jugert, Philipp

2015-11-01

Immigrant adolescents have to navigate through a complex social environment consisting of, at least, both a native and a co-ethnic community. This study used a multi-level framework to consider two research questions involving this complexity. The individual-level associations of acculturation orientations and acculturative hassles (language and sociocultural adaptation) was assessed in immigrant youths, and whether this association differs depending on the school-level acculturation orientations held by co-ethnic peers, and the school-level orientations toward immigrants held by native German peers. We then investigated whether acculturative hassles are associated with the psychosocial functioning (self-efficacy, depressive symptoms) of immigrant adolescents. The sample comprised 650 ethnic German Diaspora migrant adolescents (mean age 15.6 years, 53.7 % female) and their 787 native German peers (mean age 15.05 years, 51 % female). The results showed that contextual factors (co-ethnic acculturation orientation, native friendship preferences) moderated the association between the acculturation orientations of adolescent immigrants and both types of acculturative hassles. Acculturative hassles, in turn, were associated with the psychosocial functioning of adolescents. This research demonstrates that a person-by-context perspective is needed to better understand the adaptation of adolescent immigrants. This perspective has to take into account both the native and the co-ethnic peer environment.

Asymmetric mutations in the tetrameric R67 dihydrofolate reductase reveal high tolerance to active-site substitutions.

PubMed

Ebert, Maximilian C C J C; Morley, Krista L; Volpato, Jordan P; Schmitzer, Andreea R; Pelletier, Joelle N

2015-04-01

Type II R67 dihydrofolate reductase (DHFR) is a bacterial plasmid-encoded enzyme that is intrinsically resistant to the widely-administered antibiotic trimethoprim. R67 DHFR is genetically and structurally unrelated to E. coli chromosomal DHFR and has an unusual architecture, in that four identical protomers form a single symmetrical active site tunnel that allows only one substrate binding/catalytic event at any given time. As a result, substitution of an active-site residue has as many as four distinct consequences on catalysis, constituting an atypical model of enzyme evolution. Although we previously demonstrated that no single residue of the native active site is indispensable for function, library selection here revealed a strong bias toward maintenance of two native protomers per mutated tetramer. A variety of such "half-native" tetramers were shown to procure native-like catalytic activity, with similar KM values but kcat values 5- to 33-fold lower, illustrating a high tolerance for active-site substitutions. The selected variants showed a reduced thermal stability (Tm ∼12°C lower), which appears to result from looser association of the protomers, but generally showed a marked increase in resilience to heat denaturation, recovering activity to a significantly greater extent than the variant with no active-site substitutions. Our results suggest that the presence of two native protomers in the R67 DHFR tetramer is sufficient to provide native-like catalytic rate and thus ensure cellular proliferation. © 2014 The Protein Society.

QTL x environment interactions and latitudinal adaptation in switchgrass (Panicum virgatum)

USDA-ARS?s Scientific Manuscript database

Switchgrass (Panicum virgatum) is a polyploid C4 perennial grass that is native to North America and has been championed as a promising biofuel feedstock. It is a common member of most native prairie communities and exhibits extensive phenotypic variability and adaptation across its range, especial...

The Emotional Impact of Being Myself: Emotions and Foreign-Language Processing

ERIC Educational Resources Information Center

Ivaz, Lela; Costa, Albert; Duñabeitia, Jon Andoni

2016-01-01

Native languages are acquired in emotionally rich contexts, whereas foreign languages are typically acquired in emotionally neutral academic environments. As a consequence of this difference, it has been suggested that bilinguals' emotional reactivity in foreign-language contexts is reduced as compared with native language contexts. In the current…

Teaching complex ecological concepts through a demonstration garden Biodiversity, invasions and conservation in practice

USDA-ARS?s Scientific Manuscript database

Biodiversity encompasses the variety within and between species in an environment. Native communities host a diverse array of species and interactions between members. Invasions by non-native species reduce biodiversity and a community’s ability to support diverse assemblages, and are one of the lar...

Digital Natives? New and Old Media and Children's Outcomes

ERIC Educational Resources Information Center

Bittman, Michael; Rutherford, Leonie; Brown, Jude; Unsworth, Lens

2011-01-01

The current generation of young children has been described as "digital natives", having been born into a ubiquitous digital media environment. They are envisaged as educationally independent of the guided interaction provided by "digital immigrants": parents and teachers. This article uses data from the Longitudinal Study of…

A Garden of Learning

ERIC Educational Resources Information Center

Kirby, Tasha

2008-01-01

In order to beautify the school environment and further student learning, fourth-graders cultivated a Native Plant Learning Garden. They were responsible for designing a layout, researching garden elements, preparing the area, and planting a variety of native plants. By the completion of this inquiry-based project, students were able to clearly…

Being Black (and) Immigrant Students: When Race, Ethnicity, and Nativity Collide

ERIC Educational Resources Information Center

Mwangi, Chrystal A. George; English, Shelvia

2017-01-01

While Black immigrants share some of the racialized experiences of native-Black Americans, they also have distinctive experiences. U.S. education presents an important environment to investigate these experiences as immigrants have the fastest growing child population and these children are increasingly entering the education system. This paper…

Native Americans and the Environment: A Survey of Twentieth-Century Issues.

ERIC Educational Resources Information Center

Lewis, David Rich

1995-01-01

Land; exploitation of land; and changing Indian needs, attitudes, and religious demands define environmental issues facing modern Native Americans. Such issues are related to agriculture and ranching, forests and watersheds, hunting and fishing, water, natural resource mining and pollution, hazardous and radioactive waste storage, urbanization of…

The physiology of invasive plants in low-resource environments

PubMed Central

Funk, Jennifer L.

2013-01-01

While invasive plant species primarily occur in disturbed, high-resource environments, many species have invaded ecosystems characterized by low nutrient, water, and light availability. Species adapted to low-resource systems often display traits associated with resource conservation, such as slow growth, high tissue longevity, and resource-use efficiency. This contrasts with our general understanding of invasive species physiology derived primarily from studies in high-resource environments. These studies suggest that invasive species succeed through high resource acquisition. This review examines physiological and morphological traits of native and invasive species in low-resource environments. Existing data support the idea that species invading low-resource environments possess traits associated with resource acquisition, resource conservation or both. Disturbance and climate change are affecting resource availability in many ecosystems, and understanding physiological differences between native and invasive species may suggest ways to restore invaded ecosystems. PMID:27293610

The role of actin networks in cellular mechanosensing

NASA Astrophysics Data System (ADS)

Azatov, Mikheil

Physical processes play an important role in many biological phenomena, such as wound healing, organ development, and tumor metastasis. During these processes, cells constantly interact with and adapt to their environment by exerting forces to mechanically probe the features of their surroundings and generating appropriate biochemical responses. The mechanisms underlying how cells sense the physical properties of their environment are not well understood. In this thesis, I present my studies to investigate cellular responses to the stiffness and topography of the environment. In order to sense the physical properties of their environment, cells dynamically reorganize the structure of their actin cytoskeleton, a dynamic network of biopolymers, altering the shape and spatial distribution of protein assemblies. Several observations suggest that proteins that crosslink actin filaments may play an important role in cellular mechanosensitivity. Palladin is an actin-crosslinking protein that is found in the lamellar actin network, stress fibers and focal adhesions, cellular structures that are critical for mechanosensing of the physical environment. By virtue of its close interactions with these structures in the cell, palladin may play an important role in cell mechanics. However, the role of actin crosslinkers in general, and palladin in particular, in cellular force generation and mechanosensing is not well known. I have investigated the role of palladin in regulating the plasticity of the actin cytoskeleton and cellular force generation in response to alterations in substrate stiffness. I have shown that the expression levels of palladin modulate the forces exerted by cells and their ability to sense substrate stiffness. Perturbation experiments also suggest that palladin levels in cells altered myosin motor activity. These results suggest that the actin crosslinkers, such as palladin, and myosin motors coordinate for optimal cell function and to prevent aberrant behavior as in cancer metastasis. In addition to stiffness, the local geometry or topography of the surface has been shown to modulate the movement, morphology, and cytoskeletal organization of cells. However, the effect of topography on fluctuations of intracellular structures, which arise from motor driven activity on a viscoelastic actin network are not known. I have used nanofabricated substrates with parallel ridges to show that the cell shape, the actin cytoskeleton and focal adhesions all align along the direction of the ridges, exhibiting a biphasic dependence on the spacing between ridges. I further demonstrated that palladin bands along actin stress fibers undergo a complex diffusive motion with velocities aligned along the direction of ridges. These results provide insight into the mechanisms of cellular mechanosensing of the environment, suggesting a complex interplay between the actin cytoskeleton and cellular adhesions in coordinating cellular response to surface topography. Overall, this work has advanced our understanding of mechanisms that govern cellular responses to their physical environment.

Endothelial Progenitor Cells as a Sole Source for Ex Vivo Seeding of Tissue-Engineered Heart Valves

PubMed Central

Mettler, Bret A.; Engelmayr, George C.; Aikawa, Elena; Bischoff, Joyce; Martin, David P.; Exarhopoulos, Alexis; Moses, Marsha A.; Schoen, Frederick J.; Sacks, Michael S.

2010-01-01

Purposes: We investigated whether circulating endothelial progenitor cells (EPCs) can be used as a cell source for the creation of a tissue-engineered heart valve (TEHV). Methods: Trileaflet valved conduits were fabricated using nonwoven polyglycolic acid/poly-4-hydroxybutyrate polymer. Ovine peripheral blood EPCs were dynamically seeded onto a valved conduit and incubated for 7, 14, and 21 days. Results: Before seeding, EPCs were shown to express CD31+, eNOS+, and VE-Cadherin+ but not α-smooth muscle actin. Histological analysis demonstrated relatively homogenous cellular ingrowth throughout the valved conduit. TEHV constructs revealed the presence of endothelial cell (EC) markers and α-smooth muscle actin+ cells comparable with native valves. Protein levels were comparable with native valves and exceeded those in unseeded controls. EPC-TEHV demonstrated a temporal pattern of matrix metalloproteinases-2/9 expression and tissue inhibitors of metalloproteinase activities comparable to that of native valves. Mechanical properties of EPC-TEHV demonstrated significantly greater stiffness than that of the unseeded scaffolds and native valves. Conclusions: Circulating EPC appears to have the potential to provide both interstitial and endothelial functions and could potentially serve as a single-cell source for construction of autologous heart valves. PMID:19698056

Development and Characterization of Acellular Extracellular Matrix Scaffolds from Porcine Menisci for Use in Cartilage Tissue Engineering

PubMed Central

Chen, Ying-Chen; Chen, Ray-Neng; Jhan, Hua-Jing; Liu, Der-Zen; Ho, Hsiu-O; Mao, Yong; Kohn, Joachim

2015-01-01

Given the growing number of arthritis patients and the limitations of current treatments, there is great urgency to explore cartilage substitutes by tissue engineering. In this study, we developed a novel decellularization method for menisci to prepare acellular extracellular matrix (ECM) scaffolds with minimal adverse effects on the ECM. Among all the acid treatments, formic acid treatment removed most of the cellular contents and preserved the highest ECM contents in the decellularized porcine menisci. Compared with fresh porcine menisci, the content of DNA decreased to 4.10%±0.03%, and there was no significant damage to glycosaminoglycan (GAG) or collagen. Histological staining also confirmed the presence of ECM and the absence of cellularity. In addition, a highly hydrophilic scaffold with three-dimensional interconnected porous structure was fabricated from decellularized menisci tissue. Human chondrocytes showed enhanced cell proliferation and synthesis of chondrocyte ECM including type II collagen and GAG when cultured in this acellular scaffold. Moreover, the scaffold effectively supported chondrogenesis of human bone marrow-derived mesenchymal stem cells. Finally, in vivo implantation was conducted in rats to assess the biocompatibility of the scaffolds. No significant inflammatory response was observed. The acellular ECM scaffold provided a native environment for cells with diverse physiological functions to promote cell proliferation and new tissue formation. This study reported a novel way to prepare decellularized meniscus tissue and demonstrated the potential as scaffolds to support cartilage repair. PMID:25919905

Activation of TRPM7 channels by small molecules under physiological conditions.

PubMed

Hofmann, T; Schäfer, S; Linseisen, M; Sytik, L; Gudermann, T; Chubanov, V

2014-12-01

Transient receptor potential cation channel, subfamily M, member 7 (TRPM7) is a cation channel covalently linked to a protein kinase domain. TRPM7 is ubiquitously expressed and regulates key cellular processes such as Mg(2+) homeostasis, motility, and proliferation. TRPM7 is involved in anoxic neuronal death, cardiac fibrosis, and tumor growth. The goal of this work was to identify small molecule activators of the TRPM7 channel and investigate their mechanism of action. We used an aequorin bioluminescence-based assay to screen for activators of the TRPM7 channel. Valid candidates were further characterized using patch clamp electrophysiology. We identified 20 drug-like compounds with various structural backbones that can activate the TRPM7 channel. Among them, the δ opioid antagonist naltriben was studied in greater detail. Naltriben's action was selective among the TRP channels tested. Naltriben activates TRPM7 currents without prior depletion of intracellular Mg(2+) even under conditions of low PIP2. Moreover, naltriben interfered with the effect of the TRPM7 inhibitor NS8593. Finally, our experiments with TRPM7 variants carrying mutations in the pore, TRP, and kinase domains indicate that the site of TRPM7 activation by this small-molecule ligand is most likely located in or near the TRP domain. In conclusion, we identified the first organic small-molecule activators of TRPM7 channels, thus providing new experimental tools to study TRPM7 function in native cellular environments.

Recent Progress in the Structure Determination of GPCRs, a Membrane Protein Family with High Potential as Pharmaceutical Targets

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

Cherezov, Vadim; Abola, Enrique; Stevens, Raymond C.

2015-11-30

G protein-coupled receptors (GPCRs) constitute a highly diverse and ubiquitous family of integral membrane proteins, transmitting signals inside the cells in response to an assortment of disparate extra-cellular stimuli. Their strategic location on the cell surface and their involvement in crucial cellular and physiological processes turn these receptors into highly important pharmaceutical targets. Recent technological developments aimed at stabilization and crystallization of these receptors have led to significant breakthroughs in GPCR structure determination efforts. One of the successful approaches involved receptor stabilization with the help of a fusion partner combined with crystallization in lipidic cubic phase (LCP). The success ofmore » using an LCP matrix for crystallization is generally attributed to the creation of a more native, membrane-like stabilizing environment for GPCRs just prior to nucleation and to the formation of type I crystal lattices, thus generating highly ordered and strongly diffracting crystals. Here they describe protocols for reconstituting purified GPCRs in LCP, performing pre-crystallization assays, setting up crystallization trials in manual mode, detecting crystallization hits, optimizing crystallization conditions, harvesting, and collecting crystallographic data. The protocols provide a sensible framework for approaching crystallization of stabilized GPCRs in LCP, however, as in any crystallization experiment, extensive screening and optimization of crystallization conditions as well as optimization of protein construct and purification steps are required. The process remains risky and these protocols do not necessarily guarantee success.« less

Spatial reconstruction of single-cell gene expression data.

PubMed

Satija, Rahul; Farrell, Jeffrey A; Gennert, David; Schier, Alexander F; Regev, Aviv

2015-05-01

Spatial localization is a key determinant of cellular fate and behavior, but methods for spatially resolved, transcriptome-wide gene expression profiling across complex tissues are lacking. RNA staining methods assay only a small number of transcripts, whereas single-cell RNA-seq, which measures global gene expression, separates cells from their native spatial context. Here we present Seurat, a computational strategy to infer cellular localization by integrating single-cell RNA-seq data with in situ RNA patterns. We applied Seurat to spatially map 851 single cells from dissociated zebrafish (Danio rerio) embryos and generated a transcriptome-wide map of spatial patterning. We confirmed Seurat's accuracy using several experimental approaches, then used the strategy to identify a set of archetypal expression patterns and spatial markers. Seurat correctly localizes rare subpopulations, accurately mapping both spatially restricted and scattered groups. Seurat will be applicable to mapping cellular localization within complex patterned tissues in diverse systems.

Effect of processing on physicochemical characteristics and bioefficacy of β-lactoglobulin-epigallocatechin-3-gallate complexes.

PubMed

Lestringant, Pauline; Guri, Anilda; Gülseren, Ibrahim; Relkin, Perla; Corredig, Milena

2014-08-20

Varying amounts of epigallocatechin-3-gallate (EGCG) were encapsulated in β-lactoglobulin (β-Lg) nanoparticles, either native or processed, denoted as heated or desolvated protein. The stability, physical properties, and bioactivity of the β-Lg-EGCG complexes were tested. Native β-Lg-EGCG complexes showed comparable stability and binding efficacy (EGCG/β-Lg molar ratio of 1:1) to heated β-Lg nanoparticles (1% and 5% protein w/w). The sizes of heated and desolvated β-Lg nanoparticles were comparable, but the latter showed the highest binding affinity for EGCG. The presence of EGCG complexed with β-Lg did not affect the interfacial tension of the protein when tested at the soy oil-water interface but caused a decrease in dilational elasticity. All β-Lg complexes (native, heated, or desolvated) showed a decrease in cellular proliferation similar to that of free ECGC. In summary, protein-EGCG complexes did not alter the bioefficacy of EGCG and contributed to increased stability with storage, demonstrating the potential benefits of nanoencapsulation.

Clonal dynamics of native haematopoiesis

PubMed Central

Sun, Jianlong; Ramos, Azucena; Chapman, Brad; Johnnidis, Jonathan B.; Le, Linda; Ho, Yu-Jui; Klein, Allon; Hofmann, Oliver; Camargo, Fernando D.

2015-01-01

It is currently thought that life-long blood cell production is driven by the action of a small number of multipotent haematopoietic stem cells. Evidence supporting this view has been largely acquired through the use of functional assays involving transplantation. However, whether these mechanisms also govern native non-transplant haematopoiesis is entirely unclear. Here we have established a novel experimental model in mice where cells can be uniquely and genetically labelled in situ to address this question. Using this approach, we have performed longitudinal analyses of clonal dynamics in adult mice that reveal unprecedented features of native haematopoiesis. In contrast to what occurs following transplantation, steady-state blood production is maintained by the successive recruitment of thousands of clones, each with a minimal contribution to mature progeny. Our results demonstrate that a large number of long-lived progenitors, rather than classically defined haematopoietic stem cells, are the main drivers of steady-state haematopoiesis during most of adulthood. Our results also have implications for understanding the cellular origin of haematopoietic disease. PMID:25296256

Clonal dynamics of native haematopoiesis.

PubMed

Sun, Jianlong; Ramos, Azucena; Chapman, Brad; Johnnidis, Jonathan B; Le, Linda; Ho, Yu-Jui; Klein, Allon; Hofmann, Oliver; Camargo, Fernando D

2014-10-16

It is currently thought that life-long blood cell production is driven by the action of a small number of multipotent haematopoietic stem cells. Evidence supporting this view has been largely acquired through the use of functional assays involving transplantation. However, whether these mechanisms also govern native non-transplant haematopoiesis is entirely unclear. Here we have established a novel experimental model in mice where cells can be uniquely and genetically labelled in situ to address this question. Using this approach, we have performed longitudinal analyses of clonal dynamics in adult mice that reveal unprecedented features of native haematopoiesis. In contrast to what occurs following transplantation, steady-state blood production is maintained by the successive recruitment of thousands of clones, each with a minimal contribution to mature progeny. Our results demonstrate that a large number of long-lived progenitors, rather than classically defined haematopoietic stem cells, are the main drivers of steady-state haematopoiesis during most of adulthood. Our results also have implications for understanding the cellular origin of haematopoietic disease.

The molten globule state is unusually deformable under mechanical force

PubMed Central

Elms, Phillip J.; Chodera, John D.; Bustamante, Carlos; Marqusee, Susan

2012-01-01

Recently, the role of force in cellular processes has become more evident, and now with advances in force spectroscopy, the response of proteins to force can be directly studied. Such studies have found that native proteins are brittle, and thus not very deformable. Here, we examine the mechanical properties of a class of intermediates referred to as the molten globule state. Using optical trap force spectroscopy, we investigated the response to force of the native and molten globule states of apomyoglobin along different pulling axes. Unlike natively folded proteins, the molten globule state of apomyoglobin is compliant (large distance to the transition state); this large compliance means that the molten globule is more deformable and the unfolding rate is more sensitive to force (the application of force or tension will have a more dramatic effect on the unfolding rate). Our studies suggest that these are general properties of molten globules and could have important implications for mechanical processes in the cell. PMID:22355138

Are invasive plants more competitive than native conspecifics? Patterns vary with competitors

NASA Astrophysics Data System (ADS)

Zheng, Yulong; Feng, Yulong; Valiente-Banuet, Alfonso; Li, Yangping; Liao, Zhiyong; Zhang, Jiaolin; Chen, Yajun

2015-10-01

Invasive plants are sometimes considered to be more competitive than their native conspecifics, according to the prediction that the invader reallocates resources from defense to growth due to liberation of natural enemies [‘Evolution of Increased Competitive Ability’ (EICA) hypothesis]. However, the differences in competitive ability may depend on the identity of competitors. In order to test the effects of competitors, Ageratina adenophora plants from both native and invasive ranges competed directly, and competed with native residents from both invasive (China) and native (Mexico) ranges respectively. Invasive A. adenophora plants were more competitive than their conspecifics from native populations when competing with natives from China (interspecific competition), but not when competing with natives from Mexico. Invasive A. adenophora plants also showed higher competitive ability when grown in high-density monoculture communities of plants from the same population (intrapopulation competition). In contrast, invasive A. adenophora plants showed lower competitive ability when competing with plants from native populations (intraspecific competition). Our results indicated that in the invasive range A. adenophora has evolved to effectively cope with co-occurring natives and high density environments, contributing to invasion success. Here, we showed the significant effects of competitors, which should be considered carefully when testing the EICA hypothesis.

Are invasive plants more competitive than native conspecifics? Patterns vary with competitors.

PubMed

Zheng, Yulong; Feng, Yulong; Valiente-Banuet, Alfonso; Li, Yangping; Liao, Zhiyong; Zhang, Jiaolin; Chen, Yajun

2015-10-22

Invasive plants are sometimes considered to be more competitive than their native conspecifics, according to the prediction that the invader reallocates resources from defense to growth due to liberation of natural enemies ['Evolution of Increased Competitive Ability' (EICA) hypothesis]. However, the differences in competitive ability may depend on the identity of competitors. In order to test the effects of competitors, Ageratina adenophora plants from both native and invasive ranges competed directly, and competed with native residents from both invasive (China) and native (Mexico) ranges respectively. Invasive A. adenophora plants were more competitive than their conspecifics from native populations when competing with natives from China (interspecific competition), but not when competing with natives from Mexico. Invasive A. adenophora plants also showed higher competitive ability when grown in high-density monoculture communities of plants from the same population (intrapopulation competition). In contrast, invasive A. adenophora plants showed lower competitive ability when competing with plants from native populations (intraspecific competition). Our results indicated that in the invasive range A. adenophora has evolved to effectively cope with co-occurring natives and high density environments, contributing to invasion success. Here, we showed the significant effects of competitors, which should be considered carefully when testing the EICA hypothesis.

Introduced species as evolutionary traps

USGS Publications Warehouse

Schlaepfer, Martin A.; Sherman, P.W.; Blossey, B.; Runge, M.C.

2005-01-01

Invasive species can alter environments in such a way that normal behavioural decision-making rules of native species are no longer adaptive. The evolutionary trap concept provides a useful framework for predicting and managing the impact of harmful invasive species. We discuss how native species can respond to changes in their selective regime via evolution or learning. We also propose novel management strategies to promote the long-term co-existence of native and introduced species in cases where the eradication of the latter is either economically or biologically unrealistic.

Population variation revealed high-altitude adaptation of Tibetan mastiffs.

PubMed

Li, Yan; Wu, Dong-Dong; Boyko, Adam R; Wang, Guo-Dong; Wu, Shi-Fang; Irwin, David M; Zhang, Ya-Ping

2014-05-01

With the assistance of their human companions, dogs have dispersed into new environments during the expansion of human civilization. Tibetan Mastiff (TM), a native of the Tibetan Plateau, was derived from the domesticated Chinese native dog and, like Tibetans, has adapted to the extreme environment of high altitude. Here, we genotyped genome-wide single-nucleotide polymorphisms (SNPs) from 32 TMs and compared them with SNPs from 20 Chinese native dogs and 14 gray wolves (Canis lupus). We identified 16 genes with signals of positive selection in the TM, with 12 of these candidate genes associated with functions that have roles in adaptation to high-altitude adaptation, such as EPAS1, SIRT7, PLXNA4, and MAFG that have roles in responses to hypoxia. This study provides important information on the genetic diversity of the TM and potential mechanisms for adaptation to hypoxia.

Characteristics of Middle School Students Learning Actions in Outdoor Mathematical Activities with the Cellular Phone

ERIC Educational Resources Information Center

Daher, Wajeeh; Baya'a, Nimer

2012-01-01

Learning in the cellular phone environment enables utilizing the multiple functions of the cellular phone, such as mobility, availability, interactivity, verbal and voice communication, taking pictures or recording audio and video, measuring time and transferring information. These functions together with mathematics-designated cellular phone…

Investigation of biomineralization by Raman spectroscopy

NASA Astrophysics Data System (ADS)

Fatscher, Robert William

Biomineralization is a process in which living organism grow composite materials consisting of inorganic and organic materials. This produces a composite material consisting of both inorganic and organic components, with superior mechanical properties. In the human body bone and dentin are both examples of biominerals. In this research Raman spectroscopy was used to characterize dentin from mice and human teeth, to determine composition. In the mouse tooth samples areas of irregular dentin were found, along the inside of the tooth, to be in the process of mineralization. By analyzing the samples along these areas we were able to determine the composition of dentin and track how it changed in these area. By analysis of the mineral to matrix ratio the areas of irregular dentin were determined to have less mineral present. Observations of other organic components and collagen in increased concentrations in this area suggested these area were in the process of biomineralization. The understanding of the structure of dentin and its biomineralization process is of crucial importance when trying reproduce dentin. Scientists and engineers are able to produce dentin minerals in vitro by culturing various dental stem cells. The ability to create dentin mineral from cells could lead to methods of repairing dentin in patients, or even lead to the creation of a completely engineered tooth. While dentin-like materials can be produced in a laboratory environment, analysis and comparison of the composition of these materials must be performed to ensure the mineral produced is consistent with dentin. Mineralized nodules from six different dental stem cell lines were cultured to produce a mineralized deposit. Utilizing Raman spectroscopy, we were able to determine cell source dependent differences in a variety of dental stem cells, and compare the mineral produced to native dentin. Orthopedic implants are implants used to replace damaged bone, examples include knee, hip and dental implants. These implants are designed to osteointegrate with the native healthy tissues in order to create a functionally stable and structural interface. Biomaterials such as hydroxyapatite and titania are known to increase the rate of bone regeneration in vivo.1 By accelerating the early response of bone forming cells to these implants, better fixation is achieved between the implant and the bone, shortening recovery times and increasing the viability of these implants. In the last part of this research an investigation of osteoblasts cultured at 14 days on five different heat-treated titania substrates was investigated by Raman spectroscopy, in order to observe the initial cellular response to the titania substrates. The heat-treatment of titania changes the amount of oxygen on it's surface which in turn effects the surface energy. A change in the surface energy of a material will affect the cellular response, by culturing cells on various heat-treated titania substrates a relationship between the surface energy and cellular response can be investigated. A faster cellular response would lead to an increased rate of bone regeneration shortening healing times and allowing for better fixation of the implant.

Microfluidic hydrogels for tissue engineering.

PubMed

Huang, Guo You; Zhou, Li Hong; Zhang, Qian Cheng; Chen, Yong Mei; Sun, Wei; Xu, Feng; Lu, Tian Jian

2011-03-01

With advanced properties similar to the native extracellular matrix, hydrogels have found widespread applications in tissue engineering. Hydrogel-based cellular constructs have been successfully developed to engineer different tissues such as skin, cartilage and bladder. Whilst significant advances have been made, it is still challenging to fabricate large and complex functional tissues due mainly to the limited diffusion capability of hydrogels. The integration of microfluidic networks and hydrogels can greatly enhance mass transport in hydrogels and spatiotemporally control the chemical microenvironment of cells, mimicking the function of native microvessels. In this review, we present and discuss recent advances in the fabrication of microfluidic hydrogels from the viewpoint of tissue engineering. Further development of new hydrogels and microengineering technologies will have a great impact on tissue engineering.

Biotic and abiotic controls of argentine ant invasion success at local and landscape scales

USGS Publications Warehouse

Menke, S.B.; Fisher, R.N.; Jetz, W.; Holway, D.A.

2007-01-01

Although the ecological success of introduced species hinges on biotic interactions and physical conditions, few experimental studies - especially on animals - have simultaneously investigated the relative importance of both types of factors. The lack of such research may stem from the common assumption that native and introduced species exhibit similar environmental tolerances. Here we combine experimental and spatial modeling approaches (1) to determine the relative importance of biotic and abiotic controls of Argentine ant (Linepithema humile) invasion success, (2) to examine how the importance of these factors changes with spatial scale in southern California (USA), and (3) to assess how Argentine ants differ from native ants in their environmental tolerances. A factorial field experiment that combined native ant removal with irrigation revealed that Argentine ants failed to invade any dry plots (even those lacking native ants) but readily invaded all moist plots. Native ants slowed the spread of Argentine ants into irrigated plots but did not prevent invasion. In areas without Argentine ants, native ant species showed variable responses to irrigation. At the landscape scale, Argentine ant occurrence was positively correlated with minimum winter temperature (but not precipitation), whereas native ant diversity increased with precipitation and was negatively correlated with minimum winter temperature. These results are of interest for several reasons. First, they demonstrate that fine-scale differences in the physical environment can eclipse biotic resistance from native competitors in determining community susceptibility to invasion. Second, our results illustrate surprising complexities with respect to how the abiotic factors limiting invasion can change with spatial scale, and third, how native and invasive species can differ in their responses to the physical environment. Idiosyncratic and scale-dependent processes complicate attempts to forecast where introduced species will occur and how their range limits may shift as a result of climate change. ?? 2007 by the Ecological Society of America.

Perception of Native English Reduced Forms in Adverse Environments by Chinese Undergraduate Students

ERIC Educational Resources Information Center

Wong, Simpson W. L.; Tsui, Jenny K. Y.; Chow, Bonnie Wing-Yin; Leung, Vina W. H.; Mok, Peggy; Chung, Kevin Kien-Hoa

2017-01-01

Previous research has shown that learners of English-as-a-second-language (ESL) have difficulties in understanding connected speech spoken by native English speakers. Extending from past research limited to quiet listening condition, this study examined the perception of English connected speech presented under five adverse conditions, namely…

Facilitation and interference of seedling establishment by a native legume before and after wildfire

Treesearch

Erin Goergen; Jeanne C. Chambers

2011-01-01

In semi-arid ecosystems, heterogeneous resources can lead to variable seedling recruitment. Existing vegetation can influence seedling establishment by modifying the resource and physical environment. We asked how a native legume, Lupinus argenteus, modifies microenvironments in unburned and burned sagebrush steppe, and if L. argenteus presence facilitates seedling...

The multitrophic consequences of concurrent insect invasions: a range-expanding herbivore and its associated parasitoid affect native tritrophic interactions

USDA-ARS?s Scientific Manuscript database

Global climatic changes may lead to the arrival of range-expanding species into new environments. Species from different trophic levels sharing the same climatic niche may invade new habitats simultaneously or in quick succession, causing the formation of multiple novel interactions into native food...

Android: Call C Functions with the Native Development Kit (NDK)

DTIC Science & Technology

2016-09-01

guide is intended to assist programmers with how to attach an NDK plugin to an Android Integrated Development Environment and how to call C functions...written in Java to interact with native C/C++. This guide is intended to take programmers through adding an NDK package into an Android Studio

Host-induced phenotypic diversification in Phytophthora ramorum

Treesearch

Takao Kasuga; Mai Bui; Christine Shoemaker; Elizabeth Bernhardt; Tedmund Swiecki; Kamyar Aram; David Rizzo; Melina Kozanitas; Matteo Garbelotto

2013-01-01

Forestry, agriculture, and native ecosystems face ever-increasing threats by invasive species. Not all introduced species are, however, invasive. In order to establish and persist in a non-native land, introduced species have to adapt to different environments, unfamiliar food, and predators. There are a number of examples where invasive species evolved quickly in non-...

Competence linguistique et environnement social (Linguistic Competence and Social Environment).

ERIC Educational Resources Information Center

Laflamme, Simon; Berger, Jacques

1988-01-01

A study found native French-speaking and native English-speaking university students had similar writing skill levels and error patterns despite their position as language-minority or language-majority members of society. It is concluded that language competency is not necessarily linked to language difficulty or to the position of the language.…

Succeeding in School: The Online Reflections of Native American and Other Minority Students

ERIC Educational Resources Information Center

Zyromski, Brett; Bryant, Alfred, Jr.; Gerler, Edwin R., Jr.

2011-01-01

This phenomenological study of students' online responses to the Succeeding in School program offers rare insight into how Native American and other minority students perceived and experienced their school environment. Students' strategies regarding behavior and attitude changes they would use to improve their success and counseling implications…

Teaching Values in Everything We Do: The Nativity Experience.

ERIC Educational Resources Information Center

Daly, Jennifer Grumhaus

1996-01-01

Nativity Prep, a small, inner-city Roman Catholic middle school seeks to provide an environment that helps students excel in their studies and their personal development. The school has few discipline problems due to its small size; its strict, highly structured academic climate; its underpaid and devoted faculty; and its practice of praying…

Wellness in the Workplace: Building a More Productive Institution.

ERIC Educational Resources Information Center

Crazy Bull, Cheryl; Prue, Alex Sr.

2003-01-01

Discusses the challenges unique to Native Americans in the workplace. Asserts that the effects of high rates of poverty, health problems, and violence in Native communities are often visible at the office. Offers suggestions for using cultural healing strategies in the workplace to create an environment of respect and support. (NB)

Topic Appropriateness in Cross-Cultural Social Conversations.

ERIC Educational Resources Information Center

Hinkel, Eli

A group of university students consisting of native speakers of Chinese (n=63), Japanese (n=33), Korean (n=21), Indonesian (n=20), and Arabic (n=13) with relatively extensive exposure to the American university environment and a control group of 20 native English-speakers were asked to rank the social appropriateness of 104 conversation topics.…

Dispersal and selection mediate hybridization between a native and invasive species

USGS Publications Warehouse

Kovach, Ryan P.; Muhlfeld, Clint C.; Boyer, Matthew C.; Lowe, Winsor H.; Allendorf, Fred W.; Luikart, Gordon

2015-01-01

Hybridization between native and non-native species has serious biological consequences, but our understanding of how dispersal and selection interact to influence invasive hybridization is limited. Here, we document the spread of genetic introgression between a native (Oncorhynchus clarkii) and invasive (Oncorhynchus mykiss) trout, and identify the mechanisms influencing genetic admixture. In two populations inhabiting contrasting environments, non-native admixture increased rapidly from 1984 to 2007 and was driven by surprisingly consistent processes. Individual admixture was related to two phenotypic traits associated with fitness: size at spawning and age of juvenile emigration. Fish with higher non-native admixture were larger and tended to emigrate at a younger age—relationships that are expected to confer fitness advantages to hybrid individuals. However, strong selection against non-native admixture was evident across streams and cohorts (mean selection coefficient against genotypes with non-native alleles (s) ¼ 0.60; s.e. ¼ 0.10). Nevertheless, hybridization was promoted in both streams by the continuous immigration of individuals with high levels of non-native admixture from other hybrid source populations. Thus, antagonistic relationships between dispersal and selection are mediating invasive hybridization between these fish, emphasizing that data on dispersal and natural selection are needed to fully understand the dynamics of introgression between native and non-native species. .

Rupturing Giant Plasma Membrane Vesicles to Form Micron-sized Supported Cell Plasma Membranes with Native Transmembrane Proteins.

PubMed

Chiang, Po-Chieh; Tanady, Kevin; Huang, Ling-Ting; Chao, Ling

2017-11-09

Being able to directly obtain micron-sized cell blebs, giant plasma membrane vesicles (GPMVs), with native membrane proteins and deposit them on a planar support to form supported plasma membranes could allow the membrane proteins to be studied by various surface analytical tools in native-like bilayer environments. However, GPMVs do not easily rupture on conventional supports because of their high protein and cholesterol contents. Here, we demonstrate the possibility of using compression generated by the air-water interface to efficiently rupture GPMVs to form micron-sized supported membranes with native plasma membrane proteins. We demonstrated that not only lipid but also a native transmembrane protein in HeLa cells, Aquaporin 3 (AQP3), is mobile in the supported membrane platform. This convenient method for generating micron-sized supported membrane patches with mobile native transmembrane proteins could not only facilitate the study of membrane proteins by surface analytical tools, but could also enable us to use native membrane proteins for bio-sensing applications.

Gender differences in resource use and evaluation of attributes of places of resource use by Native Americans and Caucasians from Western Idaho: relevance to risk evaluations.

PubMed

Burger, Joanna; Gochfeld, Michael

2010-01-01

A substantial body of literature deals with exposure differences between men and women, and how men and women perceive environmental risk, but far less attention has been devoted to how men and women use the environment and how they evaluate the features of natural environments. The objective of this study was to examine gender differences in the perceptions of environmental quality and resource use for Native Americans and Caucasians interviewed at an Indian festival in northwestern Idaho. More individuals engaged in fishing than any other consumptive activity, and more people engaged in camping and hiking than other nonconsumptive activities. For both ethnic groups, significantly more men hunted than women, although a higher percentage of Native Americans of both genders hunted than did Caucasians. Although significantly more Caucasian men fished than women (63 vs. 41%), there were no marked differences in fishing for Native Americans. Significantly more Native American women gathered herbs (57%) compared to men (37%). There were no significant gender differences in nonconsumptive activities (camping, hiking, biking, bird watching, or picnicking). For those who engaged in consumptive and nonconsumptive activities, however, there were few gender differences in the frequency of these activities, except for fishing, hunting, and crabbing by Caucasians (men had higher rates) and collecting berries and herbs for Native Americans (women had higher rates). When asked to evaluate environmental characteristics or attributes on a scale of 1 (less important) to 5 (very important), unpolluted water, clean air, no visible smog, unpolluted groundwater, and appears unspoiled were rated the highest. There were few significant gender differences in these evaluations for Native Americans, but there were significant gender differences for Caucasians: Women rated most features higher than did men (except for natural tidal flow). These data indicate a need to evaluate not only consumption rate differences between men and women, but also nonconsumptive activities, as well as resource values and perceptions, when managing environments and determining potential risk from exposure.

Distinct Cellular Locations of Carbonic Anhydrases Mediate Carbon Dioxide Control of Stomatal Movements1[OPEN

PubMed Central

Hu, Honghong; Rappel, Wouter-Jan; Occhipinti, Rossana; Ries, Amber; Böhmer, Maik; You, Lei; Xiao, Chuanlei; Engineer, Cawas B.; Boron, Walter F.; Schroeder, Julian I.

2015-01-01

Elevated carbon dioxide (CO2) in leaves closes stomatal apertures. Research has shown key functions of the β-carbonic anhydrases (βCA1 and βCA4) in rapid CO2-induced stomatal movements by catalytic transmission of the CO2 signal in guard cells. However, the underlying mechanisms remain unclear, because initial studies indicate that these Arabidopsis (Arabidopsis thaliana) βCAs are targeted to distinct intracellular compartments upon expression in tobacco (Nicotiana benthamiana) cells. Which cellular location of these enzymes plays a key role in native guard cells in CO2-regulated stomatal movements remains unknown. Here, we express fluorescently tagged CAs in guard cells of ca1ca4 double-mutant plants and show that the specific locations of βCA4 at the plasma membrane and βCA1 in native guard cell chloroplasts each can mediate rapid CO2 control of stomatal movements. Localization and complementation analyses using a mammalian αCAII-yellow fluorescent protein in guard cells further show that cytoplasmic localization is also sufficient to restore CO2 regulation of stomatal conductance. Mathematical modeling of cellular CO2 catalysis suggests that the dynamics of the intracellular HCO3− concentration change in guard cells can be driven by plasma membrane and cytoplasmic localizations of CAs but not as clearly by chloroplast targeting. Moreover, modeling supports the notion that the intracellular HCO3− concentration dynamics in guard cells are a key mechanism in mediating CO2-regulated stomatal movements but that an additional chloroplast role of CAs exists that has yet to be identified. PMID:26243620

Gas Transfer in Cellularized Collagen-Membrane Gas Exchange Devices.

PubMed

Lo, Justin H; Bassett, Erik K; Penson, Elliot J N; Hoganson, David M; Vacanti, Joseph P

2015-08-01

Chronic lower respiratory disease is highly prevalent in the United States, and there remains a need for alternatives to lung transplant for patients who progress to end-stage lung disease. Portable or implantable gas oxygenators based on microfluidic technologies can address this need, provided they operate both efficiently and biocompatibly. Incorporating biomimetic materials into such devices can help replicate native gas exchange function and additionally support cellular components. In this work, we have developed microfluidic devices that enable blood gas exchange across ultra-thin collagen membranes (as thin as 2 μm). Endothelial, stromal, and parenchymal cells readily adhere to these membranes, and long-term culture with cellular components results in remodeling, reflected by reduced membrane thickness. Functionally, acellular collagen-membrane lung devices can mediate effective gas exchange up to ∼288 mL/min/m(2) of oxygen and ∼685 mL/min/m(2) of carbon dioxide, approaching the gas exchange efficiency noted in the native lung. Testing several configurations of lung devices to explore various physical parameters of the device design, we concluded that thinner membranes and longer gas exchange distances result in improved hemoglobin saturation and increases in pO2. However, in the design space tested, these effects are relatively small compared to the improvement in overall oxygen and carbon dioxide transfer by increasing the blood flow rate. Finally, devices cultured with endothelial and parenchymal cells achieved similar gas exchange rates compared with acellular devices. Biomimetic blood oxygenator design opens the possibility of creating portable or implantable microfluidic devices that achieve efficient gas transfer while also maintaining physiologic conditions.

Distinct Cellular Locations of Carbonic Anhydrases Mediate Carbon Dioxide Control of Stomatal Movements

DOE PAGES

Hu, Honghong; Rappel, Wouter-Jan; Occhipinti, Rossana; ...

2015-09-28

Elevated carbon dioxide (CO 2) in leaves closes stomatal apertures. Research has shown key functions of the β-carbonic anhydrases (βCA1 and βCA4) in rapid CO 2-induced stomatal movements by catalytic transmission of the CO 2 signal in guard cells. But, the underlying mechanisms remain unclear, because initial studies indicate that these Arabidopsis (Arabidopsis thaliana) βCAs are targeted to distinct intracellular compartments upon expression in tobacco (Nicotiana benthamiana) cells. Which cellular location of these enzymes plays a key role in native guard cells in CO 2-regulated stomatal movements remains unknown. We express fluorescently tagged CAs in guard cells of ca1ca4 double-mutantmore » plants and show that the specific locations of βCA4 at the plasma membrane and βCA1 in native guard cell chloroplasts each can mediate rapid CO 2 control of stomatal movements. Localization and complementation analyses using a mammalian αCAII-yellow fluorescent protein in guard cells further show that cytoplasmic localization is also sufficient to restore CO 2 regulation of stomatal conductance. Mathematical modeling of cellular CO 2 catalysis suggests that the dynamics of the intracellular HCO 3 - concentration change in guard cells can be driven by plasma membrane and cytoplasmic localizations of CAs but not as clearly by chloroplast targeting. Therefore, modeling supports the notion that the intracellular HCO 3 - concentration dynamics in guard cells are a key mechanism in mediating CO 2 -regulated stomatal movements but that an additional chloroplast role of CAs exists that has yet to be identified.« less

Cellular thermotolerance is inheritable from Holstein cattle cloned with ooplasts of Taiwan native yellow cattle.

PubMed

Kesorn, Piyawit; Lee, Jai-Wei; Wu, Hung-Yi; Ju, Jyh-Cherng; Peng, Shao-Yu; Liu, Shyh-Shyan; Wu, Hsi-Hsun; Shen, Perng-Chih

2017-01-15

We have previously demonstrated that the somatic cells from cattle cloned with Holstein (H) donor cells and Taiwan native yellow cattle (Y) ooplasm (Yo-Hd) had better thermotolerance than those from cattle cloned with both Holstein donor cells and ooplasm (Ho-Hd). The present study aimed to investigate whether the cellular thermotolerance of these cloned cattle is transmissible to their offspring (Ho-Hd-F1 and Yo-Hd-F1). Thermotolerance of ear fibroblasts derived from these cloned cattle and their offspring were analyzed. Polymorphisms in mitochondrial DNA (mtDNA) D-loop of ear fibroblasts derived from Yo-Hd and Yo-Hd-F1 indicated that the cytoplasm is originated from Bos indicus (Y). After heat shock, the apoptotic rates, B-cell lymphoma 2-associated X protein/B-cell lymphoma 2 ratios, and relative expression levels of cysteine-aspartic proteases (caspases)-3, -8, and -9 of ear fibroblasts with Y-originated cytoplasm (including Y, Yo-Hd, and Yo-Hd-F1) were lower (P < 0.05) than those of ear fibroblasts with H-originated cytoplasm (including H, Ho-Hd, and Ho-Hd-F1). In contrast, the relative level of HSP-70 was higher (P < 0.05) in ear fibroblasts with Y-originated cytoplasm than that of with H-originated cytoplasm. Based on our results, thermotolerance of ear fibroblasts derived from Yo-Hd and Yo-Hd-F1 cattle is better and can be transmitted, at least at the cellular level, to their offspring. Copyright © 2016 Elsevier Inc. All rights reserved.

Gene, Immune and Cellular Responses to Single and Combined Space Flight Conditions-B (TripleLux-B):

NASA Image and Video Library

2015-03-31

ISS043E070945 (03/31/2015) --- ESA (European Space Agency) astronaut Samantha Cristoforetti, Expedition 43 flight engineer aboard the International Space Station, is seen working on a science experiment that includes photographic documentation of Cellular Responses to Single and Combined Space Flight Conditions. Some effects of the space environment level appear to act at the cellular level and it is important to understand the underlying mechanisms of these effects. This science project uses invertebrate hemocytes to focus on two aspects of cellular function which may have medical importance. The synergy between the effects of the space radiation environment and microgravity on cellular function is the goal of this experiment along with studying the impairment of immune functions under spaceflight conditions.

The Protein Kingdom Extended: Ordered and Intrinsically Disordered Proteins, Their Folding, Supramolecular Complex Formation, and Aggregation

PubMed Central

Turoverov, Konstantin K.; Kuznetsova, Irina M.; Uversky, Vladimir N.

2010-01-01

The native state of a protein is usually associated with a compact globular conformation possessing a rigid and highly ordered structure. At the turn of the last century certain studies arose which concluded that many proteins cannot, in principle, form a rigid globular structure in an aqueous environment, but they are still able to fulfill their specific functions — i.e., they are native. The existence of the disordered regions allows these proteins to interact with their numerous binding partners. Such interactions are often accompanied by the formation of complexes that possess a more ordered structure than the original components. The functional diversity of these proteins, combined with the variability of signals related to the various intra-and intercellular processes handled by these proteins and their capability to produce multi-variant and multi-directional responses allow them to form a unique regulatory net in a cell. The abundance of disordered proteins inside the cell is precisely controlled at the synthesis and clearance levels as well as via interaction with specific binding partners and posttranslational modifications. Another recently recognized biologically active state of proteins is the functional amyloid. The formation of such functional amyloids is tightly controlled and therefore differs from the uncontrolled formation of pathogenic amyloids which are associated with the pathogenesis of several conformational diseases, the development of which is likely to be determined by the failures of the cellular regulatory systems rather than by the formation of the proteinaceous deposits and/or by the protofibril toxicity. PMID:20097220

Binding affinity of amyloid oligomers to cellular membranes is a generic indicator of cellular dysfunction in protein misfolding diseases

PubMed Central

Evangelisti, Elisa; Cascella, Roberta; Becatti, Matteo; Marrazza, Giovanna; Dobson, Christopher M.; Chiti, Fabrizio; Stefani, Massimo; Cecchi, Cristina

2016-01-01

The conversion of peptides or proteins from their soluble native states into intractable amyloid deposits is associated with a wide range of human disorders. Misfolded protein oligomers formed during the process of aggregation have been identified as the primary pathogenic agents in many such conditions. Here, we show the existence of a quantitative relationship between the degree of binding to neuronal cells of different types of oligomers formed from a model protein, HypF-N, and the GM1 content of the plasma membranes. In addition, remarkably similar behavior is observed for oligomers of the Aβ42 peptide associated with Alzheimer’s disease. Further analysis has revealed the existence of a linear correlation between the level of the influx of Ca2+ across neuronal membranes that triggers cellular damage, and the fraction of oligomeric species bound to the membrane. Our findings indicate that the susceptibility of neuronal cells to different types of misfolded oligomeric assemblies is directly related to the extent of binding of such oligomers to the cellular membrane. PMID:27619987

Interplay of secondary structures and side-chain contacts in the denatured state of BBA1

NASA Astrophysics Data System (ADS)

Wen, Edward Z.; Luo, Ray

2004-08-01

The denatured state of a miniprotein BBA1 is studied under the native condition with the AMBER/Poisson-Boltzmann energy model and with the self-guided enhanced sampling technique. Forty independent trajectories are collected to sample the highly diversified denatured structures. Our simulation data show that the denatured BBA1 contains high percentage of native helix and native turn, but low percentage of native hairpin. Conditional population analysis indicates that the native helix formation and the native hairpin formation are not cooperative in the denatured state. Side-chain analysis shows that the native hydrophobic contacts are more preferred than the non-native hydrophobic contacts in the denatured BBA1. In contrast, the salt-bridge contacts are more or less nonspecific even if their populations are higher than those of hydrophobic contacts. Analysis of the trajectories shows that the native helix mostly initiates near the N terminus and propagates to the C terminus, and mostly forms from 310-helix/turn to α helix. The same analysis shows that the native turn is important but not necessary in its formation in the denatured BBA1. In addition, the formations of the two strands in the native hairpin are rather asymmetric, demonstrating the likely influence of the protein environment. Energetic analysis shows that the native helix formation is largely driven by electrostatic interactions in denatured BBA1. Further, the native helix formation is associated with the breakup of non-native salt-bridge contacts and the accumulation of native salt-bridge contacts. However, the native hydrophobic contacts only show a small increase upon the native helix formation while the non-native hydrophobic contacts stay essentially the same, different from the evolution of hydrophobic contacts observed in an isolated helix folding.

Cell-laden composite suture threads for repairing damaged tendons.

PubMed

Costa-Almeida, Raquel; Domingues, Rui M A; Fallahi, Afsoon; Avci, Huseyin; Yazdi, Iman K; Akbari, Mohsen; Reis, Rui L; Tamayol, Ali; Gomes, Manuela E; Khademhosseini, Ali

2018-04-01

Tendons have limited regenerative capacity due to their low cellularity and hypovascular nature, which results in poor clinical outcomes of presently used therapies. As tendon injuries are often observed in active adults, it poses an increasing socio-economic burden on healthcare systems. Currently, suture threads are used during surgical repair to anchor the tissue graft or to connect injured ends. Here, we created composite suture threads coated with a layer of cell-laden hydrogel that can be used for bridging the injured tissue aiming at tendon regeneration. In addition, the fibres can be used to engineer 3-dimensional constructs through textile processes mimicking the architecture and mechanical properties of soft tissues, including tendons and ligaments. Encapsulated human tendon-derived cells migrated within the hydrogel and aligned at the surface of the core thread. An up-regulation of tendon-related genes (scleraxis and tenascin C) and genes involved in matrix remodelling (matrix metalloproteinases 1, matrix metalloproteinases 2) was observed. Cells were able to produce a collagen-rich matrix, remodelling their micro-environment, which is structurally comparable to native tendon tissue. Copyright © 2017 John Wiley & Sons, Ltd.

LRAT-specific domain facilitates vitamin A metabolism by domain swapping in HRASLS3

DOE PAGES

Golczak, Marcin; Sears, Avery E.; Kiser, Philip D.; ...

2014-11-10

Cellular uptake of vitamin A, production of visual chromophore and triglyceride homeostasis in adipocytes depend on two representatives of the vertebrate N1pC/P60 protein family, lecithin:retinol acyltransferase (LRAT) and HRAS-like tumor suppressor 3 (HRASLS3). Both proteins function as lipid-metabolizing enzymes but differ in their substrate preferences and dominant catalytic activity. The mechanism of this catalytic diversity is not understood. In this paper, by using a gain-of-function approach, we identified a specific sequence responsible for the substrate specificity of N1pC/P60 proteins. A 2.2-Å crystal structure of the HRASLS3-LRAT chimeric enzyme in a thioester catalytic intermediate state revealed a major structural rearrangement accompaniedmore » by three-dimensional domain swapping dimerization not observed in native HRASLS proteins. Structural changes affecting the active site environment contributed to slower hydrolysis of the catalytic intermediate, supporting efficient acyl transfer. Finally, these findings reveal structural adaptation that facilitates selective catalysis and mechanism responsible for diverse substrate specificity within the LRAT-like enzyme family.« less

Correlation of Electron-Transfer Rates with the Surface Density of States of Native and Anodically Grown Oxide Films on Titanium

DTIC Science & Technology

1990-11-16

materials. v :67:RiB T7;N, AVAILA81UTY CF ABS-.RAC- 21. ABSTRAC7 SEC-RTY C .SSi~ CAT ;CN X NC_SSF:E- /UNL:MITE- : C SA.ME AS ;P’ C C jSE’S Unclassified i...value in ambient environments. Localized breakdown of the native film occurs in chemically aggresive environments (e.g., aqueous Br- solutions...oxide film, Fig. 1 (c), show highly rectifying behavior , in agreement with expectations for a large band gap semiconductor. The tunneling current at each

Comparative analysis of the immune responses induced by native versus recombinant versions of the ASP-based vaccine against the bovine intestinal parasite Cooperia oncophora.

PubMed

González-Hernández, Ana; Borloo, Jimmy; Peelaers, Iris; Casaert, Stijn; Leclercq, Georges; Claerebout, Edwin; Geldhof, Peter

2018-01-01

The protective capacities of a native double-domain activation-associated secreted protein (ndd-ASP)-based vaccine against the cattle intestinal nematode Cooperia oncophora has previously been demonstrated. However, protection analysis upon vaccination with a recombinantly produced antigen has never been performed. Therefore, the aim of the current study was to test the protective potential of a Pichia-produced double-domain ASP (pdd-ASP)-based vaccine against C. oncophora. Additionally, we aimed to compare the cellular and humoral mechanisms underlying the vaccine-induced responses by the native (ndd-ASP) and recombinant vaccines. Immunisation of cattle with the native C. oncophora vaccine conferred significant levels of protection after an experimental challenge infection, whereas the recombinant vaccine did not. Moreover, vaccination with ndd-ASP resulted in a higher proliferation of CD4-T cells both systemically and in the small intestinal mucosa when compared with animals vaccinated with the recombinant antigen. In terms of humoral response, although both native and recombinant vaccines induced similar levels of antibodies, animals vaccinated with the native vaccine were able to raise antibodies with greater specificity towards ndd-ASP in comparison with antibodies raised by vaccination with the recombinant vaccine, suggesting a differential immune recognition towards the ndd-ASP and pdd-ASP. Finally, the observation that animals displaying antibodies with higher percentages of recognition towards ndd-ASP also exhibited the lowest egg counts suggests a potential relationship between antibody specificity and protection. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Exploring the relevance of gas-phase structures to biology: cold ion spectroscopy of the decapeptide neurokinin A.

PubMed

Pereverzev, A Y; Boyarkin, O V

2017-02-01

Linking the intrinsic tertiary structures of biomolecules to their native geometries is a central prerequisite for making gas-phase studies directly relevant to biology. The isolation of molecules in the gas phase eliminates hydrophilic interactions with solvents, to some extent mimicking a hydrophobic environment. Intrinsic structures therefore may resemble native ones for peptides that in vivo reside in a hydrophobic environment (e.g., binding pockets of receptors). In this study, we investigate doubly protonated neurokinin A (NKA) using IR-UV double resonance cold ion spectroscopy and find only five conformers of this decapeptide in the gas phase. In contrast, NMR data show that in aqueous solutions, NKA exhibits high conformational heterogeneity, which reduces to a few well-defined structures in hydrophobic micelles. Do the gas-phase structures of NKA resemble these native structures? The IR spectra reported here allow the validation of future structural calculations that may answer this question.

Low Predictability of Colour Polymorphism in Introduced Guppy (Poecilia reticulata) Populations in Panama

PubMed Central

Martínez, Celestino; Chavarría, Carmen; Sharpe, Diana M. T.; De León, Luis Fernando

2016-01-01

Colour polymorphism is a recurrent feature of natural populations, and its maintenance has been studied in a range of taxa in their native ranges. However, less is known about whether (and how) colour polymorphism is maintained when populations are removed from their native environments, as in the case of introduced species. We here address this issue by analyzing variation in colour patterns in recently-discovered introduced populations of the guppy (Poecilia reticulata) in Panama. Specifically, we use classic colour analysis to estimate variation in the number and the relative area of different colour spots across low predation sites in the introduced Panamanian range of the species. We then compare this variation to that found in the native range of the species under low- and high predation regimes. We found aspects of the colour pattern that were both consistent and inconsistent with the classical paradigm of colour evolution in guppies. On one hand, the same colours that dominated in native populations (orange, iridescent and black) were also the most dominant in the introduced populations in Panama. On the other, there were no clear differences between either introduced-low and native low- and high predation populations. Our results are therefore only partially consistent with the traditional role of female preference in the absence of predators, and suggest that additional factors could influence colour patterns when populations are removed from their native environments. Future research on the interaction between female preference and environmental variability (e.g. multifarious selection), could help understand adaptive variation in this widely-introduced species, and the contexts under which variation in adaptive traits parallels (or not) variation in the native range. PMID:26863538

Low Predictability of Colour Polymorphism in Introduced Guppy (Poecilia reticulata) Populations in Panama.

PubMed

Martínez, Celestino; Chavarría, Carmen; Sharpe, Diana M T; De León, Luis Fernando

2016-01-01

Colour polymorphism is a recurrent feature of natural populations, and its maintenance has been studied in a range of taxa in their native ranges. However, less is known about whether (and how) colour polymorphism is maintained when populations are removed from their native environments, as in the case of introduced species. We here address this issue by analyzing variation in colour patterns in recently-discovered introduced populations of the guppy (Poecilia reticulata) in Panama. Specifically, we use classic colour analysis to estimate variation in the number and the relative area of different colour spots across low predation sites in the introduced Panamanian range of the species. We then compare this variation to that found in the native range of the species under low- and high predation regimes. We found aspects of the colour pattern that were both consistent and inconsistent with the classical paradigm of colour evolution in guppies. On one hand, the same colours that dominated in native populations (orange, iridescent and black) were also the most dominant in the introduced populations in Panama. On the other, there were no clear differences between either introduced-low and native low- and high predation populations. Our results are therefore only partially consistent with the traditional role of female preference in the absence of predators, and suggest that additional factors could influence colour patterns when populations are removed from their native environments. Future research on the interaction between female preference and environmental variability (e.g. multifarious selection), could help understand adaptive variation in this widely-introduced species, and the contexts under which variation in adaptive traits parallels (or not) variation in the native range.

Chitosan based hydrogels: characteristics and pharmaceutical applications

PubMed Central

Ahmadi, F.; Oveisi, Z.; Samani, S. Mohammadi; Amoozgar, Z.

2015-01-01

Hydrogel scaffolds serve as semi synthetic or synthetic extra cellular matrix to provide an amenable environment for cellular adherence and cellular remodeling in three dimensional structures mimicking that of natural cellular environment. Additionally, hydrogels have the capacity to carry small molecule drugs and/or proteins, growth factors and other necessary components for cell growth and differentiation. In the context of drug delivery, hydrogels can be utilized to localize drugs, increase drugs concentration at the site of action and consequently reduce off-targeted side effects. The current review aims to describe and classify hydrogels and their methods of production. The main highlight is chitosan-based hydrogels as biocompatible and medically relevant hydrogels for drug delivery. PMID:26430453

Non-native plants add to the British flora without negative consequences for native diversity.

PubMed

Thomas, Chris D; Palmer, G

2015-04-07

Plants are commonly listed as invasive species, presuming that they cause harm at both global and regional scales. Approximately 40% of all species listed as invasive within Britain are plants. However, invasive plants are rarely linked to the national or global extinction of native plant species. The possible explanation is that competitive exclusion takes place slowly and that invasive plants will eventually eliminate native species (the "time-to-exclusion hypothesis"). Using the extensive British Countryside Survey Data, we find that changes to plant occurrence and cover between 1990 and 2007 at 479 British sites do not differ between native and non-native plant species. More than 80% of the plant species that are widespread enough to be sampled are native species; hence, total cover changes have been dominated by native species (total cover increases by native species are more than nine times greater than those by non-native species). This implies that factors other than plant "invasions" are the key drivers of vegetation change. We also find that the diversity of native species is increasing in locations where the diversity of non-native species is increasing, suggesting that high diversities of native and non-native plant species are compatible with one another. We reject the time-to-exclusion hypothesis as the reason why extinctions have not been observed and suggest that non-native plant species are not a threat to floral diversity in Britain. Further research is needed in island-like environments, but we question whether it is appropriate that more than three-quarters of taxa listed globally as invasive species are plants.

Are invasive plants more competitive than native conspecifics? Patterns vary with competitors

PubMed Central

Zheng, Yulong; Feng, Yulong; Valiente-Banuet, Alfonso; Li, Yangping; Liao, Zhiyong; Zhang, Jiaolin; Chen, Yajun

2015-01-01

Invasive plants are sometimes considered to be more competitive than their native conspecifics, according to the prediction that the invader reallocates resources from defense to growth due to liberation of natural enemies [‘Evolution of Increased Competitive Ability’ (EICA) hypothesis]. However, the differences in competitive ability may depend on the identity of competitors. In order to test the effects of competitors, Ageratina adenophora plants from both native and invasive ranges competed directly, and competed with native residents from both invasive (China) and native (Mexico) ranges respectively. Invasive A. adenophora plants were more competitive than their conspecifics from native populations when competing with natives from China (interspecific competition), but not when competing with natives from Mexico. Invasive A. adenophora plants also showed higher competitive ability when grown in high-density monoculture communities of plants from the same population (intrapopulation competition). In contrast, invasive A. adenophora plants showed lower competitive ability when competing with plants from native populations (intraspecific competition). Our results indicated that in the invasive range A. adenophora has evolved to effectively cope with co-occurring natives and high density environments, contributing to invasion success. Here, we showed the significant effects of competitors, which should be considered carefully when testing the EICA hypothesis. PMID:26489964

Native plants fare better against an introduced competitor with native microbes and lower nitrogen availability

PubMed Central

Shivega, W. Gaya

2017-01-01

Abstract While the soil environment is generally acknowledged as playing a role in plant competition, the relative importance of soil resources and soil microbes in determining outcomes of competition between native and exotic plants has rarely been tested. Resilience of plant communities to invasion by exotic species may depend on the extent to which native and exotic plant performance are mediated by abiotic and biotic components of the soil. We used a greenhouse experiment to compare performance of two native prairie plant species and one exotic species, when grown in intraspecific competition and when each native was grown in interspecific competition with the exotic species, in the presence and absence of a native prairie soil community, and when nitrogen availability was elevated or was maintained at native prairie levels. We found that elevated nitrogen availability was beneficial to the exotic species and had no effect on or was detrimental to the native plant species, that the native microbial community was beneficial to the native plant species and either had no effect or was detrimental to the exotic species and that intraspecific competition was stronger than interspecific competition for the exotic plant species and vice versa for the natives. Our results demonstrate that soil nitrogen availability and the soil microbial community can mediate the strength of competition between native and exotic plant species. We found no evidence for native microbes enhancing the performance of the exotic plant species. Instead, loss of the native soil microbial community appears to reinforce the negative effects of elevated N on native plant communities and its benefits to exotic invasive species. Resilience of plant communities to invasion by exotic plant species is facilitated by the presence of an intact native soil microbial community and weakened by anthropogenic inputs of nitrogen. PMID:28122737

Ecological disequilibrium drives insect pest and pathogen accumulation in non-native trees

PubMed Central

Burgess, Treena I.; Le Roux, Johannes J.; Richardson, David M.; Slippers, Bernard; Wingfield, Michael J.

2017-01-01

Abstract Non-native trees have become dominant components of many landscapes, including urban ecosystems, commercial forestry plantations, fruit orchards and as invasives in natural ecosystems. Often, these trees have been separated from their natural enemies (i.e. insects and pathogens) leading to ecological disequilibrium, that is, the immediate breakdown of historically co-evolved interactions once introduced into novel environments. Long-established, non-native tree plantations provide useful experiments to explore the dimensions of such ecological disequilibria. We quantify the status quo of non-native insect pests and pathogens catching up with their tree hosts (planted Acacia, Eucalyptus and Pinus species) in South Africa, and examine which native South African enemy species utilize these trees as hosts. Interestingly, pines, with no confamilial relatives in South Africa and the longest residence time (almost two centuries), have acquired only one highly polyphagous native pathogen. This is in contrast to acacias and eucalypts, both with many native and confamilial relatives in South Africa that have acquired more native pathogens. These patterns support the known role of phylogenetic relatedness of non-native and native floras in influencing the likelihood of pathogen shifts between them. This relationship, however, does not seem to hold for native insects. Native insects appear far more likely to expand their feeding habits onto non-native tree hosts than are native pathogens, although they are generally less damaging. The ecological disequilibrium conditions of non-native trees are deeply rooted in the eco-evolutionary experience of the host plant, co-evolved natural enemies and native organisms from the introduced range. We should expect considerable spatial and temporal variation in ecological disequilibrium conditions among non-native taxa, which can be significantly influenced by biosecurity and management practices. PMID:28013250

Rating the YouTube Indian: Viewer Ratings of Native American Portrayals on a Viral Video Site

ERIC Educational Resources Information Center

Kopacz, Maria A.; Lawton, Bessie Lee

2011-01-01

Online outlets for user-generated content (UGC) like YouTube have created environments for alternative depictions of marginalized groups, as UGC can be contributed by anyone with basic technology access. Preliminary findings on UGC relating to Native Americans confirm some favorable departures from the distortions prevalent in the old media. The…

Beneficial fungal interactions resulting in accelerated germination of Astragalus utahensis, a hard-seeded legume

Treesearch

Sean D. Eldredge

2007-01-01

Seed germination is pivotal in the life cycle of native plants in a restorative context because initiation of the metabolic processes critical to establishment is key to survival in such a competitive environment. Dormancy characteristics of some native plants including the subject species, Astragalus utahensis, have evolved mechanisms to control...

Natural mixing of species: novel plant–animal communities on Caribbean Islands

Treesearch

Ariel E. Lugo; T.A. Carlo; Jr. Wunderle

2012-01-01

Global anthropogenic activities are responsible for the modification of landscapes, creation of novel environments and movement of species across biogeographic regions. A consequence of this activity is the mixing of native and introduced species and the formation of novel biotic communities. We review the ecological consequences of the mixing of native and introduced...

Maternal Gambling, Parenting, and Child Behavioral Functioning in Native American Families

ERIC Educational Resources Information Center

Momper, Sandra L.; Jackson, Aurora P.

2007-01-01

Using data from a sample of 150 Native American mothers of a child 6 to 15 years old, this study examined the relations between and among mothers' gambling, parenting in the home environment, social supports, and child behavior problems. Respondents were recruited from a tribal casino on a Great Lakes Indian reservation. Results indicate that…

Collaborative Learning and Support Environment for Teachers in Native American Pueblo Schools in New Mexico

ERIC Educational Resources Information Center

Kilde, Josephine

2016-01-01

Teachers in rural Native American Pueblo schools in New Mexico lack professional development opportunities due to the long distances between the Pueblos and academic institutions. Previously, most schools received "hit and run" professional development sessions conducted once or twice a year that did not address the real issues faced by…

Valuing Native American Tribal Elders and Stories for Sustainability Study

ERIC Educational Resources Information Center

Gritter, Kristine; Scheurerman, Richard; Strong, Cindy; Schuster, Carrie Jim; Williams, Tracy

2016-01-01

This article outlines a framework the authors have used to infuse sustainability study into humanities teaching at the middle school level. Native American tribal elders can act as co-teachers in such classrooms, and the place-based stories that shaped their views of the environment can serve as important classroom texts to investigate sustainable…

Common pathways by which non-native forest insects move internationally and domestically

Treesearch

Nicolas Meurisse; Davide Rassati; Brett P. Hurley; Eckehard G. Brockerhoff; Robert A. Haack

2018-01-01

International trade and movement of people are largely responsible for increasing numbers of non-native insect introductions to new environments. For forest insects, trade in live plants and transport of wood packaging material (WPM) are considered the most important pathways facilitating long-distance invasions. These two pathways as well as trade in firewood, logs,...

Iowa's Environment.

ERIC Educational Resources Information Center

Ruth, Amy, Ed.

1994-01-01

This theme issue explores the changes in Iowa's environment. When Native Americans lived in Iowa hundreds of years ago, the land was rich in tall grasslands, fertile soil, wildlife, wetlands, and unpolluted waters. When European-American pioneers settled Iowa in 1833, they changed the environment in order to survive. The first article in this…

Design and Implementation of an Intelligent Virtual Environment for Improving Speaking and Listening Skills

ERIC Educational Resources Information Center

Hassani, Kaveh; Nahvi, Ali; Ahmadi, Ali

2016-01-01

In this paper, we present an intelligent architecture, called intelligent virtual environment for language learning, with embedded pedagogical agents for improving listening and speaking skills of non-native English language learners. The proposed architecture integrates virtual environments into the Intelligent Computer-Assisted Language…

What Is Life? What Was Life? What Will Life Be?

NASA Astrophysics Data System (ADS)

Deamer, D.

Our laboratory is exploring self-assembly processes and polymerization reactions of organic compounds in natural geothermal environments and related laboratory simulations. Although the physical environment that fostered primitive cellular life is still largely unconstrained, we can be reasonably confident that liquid water was required, together with a source of organic compounds and energy to drive polymerization reactions. There must also have been a process by which the compounds were sufficiently concentrated to undergo physical and chemical interactions. In earlier work we observed that macromolecules such as nucleic acids and proteins are readily encapsulated in membranous boundaries during wet-dry cycles such as those that would occur at the edges of geothermal springs or tide pools. The resulting structures are referred to as protocells, in that they exhibit certain properties of living cells and are models of the kinds of encapsulated macromolecular systems that would have led toward the first forms of cellular life. However, the assembly of protocells is markedly inhibited by conditions associated with extreme environments: High temperature, high salt concentrations, and low pH ranges. From a biophysical perspective, it follows that the most plausible planetary environment for the origin of cellular life would be an aqueous phase at moderate temperature ranges and low ionic strength, having a pH value near neutrality and divalent cations at submillimolar concentrations. This suggestion is in marked contrast to the view that life most likely began in a geothermal or marine environment, perhaps even the extreme environment of a hydrothermal vent. A more plausible site for the origin of cellular life would be fresh water pools maintained by rain falling on volcanic land masses resembling present-day Hawaii and Iceland. After the first cellular life was able to establish itself in a relatively benign environment, it would rapidly begin to adapt through Darwinian selection to more rigorous environments, including the extreme temperatures, salt concentrations and pH ranges that we now associate with the limits of life on the Earth.

Hodgkin lymphoma incidence in California Hispanics: Influence of nativity and tumor Epstein–Barr virus

PubMed Central

Clarke, C. A.; Chang, E. T.; Yang, J.; Gomez, S. L.; Keegan, T. H.

2017-01-01

Purpose For classical Hodgkin lymphoma (HL), migrant studies could elucidate contributions of environmental factors (including Epstein–Barr virus (EBV)) to the lower rates in non-whites. Given the well-described etiologic complexity of HL, this research requires a large, immigrant population, such as California Hispanics. Methods With 1988–2004 California Cancer Registry data (2,595 Hispanic, 8,637 white HL cases) and tumor cell EBV status on a subset (218 Hispanics, 656 whites), we calculated ethnicity- and nativity-specific HL incidence rates simultaneously by age, sex, and histologic subtype, and tumor cell EBV prevalence. Results Compared with white rates, Hispanic HL rates were lower overall (70 %) and for nodular sclerosis HL, particularly among young adults (60–65 % for females). However, they were higher among children (200 %) and older adults, and for mixed cellularity HL. Compared with rates in foreign-born Hispanics, rates in US-born Hispanics were higher among young adults (>threefold in females), lower for children and adults over age 70, and consistently intermediate compared with rates in whites. EBV tumor prevalence was 67, 32, and 23 % among foreign-born Hispanics, US-born Hispanics, and whites, respectively, although with variation by age, sex, and histology. Conclusions Findings strongly implicate environmental influences, such as nativity-related sociodemographic differences, on HL occurrence. In addition, lower young adult rates and higher EBV prevalence in US-born Hispanics than in whites raise questions about the duration/extent of environmental change for affecting HL rates and also point to ethnic differences in genetic susceptibility. Lesser variation in mixed cellularity HL rates and greater variation in rates for females across groups suggest less modifiable factors interacting with environmental influences. PMID:24722952

A review of Ruffe (Gymnocephalus cernuus) life history in its ...

EPA Pesticide Factsheets

Ruffe (Gymnocephalus cernuus) have caused and have the potential to cause great ecological damage as invasive species in North America, parts of the European Union, Scandinavian countries, and the United Kingdom. The objectives of this review are to define the Ruffe's native and non-native range, examine the life history requirements of Ruffe, explore the Ruffe life cycle, and differentiate between the life stages. We compare Ruffe in their native range to Ruffe in their non-native range to determine if there are any differences in habitat, size, age, genotype, or migratory patterns in the winter. Literature from both the native and non-native ranges of Ruffe, with a particular emphasis on rare translated literature, is used. Ruffe have variability and plasticity in their chemical, physical, biological, and habitat requirements in their native and non-native ranges. Adult Ruffe have a suite of characteristics that make them adaptable to novel environments, including age and size at maturity, maximum age and length (and/ or weight), reproduction type, genotype, feeding habits, seasonal movements, and spawning movements. There is variability among these characteristics seen between the Ruffe's native, non-native North American, and European non-native populations. Based on the Ruffe's variable life history strategies and their recent range expansion, all of the Great Lakes and many other regions in the U.K., Europe, and Scandinavian countries could be vulnerable t

Dispersal and selection mediate hybridization between a native and invasive species.

PubMed

Kovach, Ryan P; Muhlfeld, Clint C; Boyer, Matthew C; Lowe, Winsor H; Allendorf, Fred W; Luikart, Gordon

2015-01-22

Hybridization between native and non-native species has serious biological consequences, but our understanding of how dispersal and selection interact to influence invasive hybridization is limited. Here, we document the spread of genetic introgression between a native (Oncorhynchus clarkii) and invasive (Oncorhynchus mykiss) trout, and identify the mechanisms influencing genetic admixture. In two populations inhabiting contrasting environments, non-native admixture increased rapidly from 1984 to 2007 and was driven by surprisingly consistent processes. Individual admixture was related to two phenotypic traits associated with fitness: size at spawning and age of juvenile emigration. Fish with higher non-native admixture were larger and tended to emigrate at a younger age--relationships that are expected to confer fitness advantages to hybrid individuals. However, strong selection against non-native admixture was evident across streams and cohorts (mean selection coefficient against genotypes with non-native alleles (s) = 0.60; s.e. = 0.10). Nevertheless, hybridization was promoted in both streams by the continuous immigration of individuals with high levels of non-native admixture from other hybrid source populations. Thus, antagonistic relationships between dispersal and selection are mediating invasive hybridization between these fish, emphasizing that data on dispersal and natural selection are needed to fully understand the dynamics of introgression between native and non-native species. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Imported fire ants near the edge of their range: disturbance and moisture determine prevalence and impact of an invasive social insect.

PubMed

LeBrun, Edward G; Plowes, Robert M; Gilbert, Lawrence E

2012-07-01

1. Habitat disturbance and species invasions interact in natural systems, making it difficult to isolate the primary cause of ecosystem degradation. A general understanding requires case studies of how disturbance and invasion interact across a variety of ecosystem - invasive species combinations. 2. Dramatic losses in ant diversity followed the invasion of central Texas by red imported fire ants (Solenopsis invicta). However, recent manipulative studies in Florida revealed no effect on ant diversity following the removal of S. invicta from a disturbed pasture habitat, but moderate loss of diversity associated with their introduction into undisturbed habitat and no invasion occurred without disturbance. Thus, the importance of S. invicta in driving diversity loss and its ability to invade undisturbed systems is unresolved. 3. We examine the distribution and abundance of a large monogyne S. invicta population and its association with the co-occurring ant assemblage at a site in south Texas close to the aridity tolerance limit of S. invicta. 4. We document that moisture modulates S. invicta densities. Further, soil disturbing habitat manipulations greatly increase S. invicta population densities. However, S. invicta penetrates all habitats regardless of soil disturbance history. In contrast, controlled burns depress S. invicta densities. 5. In habitats where S. invicta is prevalent, it completely replaces native fire ants. However, S. invicta impacts native ants as a whole less strongly. Intriguingly, native ants responded distinctly to S. invicta in different environments. In wet, undisturbed environments, high S. invicta abundance disrupts the spatial structure of the ant assemblage by increasing clumping and is associated with reduced species density, while in dry-disturbed habitats, sites with high S. invicta abundance possess high numbers of native species. Analyses of co-occurrence indicate that reduced species density in wet-undisturbed sites arises from negative species interactions between native ants and S. invicta. However, these same data suggest that the high native species density of abundant S. invicta sites in dry-disturbed environments does not result from facilitation. 6. Monogyne S. invicta populations play different roles in different environments, driving ant diversity loss in some, but being largely symptomatic of habitat disturbance in others. © 2012 The Authors. Journal of Animal Ecology © 2012 British Ecological Society.

Bioengineering pediatric scaffold-free auricular cartilaginous constructs.

PubMed

Akbari, Pedram; Waldman, Stephen D; Cushing, Sharon L; Papsin, Blake C; Propst, Evan J; Weber, Joanna F; Yeger, Herman; Farhat, Walid A

2017-05-01

The use of exogenous materials as scaffolds in cartilage tissue engineering has limited the clinical application of resultant constructs due to the risk of postoperative complications. In an effort to minimize such complications, we aim to generate human, scaffold-free auricular cartilaginous constructs. Laboratory study using pediatric auricular cartilage. Remnant, normal pediatric auricular cartilage samples that would have otherwise been discarded were collected and digested to free cells. Harvested cells were cultured and expanded in vitro for two passages and plated as micromass cultures. The culture medium was replaced with a chemically defined chondrogenic medium, and cellular monolayers surrounding micromass cultures were continuously scraped off. Constructs were allowed to mature for a period of 8 weeks. Micromass constructs showed mechanical stability and structurally resembled native auricular tissue, with a perichondrium-like layer of cells surrounding the inner cartilaginous zone. Constructs accumulated equivalent sulphated glycosaminoglycan and 50% of collagen content compared to native auricular cartilage by mass, while displaying 156% more cellularity. High-density micromass cultures of pediatric auricular chondrocytes can generate stable cartilaginous constructs following prolonged chondrogenic inductions in vitro. This technique is an essential step toward the development of three-dimensional constructs to recreate clinically applicable auricular cartilaginous constructs. NA. Laryngoscope, 127:E153-E158, 2017. © 2016 The American Laryngological, Rhinological and Otological Society, Inc.

In vitro reconstruction of hybrid vascular tissue. Hierarchic and oriented cell layers.

PubMed

Kanda, K; Matsuda, T; Oka, T

1993-01-01

Hybrid vascular tissue was hierarchically reconstructed in vitro. A hybrid medial layer composed of type I collagen gel, in which SMCs derived from a mongrel dog were embedded, was formed on the inner surface of a compliant porous polyurethane graft (internal diameter = 3 mm). Endothelial cells (ECs) from the same animal were seeded and cultured on the hybrid media to build an intimal layer. Subsequently, hierarchically structured grafts constructed in this manner were subjected to pulsatile flow (flow rate: 8.5 ml/min; frequency: 60 rpm; amplitude: 5% of graft outer diameter) of culture medium (Medium 199 supplemented with 20% fetal calf serum). After stress loading for as long as 10 days, tissues were morphologically investigated with a light microscope and a scanning electron microscope. Inner surfaces of the hybrid tissues were covered with EC monolayers that aligned along the direction of the flow (i.e., longitudinally). However, SMCs beneath the intima aligned in the circumferential direction. These cellular orientations resembled those in native muscular arteries. The pulsatile stress loaded hybrid tissue mimicked native muscular arteries with respect to hierarchic structure and cellular orientation. In vitro mechanical stress loading on a hybrid graft might provide a high degree of integrity in terms of tissue structure that promises high tolerance toward hydrodynamic stress and regulation of vasomotor tone upon implantation.

Practice-Informed Approaches to Addressing Substance Abuse and Trauma Exposure in Urban Native Families Involved with Child Welfare.

PubMed

Lucero, Nancy M; Bussey, Marian

2015-01-01

Similar to families from other groups, urban-based American Indian and Alaska Native ("Native") family members involved with the child welfare system due to substance abuse issues are also often challenged by untreated trauma exposure. The link between these conditions and the history of genocidal policies aimed at destroying Native family ties, as well as experiences of ongoing discrimination, bring added dimensions for consideration when pro- viding services to these families. Practice-based evidence indicates that the trauma-informed and culturally responsive model developed by the Denver Indian Family Resource Center (DIFRC) shows promise in reducing out-of-home placements and re-referrals in urban Native families with substance abuse and child welfare concerns, while also increasing caregiver capabilities, family safety, and child well-being. This article provides strategies from the DIFRC approach that non-Native caseworkers and supervisors can utilize to create an environment in their own agencies that supports culturally based practice with Native families while incorporating a trauma-informed understanding of service needs of these families. Casework consistent with this approach demonstrates actions that meet the Active Efforts requirement of the Indian Child Welfare Act (ICWA) as well as sound clinical practice. Intensive and proactive case management designed specifically for families with high levels of service needs is a key strategy when combined with utilizing a caseworker brief screening tool for trauma exposure; training caseworkers to recognize trauma symptoms, making timely referrals to trauma treatment by behavioral health specialists experienced in working with Native clients, and providing a consistent service environment that focuses on client safety and worker trustworthiness. Finally, suggestions are put forth for agencies seeking to enhance their cultural responsiveness and include increasing workers' understanding of cultural values, worldview, and historical issues; working from a relational perspective; listening deeply to families' experiences; and being open to incorporating traditional healing and cultural practice into service plans.

A generic screening platform for inhibitors of virus induced cell fusion using cellular electrical impedance

PubMed Central

Watterson, Daniel; Robinson, Jodie; Chappell, Keith J.; Butler, Mark S.; Edwards, David J.; Fry, Scott R.; Bermingham, Imogen M.; Cooper, Matthew A.; Young, Paul R.

2016-01-01

Fusion of the viral envelope with host cell membranes is an essential step in the life cycle of all enveloped viruses. Despite such a clear target for antiviral drug development, few anti-fusion drugs have progressed to market. One significant hurdle is the absence of a generic, high-throughput, reproducible fusion assay. Here we report that real time, label-free measurement of cellular electrical impedance can quantify cell-cell fusion mediated by either individually expressed recombinant viral fusion proteins, or native virus infection. We validated this approach for all three classes of viral fusion and demonstrated utility in quantifying fusion inhibition using antibodies and small molecule inhibitors specific for dengue virus and respiratory syncytial virus. PMID:26976324

Inhibiting host-pathogen interactions using membrane-based nanostructures.

PubMed

Bricarello, Daniel A; Patel, Mira A; Parikh, Atul N

2012-06-01

Virulent strains of bacteria and viruses recognize host cells by their plasma membrane receptors and often exploit the native translocation machinery to invade the cell. A promising therapeutic concept for early interruption of pathogen infection is to subvert this pathogenic trickery using exogenously introduced decoys that present high-affinity mimics of cellular receptors. This review highlights emerging applications of molecularly engineered lipid-bilayer-based nanostructures, namely (i) functionalized liposomes, (ii) supported colloidal bilayers or protocells and (iii) reconstituted lipoproteins, which display functional cellular receptors in optimized conformational and aggregative states. These decoys outcompete host cell receptors by preferentially binding to and neutralizing virulence factors of both bacteria and viruses, thereby promising a new approach to antipathogenic therapy. Copyright © 2012 Elsevier Ltd. All rights reserved.

Photocrosslinking approaches to interactome mapping

PubMed Central

Pham, Nam D.; Parker, Randy B.; Kohler, Jennifer J.

2012-01-01

Photocrosslinking approaches can be used to map interactome networks within the context of living cells. Photocrosslinking methods rely on use of metabolic engineering or genetic code expansion to incorporate photocrosslinking analogs of amino acids or sugars into cellular biomolecules. Immunological and mass spectrometry techniques are used to analyze crosslinked complexes, thereby defining specific interactomes. Because photocrosslinking can be conducted in native, cellular settings, it can be used to define context-dependent interactions. Photocrosslinking methods are also ideally suited for determining interactome dynamics, mapping interaction interfaces, and identifying transient interactions in which intrinsically disordered proteins and glycoproteins engage. Here we discuss the application of cell-based photocrosslinking to the study of specific problems in immune cell signaling, transcription, membrane protein dynamics, nucleocytoplasmic transport, and chaperone-assisted protein folding. PMID:23149092

Measurement uncertainty evaluation of cellular spheroids surface tension in compressing tests using Young-Laplace equation

NASA Astrophysics Data System (ADS)

Beatrici, Anderson; Santos Baptista, Leandra; Mauro Granjeiro, José

2018-03-01

Regenerative Medicine comprises the Biotechnology, Tissue Engineering and Biometrology for stem cell therapy. Starting from stem cells extracted from the patient, autologous implant, these cells are cultured and differentiated into other tissues, for example, articular cartilage. These cells are reorganized into microspheres (cell spheroids). Such tissue units are recombined into functional tissues constructs that can be implanted in the injured region for regeneration. It is necessary the biomechanical characterization of these constructed to determine if their properties are similar to native tissue. In this study was carried out the modeling of the calculation of uncertainty of the surface tension of cellular spheroids with the use of the Young-Laplace equation. We obtained relative uncertainties about 10%.

Clinical learning environment and supervision of international nursing students: A cross-sectional study.

PubMed

Mikkonen, Kristina; Elo, Satu; Miettunen, Jouko; Saarikoski, Mikko; Kääriäinen, Maria

2017-05-01

Previously, it has been shown that the clinical learning environment causes challenges for international nursing students, but there is a lack of empirical evidence relating to the background factors explaining and influencing the outcomes. To describe international and national students' perceptions of their clinical learning environment and supervision, and explain the related background factors. An explorative cross-sectional design was used in a study conducted in eight universities of applied sciences in Finland during September 2015-May 2016. All nursing students studying English language degree programs were invited to answer a self-administered questionnaire based on both the clinical learning environment, supervision and nurse teacher scale and Cultural and Linguistic Diversity scale with additional background questions. Participants (n=329) included international (n=231) and Finnish (n=98) nursing students. Binary logistic regression was used to identify background factors relating to the clinical learning environment and supervision. International students at a beginner level in Finnish perceived the pedagogical atmosphere as worse than native speakers. In comparison to native speakers, these international students generally needed greater support from the nurse teacher at their university. Students at an intermediate level in Finnish reported two times fewer negative encounters in cultural diversity at their clinical placement than the beginners. To facilitate a successful learning experience, international nursing students require a sufficient level of competence in the native language when conducting clinical placements. Educational interventions in language education are required to test causal effects on students' success in the clinical learning environment. Copyright © 2017 Elsevier Ltd. All rights reserved.

Report on the National Eye Institute’s Audacious Goals Initiative: Creating a Cellular Environment for Neuroregeneration

PubMed Central

Stevens, Beth

2018-01-01

Abstract The cellular environment of the CNS is non-permissive for growth and regeneration. In the retina, transplantation of stem cells has been limited by inefficient survival and integration into existing circuits. In November 2016, as part of the National Eye Institute’s Audacious Goals Initiative (AGI), a diverse collection of investigators gathered for a workshop devoted to articulating the gaps in knowledge, barriers to progress, and ideas for new approaches to understanding cellular environments within the retina and how these environments may be manipulated. In doing so, the group identified the areas of (1) retinal and optic nerve glia, (2) microglia and inflammation, and the (3) extracellular matrix (ECM) and retinal vasculature as key to advancing our understanding and manipulation of the retinal microenvironments. We summarize here the findings of the workshop for the broader scientific community. PMID:29766041

A scientific role for Space Station Freedom: Research at the cellular level

NASA Technical Reports Server (NTRS)

Johnson, Terry C.; Brady, John N.

1993-01-01

The scientific importance of Space Station Freedom is discussed in light of the valuable information that can be gained in cellular and developmental biology with regard to the microgravity environment on the cellular cytoskeleton, cellular responses to extracellular signal molecules, morphology, events associated with cell division, and cellular physiology. Examples of studies in basic cell biology, as well as their potential importance to concerns for future enabling strategies, are presented.

Integration of Stem Cell to Chondrocyte-Derived Cartilage Matrix in Healthy and Osteoarthritic States in the Presence of Hydroxyapatite Nanoparticles.

PubMed

Dua, Rupak; Comella, Kristin; Butler, Ryan; Castellanos, Glenda; Brazille, Bryn; Claude, Andrew; Agarwal, Arvind; Liao, Jun; Ramaswamy, Sharan

2016-01-01

We investigated the effectiveness of integrating tissue engineered cartilage derived from human bone marrow derived stem cells (HBMSCs) to healthy as well as osteoarthritic cartilage mimics using hydroxyapatite (HA) nanoparticles immersed within a hydrogel substrate. Healthy and diseased engineered cartilage from human chondrocytes (cultured in agar gels) were integrated with human bone marrow stem cell (HBMSC)-derived cartilaginous engineered matrix with and without HA, and evaluated after 28 days of growth. HBMSCs were seeded within photopolymerizable poly (ethylene glycol) diacrylate (PEGDA) hydrogels. In addition, we also conducted a preliminary in vivo evaluation of cartilage repair in rabbit knee chondral defects treated with subchondral bone microfracture and cell-free PEGDA with and without HA. Under in vitro conditions, the interfacial shear strength between tissue engineered cartilage derived from HBMSCs and osteoarthritic chondrocytes was significantly higher (p < 0.05) when HA nanoparticles were incorporated within the HBMSC culture system. Histological evidence confirmed a distinct spatial transition zone, rich in calcium phosphate deposits. Assessment of explanted rabbit knees by histology demonstrated that cellularity within the repair tissues that had filled the defects were of significantly higher number (p < 0.05) when HA was used. HA nanoparticles play an important role in treating chondral defects when osteoarthritis is a co-morbidity. We speculate that the calcified layer formation at the interface in the osteoarthritic environment in the presence of HA is likely to have attributed to higher interfacial strength found in vitro. From an in vivo standpoint, the presence of HA promoted cellularity in the tissues that subsequently filled the chondral defects. This higher presence of cells can be considered important in the context of accelerating long-term cartilage remodeling. We conclude that HA nanoparticles play an important role in engineered to native cartilage integration and cellular processes.

Phenotypic Characterization of Prostate Cancer LNCaP Cells Cultured within a Bioengineered Microenvironment

PubMed Central

Sieh, Shirly; Taubenberger, Anna V.; Rizzi, Simone C.; Sadowski, Martin; Lehman, Melanie L.; Rockstroh, Anja; An, Jiyuan; Clements, Judith A.; Nelson, Colleen C.; Hutmacher, Dietmar W.

2012-01-01

Biophysical and biochemical properties of the microenvironment regulate cellular responses such as growth, differentiation, morphogenesis and migration in normal and cancer cells. Since two-dimensional (2D) cultures lack the essential characteristics of the native cellular microenvironment, three-dimensional (3D) cultures have been developed to better mimic the natural extracellular matrix. To date, 3D culture systems have relied mostly on collagen and Matrigel™ hydrogels, allowing only limited control over matrix stiffness, proteolytic degradability, and ligand density. In contrast, bioengineered hydrogels allow us to independently tune and systematically investigate the influence of these parameters on cell growth and differentiation. In this study, polyethylene glycol (PEG) hydrogels, functionalized with the Arginine-glycine-aspartic acid (RGD) motifs, common cell-binding motifs in extracellular matrix proteins, and matrix metalloproteinase (MMP) cleavage sites, were characterized regarding their stiffness, diffusive properties, and ability to support growth of androgen-dependent LNCaP prostate cancer cells. We found that the mechanical properties modulated the growth kinetics of LNCaP cells in the PEG hydrogel. At culture periods of 28 days, LNCaP cells underwent morphogenic changes, forming tumor-like structures in 3D culture, with hypoxic and apoptotic cores. We further compared protein and gene expression levels between 3D and 2D cultures upon stimulation with the synthetic androgen R1881. Interestingly, the kinetics of R1881 stimulated androgen receptor (AR) nuclear translocation differed between 2D and 3D cultures when observed by immunofluorescent staining. Furthermore, microarray studies revealed that changes in expression levels of androgen responsive genes upon R1881 treatment differed greatly between 2D and 3D cultures. Taken together, culturing LNCaP cells in the tunable PEG hydrogels reveals differences in the cellular responses to androgen stimulation between the 2D and 3D environments. Therefore, we suggest that the presented 3D culture system represents a powerful tool for high throughput prostate cancer drug testing that recapitulates tumor microenvironment. PMID:22957009

Parasites of native and exotic freshwater fishes in south-western Australia.

PubMed

Lymbery, A J; Hassan, M; Morgan, D L; Beatty, S J; Doupé, R G

2010-05-01

In this study, 1429 fishes of 18 different species (12 native and six exotic) were sampled from 29 localities to compare the levels of parasitism between native and exotic fish species and to examine the relationship between environmental degradation and parasite diversity. Forty-four putative species of parasites were found and most of these appear to be native parasites, which have not previously been described. Two parasite species, Lernaea cyprinacea and Ligula intestinalis, are probably introduced. Both were found on or in a range of native fish species, where they may cause severe disease. Levels of parasitism and parasite diversity were significantly greater in native fishes than in exotic species, and this may contribute to an enhanced demographic performance and competitive ability in invading exotics. Levels of parasitism and parasite diversity in native fishes were negatively related to habitat disturbance, in particular to a suite of factors that indicate increased human use of the river and surrounding environment. This was due principally to the absence in more disturbed habitats of a number of species of endoparasites with complex life cycles, involving transmission between different host species.

Environmental and Biotic Correlates to Lionfish Invasion Success in Bahamian Coral Reefs

PubMed Central

Anton, Andrea; Simpson, Michael S.; Vu, Ivana

2014-01-01

Lionfish (Pterois volitans), venomous predators from the Indo-Pacific, are recent invaders of the Caribbean Basin and southeastern coast of North America. Quantification of invasive lionfish abundances, along with potentially important physical and biological environmental characteristics, permitted inferences about the invasion process of reefs on the island of San Salvador in the Bahamas. Environmental wave-exposure had a large influence on lionfish abundance, which was more than 20 and 120 times greater for density and biomass respectively at sheltered sites as compared with wave-exposed environments. Our measurements of topographic complexity of the reefs revealed that lionfish abundance was not driven by habitat rugosity. Lionfish abundance was not negatively affected by the abundance of large native predators (or large native groupers) and was also unrelated to the abundance of medium prey fishes (total length of 5–10 cm). These relationships suggest that (1) higher-energy environments may impose intrinsic resistance against lionfish invasion, (2) habitat complexity may not facilitate the lionfish invasion process, (3) predation or competition by native fishes may not provide biotic resistance against lionfish invasion, and (4) abundant prey fish might not facilitate lionfish invasion success. The relatively low biomass of large grouper on this island could explain our failure to detect suppression of lionfish abundance and we encourage continuing the preservation and restoration of potential lionfish predators in the Caribbean. In addition, energetic environments might exert direct or indirect resistance to the lionfish proliferation, providing native fish populations with essential refuges. PMID:25184250

Environmental and biotic correlates to lionfish invasion success in Bahamian coral reefs.

PubMed

Anton, Andrea; Simpson, Michael S; Vu, Ivana

2014-01-01

Lionfish (Pterois volitans), venomous predators from the Indo-Pacific, are recent invaders of the Caribbean Basin and southeastern coast of North America. Quantification of invasive lionfish abundances, along with potentially important physical and biological environmental characteristics, permitted inferences about the invasion process of reefs on the island of San Salvador in the Bahamas. Environmental wave-exposure had a large influence on lionfish abundance, which was more than 20 and 120 times greater for density and biomass respectively at sheltered sites as compared with wave-exposed environments. Our measurements of topographic complexity of the reefs revealed that lionfish abundance was not driven by habitat rugosity. Lionfish abundance was not negatively affected by the abundance of large native predators (or large native groupers) and was also unrelated to the abundance of medium prey fishes (total length of 5-10 cm). These relationships suggest that (1) higher-energy environments may impose intrinsic resistance against lionfish invasion, (2) habitat complexity may not facilitate the lionfish invasion process, (3) predation or competition by native fishes may not provide biotic resistance against lionfish invasion, and (4) abundant prey fish might not facilitate lionfish invasion success. The relatively low biomass of large grouper on this island could explain our failure to detect suppression of lionfish abundance and we encourage continuing the preservation and restoration of potential lionfish predators in the Caribbean. In addition, energetic environments might exert direct or indirect resistance to the lionfish proliferation, providing native fish populations with essential refuges.

Profound re-organization of cell surface proteome in equine retinal pigment epithelial cells in response to in vitro culturing.

PubMed

Szober, Christoph M; Hauck, Stefanie M; Euler, Kerstin N; Fröhlich, Kristina J H; Alge-Priglinger, Claudia; Ueffing, Marius; Deeg, Cornelia A

2012-10-31

The purpose of this study was to characterize the cell surface proteome of native compared to cultured equine retinal pigment epithelium (RPE) cells. The RPE plays an essential role in visual function and represents the outer blood-retinal barrier. We are investigating immunopathomechanisms of equine recurrent uveitis, an autoimmune inflammatory disease in horses leading to breakdown of the outer blood-retinal barrier and influx of autoreactive T-cells into affected horses' vitrei. Cell surface proteins of native and cultured RPE cells from eye-healthy horses were captured by biotinylation, analyzed by high resolution mass spectrometry coupled to liquid chromatography (LC MS/MS), and the most interesting candidates were validated by PCR, immunoblotting and immunocytochemistry. A total of 112 proteins were identified, of which 84% were cell surface membrane proteins. Twenty-three of these proteins were concurrently expressed by both cell states, 28 proteins exclusively by native RPE cells. Among the latter were two RPE markers with highly specialized RPE functions: cellular retinaldehyde-binding protein (CRALBP) and retinal pigment epithelium-specific protein 65kDa (RPE65). Furthermore, 61 proteins were only expressed by cultured RPE cells and absent in native cells. As we believe that initiating events, leading to the breakdown of the outer blood-retinal barrier, take place at the cell surface of RPE cells as a particularly exposed barrier structure, this differential characterization of cell surface proteomes of native and cultured equine RPE cells is a prerequisite for future studies.

Introduce Science to Students Using the Environment: A Guide for Teachers of Native American Students.

ERIC Educational Resources Information Center

Richau, Deborah

Written for science teachers of elementary and secondary Native American students, the guide offers 18 science-related activities that integrate science with Indian culture and life. A teacher preparation exercise is presented first to allow the teacher to look at him/herself and use the information as a tool to understanding the students'…

Non-Native Speaker Interaction Management Strategies in a Network-Based Virtual Environment

ERIC Educational Resources Information Center

Peterson, Mark

2008-01-01

This article investigates the dyad-based communication of two groups of non-native speakers (NNSs) of English involved in real time interaction in a type of text-based computer-mediated communication (CMC) tool known as a MOO. The object of this semester long study was to examine the ways in which the subjects managed their L2 interaction during…

Development of an aggressive bark beetle on novel hosts: Implications for outbreaks in an invaded range

Treesearch

Derek W. Rosenberger; Robert C. Venette; Brian H. Aukema; Jörg Müller

2018-01-01

Some subcortical insects have devastating effects on native tree communities in new ranges, despite benign interactions with their historical hosts. Examples of how insects, aggressive in their native habitat might respond in novel host environs are less common. One aggressive tree-killing insect undergoing a dramatic range shift is the mountain pine beetle (...

Exploring How Non-Native Teachers Can Use Commonalities with Students to Teach the Target Language

ERIC Educational Resources Information Center

Reynolds-Case, Anne

2012-01-01

This article presents a qualitative study demonstrating how teachers who are non-native speakers (NNS) of the target language and who have learned the target language in a similar environment as their students can use their past learning experiences as pedagogical tools in their classes. An analysis of transcripts from classrooms with NNS and…

Cold water as a climate shield to preserve native trout through the 21st Century

Treesearch

Daniel J. Isaak; Michael K. Young; David Nagel; Dona Horan

2014-01-01

Native trout are culturally and ecologically important, but also likely to undergo widespread declines as the coldwater environments they require continue to shrink in association with global warming. Much can be done to preserve these fish but efficient planning and targeting of conservations resources has been hindered by a lack of broad-scale datasets and precise...

Diseases of Monterey pine in native stands of California and in plantations of Western North America

Treesearch

Harold R. Offord

1964-01-01

The prevalence and identity of 72 pathogens occurring on Pinus radiate D. Don are described against a brief background of the native host and its environment. Records of pathogens in California herbaria, pathology notes is Forest Service files, findings of recent surveys, and publications provide the basis for an index of these pathogens. An appendix...

Strategy and Resistance: How Native American Students Engage in Accommodation in Mainstream Schools

ERIC Educational Resources Information Center

Masta, Stephanie

2018-01-01

This article explores the experiences of a group of Native American 8th graders who attend a mainstream school and how they engage in accommodation as an act of agency and resistance to protect and maintain their identities in their school environment. By using tribal critical race theory to examine these experiences, this study raises important…

Chapter 2. A sketch of the cultural-historical environment-Part 1: The pre-Columbian past

Treesearch

Kurt F. Anschuetz

2007-01-01

This chapter examines the scope and structure of current archaeological interpretations of the pre-Columbian Native American occupation and use of the Valles Caldera National Preserve (VCNP). The discussion provides useful cultural-historical background for the presentation and evaluation of the structure and organization of Native American land use history, as it is...

Native-Speaker/Non-Native-Speaker Discourse in the MOO: Topic Negotiation and Initiation in a Synchronous Text-Based Environment

ERIC Educational Resources Information Center

Schwienhorst, Klaus

2004-01-01

A number of researchers in computer-mediated communication have pointed towards its potential to stimulate learner participation and engagement in the classroom. However, in many cases only anecdotal reports were provided. In addition, it is unclear whether the pedagogical set-up or the technology involved is responsible for changes in learner…

Native American Ethnicity and Childhood Maltreatment as Variables in Perceptions and Adjustments to Boot Camp vs. "Traditional" Correctional Settings

ERIC Educational Resources Information Center

Gover, Angela R.

2005-01-01

A sample of 302 juveniles confined in two separate correctional facilities in a Western plains state was assessed to examine the relationship between child maltreatment and other delinquency risk factors, and Native American ethnicity on perceptions of the institutional environments and psychological adjustment in a boot camp and traditional…

Effect of heated naringenin on immunomodulatory properties and cellular antioxidant activity.

PubMed

Maatouk, Mouna; Elgueder, Dorra; Mustapha, Nadia; Chaaban, Hind; Bzéouich, Imen Mokdad; Loannou, Irina; Kilani, Soumaya; Ghoul, Mohamed; Ghedira, Kamel; Chekir-Ghedira, Leila

2016-11-01

Naringenin is one of the most popular flavonoids derived from citrus. It has been reported to be an effective anti-inflammatory compound. Citrus fruit may be used raw, cooked, stewed, or boiled. The present study was conducted to investigate the effect of thermal processes on naringenin in its immunomodulatory and cellular antioxidant activities. The effects of flavonoids on B and T cell proliferation were assessed on splenocytes stimulated or not with mitogens. However, their effects on cytotoxic T lymphocyte (CTL) and natural killer (NK) activities were assessed in splenocytes co-incubated with target cells. The amount of nitric oxide production and the lysosomal enzyme activity were evaluated in vitro on mouse peritoneal macrophages. Cellular antioxidant activity in splenocytes and macrophages was determined by measuring the fluorescence of the dichlorofluorescin (DCF). Our findings revealed that naringenin induces B cell proliferation and enhances NK activity. The highest concentration of native naringenin exhibits a significant proliferation of T cells, induces CTL activity, and inhibits cellular oxidation in macrophages. Conversely, it was observed that when heat-processed, naringenin improves the cellular antioxidant activity in splenocytes, increases the cytotoxic activity of NK cells, and suppresses the cytotoxicity of T cells. However, heat treatment maintains the anti-inflammatory potency of naringenin.

The ANISA Model of Education: A Critique. Issues in Native Education.

ERIC Educational Resources Information Center

Four Worlds Development Project, Lethbridge (Alberta).

The ANISA model of education (D. Streets and D. Jordan) classifies curriculum content into four areas--the physical environment, the human environment, the unknown environment, and the self--and encourages horizontal integration between content areas. The ANISA model holds that the process of learning consists of differentiation, integration, and…

Designing propagation environments in forest and native plant nurseries

Treesearch

Thomas D. Landis

2013-01-01

Propagation environments are areas that have been modified for plant growth, and can be designed using the law of limiting factors. Identifying critical factors that are most limiting to optimal plant growth is helpful when developing both bareroot and container nurseries. Propagation environments can be categorized into minimally-controlled, semi-controlled, and fully...

Diversity and Biotic Homogenization of Urban Land-Snail Faunas in Relation to Habitat Types and Macroclimate in 32 Central European Cities

PubMed Central

Horsák, Michal; Lososová, Zdeňka; Čejka, Tomáš; Juřičková, Lucie; Chytrý, Milan

2013-01-01

The effects of non-native species invasions on community diversity and biotic homogenization have been described for various taxa in urban environments, but not for land snails. Here we relate the diversity of native and non-native land-snail urban faunas to urban habitat types and macroclimate, and analyse homogenization effects of non-native species across cities and within the main urban habitat types. Land-snail species were recorded in seven 1-ha plots in 32 cities of ten countries of Central Europe and Benelux (224 plots in total). Each plot represented one urban habitat type characterized by different management and a specific disturbance regime. For each plot, we obtained January, July and mean annual temperature and annual precipitation. Snail species were classified into either native or non-native. The effects of habitat type and macroclimate on the number of native and non-native species were analysed using generalized estimating equations; the homogenization effect of non-native species based on the Jaccard similarity index and homogenization index. We recorded 67 native and 20 non-native species. Besides being more numerous, native species also had much higher beta diversity than non-natives. There were significant differences between the studied habitat types in the numbers of native and non-native species, both of which decreased from less to heavily urbanized habitats. Macroclimate was more important for the number of non-native than native species; however in both cases the effect of climate on diversity was overridden by the effect of urban habitat type. This is the first study on urban land snails documenting that non-native land-snail species significantly contribute to homogenization among whole cities, but both the homogenization and diversification effects occur when individual habitat types are compared among cities. This indicates that the spread of non-native snail species may cause biotic homogenization, but it depends on scale and habitat type. PMID:23936525

Diversity and biotic homogenization of urban land-snail faunas in relation to habitat types and macroclimate in 32 central European cities.

PubMed

Horsák, Michal; Lososová, Zdeňka; Čejka, Tomáš; Juřičková, Lucie; Chytrý, Milan

2013-01-01

The effects of non-native species invasions on community diversity and biotic homogenization have been described for various taxa in urban environments, but not for land snails. Here we relate the diversity of native and non-native land-snail urban faunas to urban habitat types and macroclimate, and analyse homogenization effects of non-native species across cities and within the main urban habitat types. Land-snail species were recorded in seven 1-ha plots in 32 cities of ten countries of Central Europe and Benelux (224 plots in total). Each plot represented one urban habitat type characterized by different management and a specific disturbance regime. For each plot, we obtained January, July and mean annual temperature and annual precipitation. Snail species were classified into either native or non-native. The effects of habitat type and macroclimate on the number of native and non-native species were analysed using generalized estimating equations; the homogenization effect of non-native species based on the Jaccard similarity index and homogenization index. We recorded 67 native and 20 non-native species. Besides being more numerous, native species also had much higher beta diversity than non-natives. There were significant differences between the studied habitat types in the numbers of native and non-native species, both of which decreased from less to heavily urbanized habitats. Macroclimate was more important for the number of non-native than native species; however in both cases the effect of climate on diversity was overridden by the effect of urban habitat type. This is the first study on urban land snails documenting that non-native land-snail species significantly contribute to homogenization among whole cities, but both the homogenization and diversification effects occur when individual habitat types are compared among cities. This indicates that the spread of non-native snail species may cause biotic homogenization, but it depends on scale and habitat type.

Experimental evidence of impacts of an invasive parakeet on foraging behavior of native birds

PubMed Central

2014-01-01

Resource competition is one potential behavioral mechanism by which invasive species can impact native species, but detecting this competition can be difficult due to the interactions that variable environmental conditions can have on species behavior. This is particularly the case in urban habitats where the disturbed environment can alter natural behavior from that in undisturbed habitats. The rose-ringed parakeet (Psittacula krameri), is an increasingly common invasive species, predominantly associated with large urban centers. Using an experimental approach, we tested the behavioral responses of native garden birds in response to the presence of a rose-ringed parakeet versus the presence of a similarly sized and dominant native bird, the great spotted woodpecker (Dendrocopos major). Parakeet presence significantly reduced feeding rates and increased vigilance among native birds compared with our control treatments. Of visits made by native birds in the presence of a parakeet, feeding was more likely to occur in sites within the parakeet range compared with sites outside, suggesting some habituation of native birds has occurred following prior exposure to parakeets but overall foraging behavior is still disrupted. The results of our study suggest that nonnative species can have complex and subtle impacts on native fauna and show that a nonnative competitor can impact native species simply through their presence near resources. PMID:24822022

Experimental evidence of impacts of an invasive parakeet on foraging behavior of native birds.

PubMed

Peck, Hannah L; Pringle, Henrietta E; Marshall, Harry H; Owens, Ian P F; Lord, Alexa M

2014-05-01

Resource competition is one potential behavioral mechanism by which invasive species can impact native species, but detecting this competition can be difficult due to the interactions that variable environmental conditions can have on species behavior. This is particularly the case in urban habitats where the disturbed environment can alter natural behavior from that in undisturbed habitats. The rose-ringed parakeet ( Psittacula krameri ), is an increasingly common invasive species, predominantly associated with large urban centers. Using an experimental approach, we tested the behavioral responses of native garden birds in response to the presence of a rose-ringed parakeet versus the presence of a similarly sized and dominant native bird, the great spotted woodpecker ( Dendrocopos major ). Parakeet presence significantly reduced feeding rates and increased vigilance among native birds compared with our control treatments. Of visits made by native birds in the presence of a parakeet, feeding was more likely to occur in sites within the parakeet range compared with sites outside, suggesting some habituation of native birds has occurred following prior exposure to parakeets but overall foraging behavior is still disrupted. The results of our study suggest that nonnative species can have complex and subtle impacts on native fauna and show that a nonnative competitor can impact native species simply through their presence near resources.

Fish species introductions provide novel insights into the patterns and drivers of phylogenetic structure in freshwaters

PubMed Central

Strecker, Angela L.; Olden, Julian D.

2014-01-01

Despite long-standing interest of terrestrial ecologists, freshwater ecosystems are a fertile, yet unappreciated, testing ground for applying community phylogenetics to uncover mechanisms of species assembly. We quantify phylogenetic clustering and overdispersion of native and non-native fishes of a large river basin in the American Southwest to test for the mechanisms (environmental filtering versus competitive exclusion) and spatial scales influencing community structure. Contrary to expectations, non-native species were phylogenetically clustered and related to natural environmental conditions, whereas native species were not phylogenetically structured, likely reflecting human-related changes to the basin. The species that are most invasive (in terms of ecological impacts) tended to be the most phylogenetically divergent from natives across watersheds, but not within watersheds, supporting the hypothesis that Darwin's naturalization conundrum is driven by the spatial scale. Phylogenetic distinctiveness may facilitate non-native establishment at regional scales, but environmental filtering restricts local membership to closely related species with physiological tolerances for current environments. By contrast, native species may have been phylogenetically clustered in historical times, but species loss from contemporary populations by anthropogenic activities has likely shaped the phylogenetic signal. Our study implies that fundamental mechanisms of community assembly have changed, with fundamental consequences for the biogeography of both native and non-native species. PMID:24452027

Sense of Belonging in School as a Protective Factor Against Drug Abuse Among Native American Urban Adolescents

PubMed Central

Napoli, Maria; Marsiglia, Flavio Francisco; Kulis, Stephen

2011-01-01

This article presents the results of a study conducted with 243 Native American students who were part of a multi-ethnic sample of adolescents attending middle school in a large urban center in the Southwest region of the United States. Native adolescents who felt a stronger sense of belonging in their school were found to report a lower lifetime use of alcohol and cigarettes, lower cigarette and marijuana use in the previous month, lower frequency of current use of these substances, fewer substances ever used, and a later age of initiation into drug use than other Native students. Research implications are discussed in relationship to school environment, culturally-grounded prevention curricula, and school social work practice. PMID:21359140

Non-native Listeners’ Recognition of High-Variability Speech Using PRESTO

PubMed Central

Tamati, Terrin N.; Pisoni, David B.

2015-01-01

Background Natural variability in speech is a significant challenge to robust successful spoken word recognition. In everyday listening environments, listeners must quickly adapt and adjust to multiple sources of variability in both the signal and listening environments. High-variability speech may be particularly difficult to understand for non-native listeners, who have less experience with the second language (L2) phonological system and less detailed knowledge of sociolinguistic variation of the L2. Purpose The purpose of this study was to investigate the effects of high-variability sentences on non-native speech recognition and to explore the underlying sources of individual differences in speech recognition abilities of non-native listeners. Research Design Participants completed two sentence recognition tasks involving high-variability and low-variability sentences. They also completed a battery of behavioral tasks and self-report questionnaires designed to assess their indexical processing skills, vocabulary knowledge, and several core neurocognitive abilities. Study Sample Native speakers of Mandarin (n = 25) living in the United States recruited from the Indiana University community participated in the current study. A native comparison group consisted of scores obtained from native speakers of English (n = 21) in the Indiana University community taken from an earlier study. Data Collection and Analysis Speech recognition in high-variability listening conditions was assessed with a sentence recognition task using sentences from PRESTO (Perceptually Robust English Sentence Test Open-Set) mixed in 6-talker multitalker babble. Speech recognition in low-variability listening conditions was assessed using sentences from HINT (Hearing In Noise Test) mixed in 6-talker multitalker babble. Indexical processing skills were measured using a talker discrimination task, a gender discrimination task, and a forced-choice regional dialect categorization task. Vocabulary knowledge was assessed with the WordFam word familiarity test, and executive functioning was assessed with the BRIEF-A (Behavioral Rating Inventory of Executive Function – Adult Version) self-report questionnaire. Scores from the non-native listeners on behavioral tasks and self-report questionnaires were compared with scores obtained from native listeners tested in a previous study and were examined for individual differences. Results Non-native keyword recognition scores were significantly lower on PRESTO sentences than on HINT sentences. Non-native listeners’ keyword recognition scores were also lower than native listeners’ scores on both sentence recognition tasks. Differences in performance on the sentence recognition tasks between non-native and native listeners were larger on PRESTO than on HINT, although group differences varied by signal-to-noise ratio. The non-native and native groups also differed in the ability to categorize talkers by region of origin and in vocabulary knowledge. Individual non-native word recognition accuracy on PRESTO sentences in multitalker babble at more favorable signal-to-noise ratios was found to be related to several BRIEF-A subscales and composite scores. However, non-native performance on PRESTO was not related to regional dialect categorization, talker and gender discrimination, or vocabulary knowledge. Conclusions High-variability sentences in multitalker babble were particularly challenging for non-native listeners. Difficulty under high-variability testing conditions was related to lack of experience with the L2, especially L2 sociolinguistic information, compared with native listeners. Individual differences among the non-native listeners were related to weaknesses in core neurocognitive abilities affecting behavioral control in everyday life. PMID:25405842

Matrix remodeling between cells and cellular interactions with collagen bundle

NASA Astrophysics Data System (ADS)

Kim, Jihan; Sun, Bo

When cells are surrounded by complex environment, they continuously probe and interact with it by applying cellular traction forces. As cells apply traction forces, they can sense rigidity of their local environment and remodel the matrix microstructure simultaneously. Previous study shows that single human carcinoma cell (MDA-MB-231) remodeled its surrounding extracellular matrix (ECM) and the matrix remodeling was reversible. In this study we examined the matrix microstructure between cells and cellular interaction between them using quantitative confocal microscopy. The result shows that the matrix microstructure is the most significantly remodeled between cells consisting of aligned, and densified collagen fibers (collagen bundle)., the result shows that collagen bundle is irreversible and significantly change micromechanics of ECM around the bundle. We further examined cellular interaction with collagen bundle by analyzing dynamics of actin and talin formation along with the direction of bundle. Lastly, we analyzed dynamics of cellular protrusion and migrating direction of cells along the bundle.

Combining blue native polyacrylamide gel electrophoresis with liquid chromatography tandem mass spectrometry as an effective strategy for analyzing potential membrane protein complexes of Mycobacterium bovis bacillus Calmette-Guérin

PubMed Central

2011-01-01

Background Tuberculosis is an infectious bacterial disease in humans caused primarily by Mycobacterium tuberculosis, and infects one-third of the world's total population. Mycobacterium bovis bacillus Calmette-Guérin (BCG) vaccine has been widely used to prevent tuberculosis worldwide since 1921. Membrane proteins play important roles in various cellular processes, and the protein-protein interactions involved in these processes may provide further information about molecular organization and cellular pathways. However, membrane proteins are notoriously under-represented by traditional two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and little is known about mycobacterial membrane and membrane-associated protein complexes. Here we investigated M. bovis BCG by an alternative proteomic strategy coupling blue native PAGE to liquid chromatography tandem mass spectrometry (LC-MS/MS) to characterize potential protein-protein interactions in membrane fractions. Results Using this approach, we analyzed native molecular composition of protein complexes in BCG membrane fractions. As a result, 40 proteins (including 12 integral membrane proteins), which were organized in 9 different gel bands, were unambiguous identified. The proteins identified have been experimentally confirmed using 2-D SDS PAGE. We identified MmpL8 and four neighboring proteins that were involved in lipid transport complexes, and all subunits of ATP synthase complex in their monomeric states. Two phenolpthiocerol synthases and three arabinosyltransferases belonging to individual operons were obtained in different gel bands. Furthermore, two giant multifunctional enzymes, Pks7 and Pks8, and four mycobacterial Hsp family members were determined. Additionally, seven ribosomal proteins involved in polyribosome complex and two subunits of the succinate dehydrogenase complex were also found. Notablely, some proteins with high hydrophobicity or multiple transmembrane helixes were identified well in our work. Conclusions In this study, we utilized LC-MS/MS in combination with blue native PAGE to characterize modular components of multiprotein complexes in BCG membrane fractions. The results demonstrated that the proteomic strategy was a reliable and reproducible tool for analysis of BCG multiprotein complexes. The identification in our study may provide some evidence for further study of BCG protein interaction. PMID:21241518

Extracellular K+ rapidly controls NaCl cotransporter phosphorylation in the native distal convoluted tubule by Cl−‐dependent and independent mechanisms

PubMed Central

Penton, David; Czogalla, Jan; Wengi, Agnieszka; Himmerkus, Nina; Loffing‐Cueni, Dominique; Carrel, Monique; Rajaram, Renuga Devi; Staub, Olivier; Bleich, Markus; Schweda, Frank

2016-01-01

Key points High dietary potassium (K+) intake dephosphorylates and inactivates the NaCl cotransporter (NCC) in the renal distal convoluted tubule (DCT).Using several ex vivo models, we show that physiological changes in extracellular K+, similar to those occurring after a K+ rich diet, are sufficient to promote a very rapid dephosphorylation of NCC in native DCT cells.Although the increase of NCC phosphorylation upon decreased extracellular K+ appears to depend on cellular Cl− fluxes, the rapid NCC dephosphorylation in response to increased extracellular K+ is not Cl−‐dependent.The Cl−‐dependent pathway involves the SPAK/OSR1 kinases, whereas the Cl− independent pathway may include additional signalling cascades. Abstract A high dietary potassium (K+) intake causes a rapid dephosphorylation, and hence inactivation, of the thiazide‐sensitive NaCl cotransporter (NCC) in the renal distal convoluted tubule (DCT). Based on experiments in heterologous expression systems, it was proposed that changes in extracellular K+ concentration ([K+]ex) modulate NCC phosphorylation via a Cl−‐dependent modulation of the with no lysine (K) kinases (WNK)‐STE20/SPS‐1‐44 related proline‐alanine‐rich protein kinase (SPAK)/oxidative stress‐related kinase (OSR1) kinase pathway. We used the isolated perfused mouse kidney technique and ex vivo preparations of mouse kidney slices to test the physiological relevance of this model on native DCT. We demonstrate that NCC phosphorylation inversely correlates with [K+]ex, with the most prominent effects occurring around physiological plasma [K+]. Cellular Cl− conductances and the kinases SPAK/OSR1 are involved in the phosphorylation of NCC under low [K+]ex. However, NCC dephosphorylation triggered by high [K+]ex is neither blocked by removing extracellular Cl−, nor by the Cl− channel blocker 4,4′‐diisothiocyano‐2,2′‐stilbenedisulphonic acid. The response to [K+]ex on a low extracellular chloride concentration is also independent of significant changes in SPAK/OSR1 phosphorylation. Thus, in the native DCT, [K+]ex directly and rapidly controls NCC phosphorylation by Cl−‐dependent and independent pathways that involve the kinases SPAK/OSR1 and a yet unidentified additional signalling mechanism. PMID:27457700

Multidimensional immunolabeling and 4D time-lapse imaging of vital ex vivo lung tissue

PubMed Central

Vierkotten, Sarah; Lindner, Michael; Königshoff, Melanie; Eickelberg, Oliver

2015-01-01

During the last decades, the study of cell behavior was largely accomplished in uncoated or extracellular matrix (ECM)-coated plastic dishes. To date, considerable cell biological efforts have tried to model in vitro the natural microenvironment found in vivo. For the lung, explants cultured ex vivo as lung tissue cultures (LTCs) provide a three-dimensional (3D) tissue model containing all cells in their natural microenvironment. Techniques for assessing the dynamic live interaction between ECM and cellular tissue components, however, are still missing. Here, we describe specific multidimensional immunolabeling of living 3D-LTCs, derived from healthy and fibrotic mouse lungs, as well as patient-derived 3D-LTCs, and concomitant real-time four-dimensional multichannel imaging thereof. This approach allowed the evaluation of dynamic interactions between mesenchymal cells and macrophages with their ECM. Furthermore, fibroblasts transiently expressing focal adhesions markers incorporated into the 3D-LTCs, paving new ways for studying the dynamic interaction between cellular adhesions and their natural-derived ECM. A novel protein transfer technology (FuseIt/Ibidi) shuttled fluorescently labeled α-smooth muscle actin antibodies into the native cells of living 3D-LTCs, enabling live monitoring of α-smooth muscle actin-positive stress fibers in native tissue myofibroblasts residing in fibrotic lesions of 3D-LTCs. Finally, this technique can be applied to healthy and diseased human lung tissue, as well as to adherent cells in conventional two-dimensional cell culture. This novel method will provide valuable new insights into the dynamics of ECM (patho)biology, studying in detail the interaction between ECM and cellular tissue components in their natural microenvironment. PMID:26092995

Born of fire - restoring sagebrush steppe

USGS Publications Warehouse

Pyke, David A.

2002-01-01

Fire is a natural feature of sagebrush grasslands in the Great Basin. The invasion of exotic annual grasses, such as Bromus tectorum (cheatgrass), has changed the environment in these ecosystems. Invasive annual grasses provide a dense and continuous source of fuel that extends the season for fires and increases the frequency of fires in the region. Frequent fires eventually eliminate the native sagebrush. These annual grasses also change soil nutrients, especially carbon and nitrogen, such that invasive annual grasses are favored over the native plants. The Forest and Rangeland Ecosystem Science Center of the U.S. Geological Survey (USGS) is studying how to reduce the problems caused by these invasive annual grasses and restore native sagebrush grasslands. The areas of research include understanding disturbance regimes, especially fire, discerning the role of nutrients in restoring native plants, determining the potential to restore forbs important for wildlife, and ascertaining the past and present use of native and nonnative plants in revegetation projects.

An Integrative Review of Mechanotransduction in Endothelial, Epithelial (Renal) and Dendritic Cells (Osteocytes)

PubMed Central

Weinbaum, Sheldon; Duan, Yi; Thi, Mia M.; You, Lidan

2013-01-01

In this review we will examine from a biomechanical and ultrastructural viewpoint how the cytoskeletal specialization of three basic cell types, endothelial cells (ECs), epithelial cells (renal tubule) and dendritic cells (osteocytes), enables the mechano-sensing of fluid flow in both their native in vivo environment and in culture, and the downstream signaling that is initiated at the molecular level in response to fluid flow. These cellular responses will be discussed in terms of basic mysteries and paradoxes encountered by each cell type. In ECs fluid shear stress (FSS) is nearly entirely attenuated by the endothelial glycocalyx that covers their apical membrane and yet FSS is communicated to both intracellular and junctional molecular components in activating a wide variety of signaling pathways. The same is true in proximal tubule (PT) cells where a dense brush border of microvilli covers the apical surface and the flow at the apical membrane is negligible. A four decade old unexplained mystery is the ability of PT epithelia to reliably reabsorb 60% of the flow entering the tubule regardless of the glomerular filtration rate. In the cortical collecting duct (CCD) the flow rates are so low that a special sensing apparatus, a primary cilia is needed to detect very small variations in tubular flow. In bone it has been a century old mystery as to how osteocytes embedded in a stiff mineralized tissue are able to sense miniscule whole tissue strains that are far smaller than the cellular level strains required to activate osteocytes in vitro. PMID:23976901

A Major Binding Protein for Leukemia Inhibitory Factor in Normal Mouse Serum: Identification as a Soluble Form of the Cellular Receptor

NASA Astrophysics Data System (ADS)

Layton, Meredith J.; Cross, Bronwyn A.; Metcalf, Donald; Ward, Larry D.; Simpson, Richard J.; Nicola, Nicos A.

1992-09-01

A protein that specifically binds leukemia inhibitory factor (LIF) has been isolated from normal mouse serum by using four successive fractionation steps: chromatography on a LIF affinity matrix, anion-exchange chromatography, size-exclusion chromatography, and preparative native gel electrophoresis. The purified LIF-binding protein (LBP) is a glycoprotein with an apparent molecular mass of 90 kDa that specifically binds 125I-labeled murine LIF with an affinity comparable to that of the low-affinity cellular LIF receptor (K_d = 600 pM). N-terminal sequencing has identified this protein as a soluble truncated form of the α chain of the cellular LIF receptor. LBP is present in normal mouse serum at high levels (1 μg/ml) and these levels are elevated in pregnant mice and reduced in neonatal mice. Since normal serum concentrations of LBP can block the biological actions of LIF in culture, LBP may serve as an inhibitor of the systemic effects of locally produced LIF.

Life-history habitat matching in invading non-native plant species

USGS Publications Warehouse

Stohlgren, T.J.; Crosier, C.; Chong, G.W.; Guenther, D.; Evangelista, P.

2005-01-01

We briefly reviewed the literature on habitat matching in invading non-native plant species. Then we hypothesized that the richness and cover of native annual and perennial plant species integrate complex local information of vegetation and soils that would help to predict invasion success by similarly adapted non-native plant species. We tested these ‘life-history habitat matching’ relationships in 603 0.1-ha plots, including 294 plots in Colorado, which were relatively high for the cover of native perennial plant species, and for 309 0.1-ha plots in southern Utah, which were relatively high in the cover of native annual plant species. We found strong positive relationships between the richness and foliar cover for both native and non-native species, whether they were annual or perennial species (0.34 > r2 < 0.53; P < 0.0001). We also found significant positive relationships between the cover of native annual species at a site and the richness (r2 = 0.13; P < 0.0001) and the foliar cover (r2 = 0.06; P < 0.0001) of non-native annual species. The proportion of non-native annual species in the flora of a plot also increased significantly with the foliar cover of native annual species. Conversely, the richness and cover of non-native annual species were significantly negatively associated with the foliar cover of native perennial species (r2 = 0.05 and 0.06, respectively; P < 0.0001). The cover of non-native annual or perennial species was not significantly correlated with soil texture variables, %N, or %C. We conclude that there may be a high degree of life-history habitat matching by non-native annual species in these study sites. Information on native annual and perennial species richness and cover may help characterize the complex soils, climate, and disturbance environment in which similarly adapted non-native plant species establish and gain foliar cover.

Academic Performance of Native and Immigrant Students: A Study Focused on the Perception of Family Support and Control, School Satisfaction, and Learning Environment

PubMed Central

Santos, Miguel A.; Godás, Agustín; Ferraces, María J.; Lorenzo, Mar

2016-01-01

The international assessment studies of key competences, such as the PISA report of the OECD, have revealed that the academic performance of Spanish students is significantly below the OECD average. In addition, it has also been confirmed that the results of immigrant students are consistently lower than those of their native counterparts. Given the context, the first objective of this work is to observe the variables (support, control, school satisfaction, and learning environment) which distinguish between retained and non-retained native and immigrant students. The second objective is to check, by comparing the retained and non-retained native and immigrant students and separating the two levels, in order to find out which of the selected variables clearly differentiate the two groups. A sample of 1359 students was used (79.8% native students and 20.2% immigrant students of Latin American origin), who were enrolled in the 5th and 6th year of Primary Education (aged 10–11 years) and in the 1st and 2nd year of Secondary Education (aged 12–13 years). The measurement scales, which undergo a psychometric analysis in the current work, have been developed in a previous research study (Lorenzo et al., 2009). The construct validity and reliability are reported (obtaining alpha indices between 0.705 and 0.787). Subsequently, and depending on the results of this analysis, inferential analyses are performed, using as independent variables the ethno-cultural origin and being retained or not, whereas, as dependent variables, the indices referring to students' perception of family support and control, as well as the assessment of the school and learning environment. Among other results, the Group × Being retained/Not being retained [F(1, 1315) = 4.67, p < 0.01] interaction should be pointed out, indicating that native non-retained subjects perceive more control than immigrants, as well as the Group × Being retained/Not being retained [F(1, 1200) = 5.49, p < 0.01] interaction, showing that native non-retained students perceive more family support. Given the results obtained, our intention is to provide solid evidence that would facilitate the design of family involvement programs, helping to improve students' educational performance. PMID:27790171

Academic Performance of Native and Immigrant Students: A Study Focused on the Perception of Family Support and Control, School Satisfaction, and Learning Environment.

PubMed

Santos, Miguel A; Godás, Agustín; Ferraces, María J; Lorenzo, Mar

2016-01-01

The international assessment studies of key competences, such as the PISA report of the OECD, have revealed that the academic performance of Spanish students is significantly below the OECD average. In addition, it has also been confirmed that the results of immigrant students are consistently lower than those of their native counterparts. Given the context, the first objective of this work is to observe the variables (support, control, school satisfaction, and learning environment) which distinguish between retained and non-retained native and immigrant students. The second objective is to check, by comparing the retained and non-retained native and immigrant students and separating the two levels, in order to find out which of the selected variables clearly differentiate the two groups. A sample of 1359 students was used (79.8% native students and 20.2% immigrant students of Latin American origin), who were enrolled in the 5th and 6th year of Primary Education (aged 10-11 years) and in the 1st and 2nd year of Secondary Education (aged 12-13 years). The measurement scales, which undergo a psychometric analysis in the current work, have been developed in a previous research study (Lorenzo et al., 2009). The construct validity and reliability are reported (obtaining alpha indices between 0.705 and 0.787). Subsequently, and depending on the results of this analysis, inferential analyses are performed, using as independent variables the ethno-cultural origin and being retained or not, whereas, as dependent variables, the indices referring to students' perception of family support and control, as well as the assessment of the school and learning environment. Among other results, the Group × Being retained/Not being retained [ F (1, 1315) = 4.67, p < 0.01] interaction should be pointed out, indicating that native non-retained subjects perceive more control than immigrants, as well as the Group × Being retained/Not being retained [ F (1, 1200) = 5.49, p < 0.01] interaction, showing that native non-retained students perceive more family support. Given the results obtained, our intention is to provide solid evidence that would facilitate the design of family involvement programs, helping to improve students' educational performance.

Competition for Shared Resources in the Cellular Chassis: Impact on Synthetic Circuits

DTIC Science & Technology

2013-11-01

glyceraldehyde dehydrogenase from E. coli and it is very abundant in the bacterial cytoplasm. The control MBP-dRFP does not display an effect on GFP ...discover how key parameters control the extent of coupling we constructed an analytical model that predicts how the concentration of one protein ( GFP ...SECURITY CLASSIFICATION OF: Protein overexpression leads to growth inhibition and decreased expression of native proteins. This effect is mostly due

COSEE-AK Ocean Science Fairs: A Science Fair Model That Grounds Student Projects in Both Western Science and Traditional Native Knowledge

ERIC Educational Resources Information Center

Dublin, Robin; Sigman, Marilyn; Anderson, Andrea; Barnhardt, Ray; Topkok, Sean Asiqluq

2014-01-01

We have developed the traditional science fair format into an ocean science fair model that promoted the integration of Western science and Alaska Native traditional knowledge in student projects focused on the ocean, aquatic environments, and climate change. The typical science fair judging criteria for the validity and presentation of the…

Pragmatic Competence and Social Power Awareness: The Case of Written and Spoken Discourse in Non-Native English Environments

ERIC Educational Resources Information Center

Pérez-Sabater, Carmen; Montero-Fleta, Begoña

2014-01-01

Following one of the new challenges suggested by the Common European Framework of Reference for Languages, a treatment was developed to enhance pragmatic competence, since this competence is not easy to acquire by non-native speakers. Within this context, we focused on pragmatic awareness in the workplace, an area of expertise in growing demand…

Range-wide conservation of Pinus aristata: A genetic collection with ecological context for proactive management today and resources for tomorrow

Treesearch

Anna W. Schoettle; Jonathan C. Coop

2017-01-01

Tree species are highly vulnerable to anthropogenic environmental change, and are increasingly being challenged by non-native pests and climate change. Rocky Mountain bristlecone pines are long-lived, exhibit delayed maturation, have low genetic diversity, and inhabit cold, high-elevation environments. They are threatened by the non-native disease white pine blister...

Native plants fare better against an introduced competitor with native microbes and lower nitrogen availability.

PubMed

Gaya Shivega, W; Aldrich-Wolfe, Laura

2017-01-24

While the soil environment is generally acknowledged as playing a role in plant competition, the relative importance of soil resources and soil microbes in determining outcomes of competition between native and exotic plants has rarely been tested. Resilience of plant communities to invasion by exotic species may depend on the extent to which native and exotic plant performance are mediated by abiotic and biotic components of the soil. We used a greenhouse experiment to compare performance of two native prairie plant species and one exotic species, when grown in intraspecific competition and when each native was grown in interspecific competition with the exotic species, in the presence and absence of a native prairie soil community, and when nitrogen availability was elevated or was maintained at native prairie levels. We found that elevated nitrogen availability was beneficial to the exotic species and had no effect on or was detrimental to the native plant species, that the native microbial community was beneficial to the native plant species and either had no effect or was detrimental to the exotic species, and that intraspecific competition was stronger than interspecific competition for the exotic plant species and vice-versa for the natives. Our results demonstrate that soil nitrogen availability and the soil microbial community can mediate the strength of competition between native and exotic plant species. We found no evidence for native microbes enhancing the performance of the exotic plant species. Instead, loss of the native soil microbial community appears to reinforce the negative effects of elevated N on native plant communities and its benefits to exotic invasive species. Resilience of plant communities to invasion by exotic plant species is facilitated by the presence of an intact native soil microbial community and weakened by anthropogenic inputs of nitrogen. Published by Oxford University Press on behalf of the Annals of Botany Company.

Morphological Effect of Doping Environment on Silicon Nanowires Grown by Plasma-Assisted Chemical Vapor Deposition

NASA Astrophysics Data System (ADS)

Lohn, Andrew J.; Cormia, Robert D.; Fryauf, David M.; Zhang, Junce; Norris, Kate J.; Kobayashi, Nobuhiko P.

2012-11-01

Physical properties of semiconductor nanowires are tied intimately to their specific morphologies such as length and diameter. We studied the growth of silicon nanowires and found their lengths and diameters to vary over orders of magnitude in different doping environments. In all cases we examined, doping resulted in increased diameters. In addition, boron doping was found to accelerate volume growth rate while arsenic and antimony both appeared to slow it down. We further studied the formation of the native oxides that cover the nanowires. X-ray photoelectron spectroscopy indicated that properties of the native oxides are also dependent on doping environment and correlated to doping-dependent shifts in apparent binding energy of the Si 2p3/2 peak illustrating that the electronic contribution is the dominant mechanism for the oxide growth.

An Online Task-Based Language Learning Environment: Is It Better for Advanced- or Intermediate-Level Second Language Learners?

ERIC Educational Resources Information Center

Arslanyilmaz, Abdurrahman

2012-01-01

This study investigates the relationship of language proficiency to language production and negotiation of meaning that non-native speakers (NNSs) produced in an online task-based language learning (TBLL) environment. Fourteen NNS-NNS dyads collaboratively completed four communicative tasks, using an online TBLL environment specifically designed…

Cell-matrix mechanical interaction in electrospun polymeric scaffolds for tissue engineering: Implications for scaffold design and performance.

PubMed

Kennedy, Kelsey M; Bhaw-Luximon, Archana; Jhurry, Dhanjay

2017-03-01

Engineered scaffolds produced by electrospinning of biodegradable polymers offer a 3D, nanofibrous environment with controllable structural, chemical, and mechanical properties that mimic the extracellular matrix of native tissues and have shown promise for a number of tissue engineering applications. The microscale mechanical interactions between cells and electrospun matrices drive cell behaviors including migration and differentiation that are critical to promote tissue regeneration. Recent developments in understanding these mechanical interactions in electrospun environments are reviewed, with emphasis on how fiber geometry and polymer structure impact on the local mechanical properties of scaffolds, how altering the micromechanics cues cell behaviors, and how, in turn, cellular and extrinsic forces exerted on the matrix mechanically remodel an electrospun scaffold throughout tissue development. Techniques used to measure and visualize these mechanical interactions are described. We provide a critical outlook on technological gaps that must be overcome to advance the ability to design, assess, and manipulate the mechanical environment in electrospun scaffolds toward constructs that may be successfully applied in tissue engineering and regenerative medicine. Tissue engineering requires design of scaffolds that interact with cells to promote tissue development. Electrospinning is a promising technique for fabricating fibrous, biomimetic scaffolds. Effects of electrospun matrix microstructure and biochemical properties on cell behavior have been extensively reviewed previously; here, we consider cell-matrix interaction from a mechanical perspective. Micromechanical properties as a driver of cell behavior has been well established in planar substrates, but more recently, many studies have provided new insights into mechanical interaction in fibrillar, electrospun environments. This review provides readers with an overview of how electrospun scaffold mechanics and cell behavior work in a dynamic feedback loop to drive tissue development, and discusses opportunities for improved design of mechanical environments that are conducive to tissue development. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Immunogold Localization of Key Metabolic Enzymes in the Anammoxosome and on the Tubule-Like Structures of Kuenenia stuttgartiensis.

PubMed

de Almeida, Naomi M; Neumann, Sarah; Mesman, Rob J; Ferousi, Christina; Keltjens, Jan T; Jetten, Mike S M; Kartal, Boran; van Niftrik, Laura

2015-07-01

Anaerobic ammonium-oxidizing (anammox) bacteria oxidize ammonium with nitrite as the terminal electron acceptor to form dinitrogen gas in the absence of oxygen. Anammox bacteria have a compartmentalized cell plan with a central membrane-bound "prokaryotic organelle" called the anammoxosome. The anammoxosome occupies most of the cell volume, has a curved membrane, and contains conspicuous tubule-like structures of unknown identity and function. It was suggested previously that the catalytic reactions of the anammox pathway occur in the anammoxosome, and that proton motive force was established across its membrane. Here, we used antibodies raised against five key enzymes of the anammox catabolism to determine their cellular location. The antibodies were raised against purified native hydroxylamine oxidoreductase-like protein kustc0458 with its redox partner kustc0457, hydrazine dehydrogenase (HDH; kustc0694), hydroxylamine oxidase (HOX; kustc1061), nitrite oxidoreductase (NXR; kustd1700/03/04), and hydrazine synthase (HZS; kuste2859-61) of the anammox bacterium Kuenenia stuttgartiensis. We determined that all five protein complexes were exclusively located inside the anammoxosome matrix. Four of the protein complexes did not appear to form higher-order protein organizations. However, the present data indicated for the first time that NXR is part of the tubule-like structures, which may stretch the whole length of the anammoxosome. These findings support the anammoxosome as the locus of catabolic reactions of the anammox pathway. Anammox bacteria are environmentally relevant microorganisms that contribute significantly to the release of fixed nitrogen in nature. Furthermore, the anammox process is applied for nitrogen removal from wastewater as an environment-friendly and cost-effective technology. These microorganisms feature a unique cellular organelle, the anammoxosome, which was proposed to contain the energy metabolism of the cell and tubule-like structures with hitherto unknown function. Here, we purified five native enzymes catalyzing key reactions in the anammox metabolism and raised antibodies against these in order to localize them within the cell. We showed that all enzymes were located within the anammoxosome, and nitrite oxidoreductase was located exclusively at the tubule-like structures, providing the first insights into the function of these subcellular structures. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

O-GlcNAc cycling: how a single sugar post-translational modification is changing the way we think about signaling networks.

PubMed

Slawson, Chad; Housley, Michael P; Hart, Gerald W

2006-01-01

O-GlcNAc is an ubiquitous post-translational protein modification consisting of a single N-acetlyglucosamine moiety linked to serine or threonine residues on nuclear and cytoplasmic proteins. Recent work has begun to uncover the functional roles of O-GlcNAc in cellular processes. O-GlcNAc modified proteins are involved in sensing the nutrient status of the surrounding cellular environment and adjusting the activity of cellular proteins accordingly. O-GlcNAc regulates cellular responses to hormones such as insulin, initiates a protective response to stress, modulates a cell's capacity to grow and divide, and regulates gene transcription. This review will focus on recent work involving O-GlcNAc in sensing the environment and regulating signaling cascades. (c) 2005 Wiley-Liss, Inc.

Ab initio folding of proteins using all-atom discrete molecular dynamics

PubMed Central

Ding, Feng; Tsao, Douglas; Nie, Huifen; Dokholyan, Nikolay V.

2008-01-01

Summary Discrete molecular dynamics (DMD) is a rapid sampling method used in protein folding and aggregation studies. Until now, DMD was used to perform simulations of simplified protein models in conjunction with structure-based force fields. Here, we develop an all-atom protein model and a transferable force field featuring packing, solvation, and environment-dependent hydrogen bond interactions. Using the replica exchange method, we perform folding simulations of six small proteins (20–60 residues) with distinct native structures. In all cases, native or near-native states are reached in simulations. For three small proteins, multiple folding transitions are observed and the computationally-characterized thermodynamics are in quantitative agreement with experiments. The predictive power of all-atom DMD highlights the importance of environment-dependent hydrogen bond interactions in modeling protein folding. The developed approach can be used for accurate and rapid sampling of conformational spaces of proteins and protein-protein complexes, and applied to protein engineering and design of protein-protein interactions. PMID:18611374

Strategies and Applications for Incorporating Physical and Chemical Signal Gradients in Tissue Engineering

PubMed Central

Singh, Milind; Berkland, Cory

2008-01-01

From embryonic development to wound repair, concentration gradients of bioactive signaling molecules guide tissue formation and regeneration. Moreover, gradients in cellular and extracellular architecture as well as in mechanical properties are readily apparent in native tissues. Perhaps tissue engineers can take a cue from nature in attempting to regenerate tissues by incorporating gradients into engineering design strategies. Indeed, gradient-based approaches are an emerging trend in tissue engineering, standing in contrast to traditional approaches of homogeneous delivery of cells and/or growth factors using isotropic scaffolds. Gradients in tissue engineering lie at the intersection of three major paradigms in the field—biomimetic, interfacial, and functional tissue engineering—by combining physical (via biomaterial design) and chemical (with growth/differentiation factors and cell adhesion molecules) signal delivery to achieve a continuous transition in both structure and function. This review consolidates several key methodologies to generate gradients, some of which have never been employed in a tissue engineering application, and discusses strategies for incorporating these methods into tissue engineering and implant design. A key finding of this review was that two-dimensional physicochemical gradient substrates, which serve as excellent high-throughput screening tools for optimizing desired biomaterial properties, can be enhanced in the future by transitioning from two dimensions to three dimensions, which would enable studies of cell–protein–biomaterial interactions in a more native tissue–like environment. In addition, biomimetic tissue regeneration via combined delivery of graded physical and chemical signals appears to be a promising strategy for the regeneration of heterogeneous tissues and tissue interfaces. In the future, in vivo applications will shed more light on the performance of gradient-based mechanical integrity and signal delivery strategies compared to traditional tissue engineering approaches. PMID:18803499

Strategies and applications for incorporating physical and chemical signal gradients in tissue engineering.

PubMed

Singh, Milind; Berkland, Cory; Detamore, Michael S

2008-12-01

From embryonic development to wound repair, concentration gradients of bioactive signaling molecules guide tissue formation and regeneration. Moreover, gradients in cellular and extracellular architecture as well as in mechanical properties are readily apparent in native tissues. Perhaps tissue engineers can take a cue from nature in attempting to regenerate tissues by incorporating gradients into engineering design strategies. Indeed, gradient-based approaches are an emerging trend in tissue engineering, standing in contrast to traditional approaches of homogeneous delivery of cells and/or growth factors using isotropic scaffolds. Gradients in tissue engineering lie at the intersection of three major paradigms in the field-biomimetic, interfacial, and functional tissue engineering-by combining physical (via biomaterial design) and chemical (with growth/differentiation factors and cell adhesion molecules) signal delivery to achieve a continuous transition in both structure and function. This review consolidates several key methodologies to generate gradients, some of which have never been employed in a tissue engineering application, and discusses strategies for incorporating these methods into tissue engineering and implant design. A key finding of this review was that two-dimensional physicochemical gradient substrates, which serve as excellent high-throughput screening tools for optimizing desired biomaterial properties, can be enhanced in the future by transitioning from two dimensions to three dimensions, which would enable studies of cell-protein-biomaterial interactions in a more native tissue-like environment. In addition, biomimetic tissue regeneration via combined delivery of graded physical and chemical signals appears to be a promising strategy for the regeneration of heterogeneous tissues and tissue interfaces. In the future, in vivo applications will shed more light on the performance of gradient-based mechanical integrity and signal delivery strategies compared to traditional tissue engineering approaches.

Engineering triterpene metabolism in tobacco

PubMed Central

Shuiqin, Wu; Zuodong, Jiang; Chase, Kempinski; Eric Nybo, S.; Husodo, Satrio; Williams, Robert

2013-01-01

Terpenes comprise a distinct class of natural products that serve a diverse range of physiological functions, provide for interactions between plants and their environment and represent a resource for many kinds of practical applications. To better appreciate the importance of terpenes to overall growth and development, and to create a production capacity for specific terpenes of industrial interest, we have pioneered the development of strategies for diverting carbon flow from the native terpene biosynthetic pathways operating in the cytosol and plastid compartments of tobacco for the generation of specific classes of terpenes. In the current work, we demonstrate how difficult it is to divert the 5-carbon intermediates DMAPP and IPP from the mevalonate pathway operating in the cytoplasm for triterpene biosynthesis, yet diversion of the same intermediates from the methylerythritol phosphate pathway operating in the plastid compartment leads to the accumulation of very high levels of the triterpene squalene. This was assessed by the co-expression of an avian farnesyl diphosphate synthase and yeast squalene synthase genes targeting metabolism in the cytoplasm or chloroplast. We also evaluated the possibility of directing this metabolism to the secretory trichomes of tobacco by comparing the effects of trichome-specific gene promoters to strong, constitutive viral promoters. Surprisingly, when transgene expression was directed to trichomes, high-level squalene accumulation was observed, but overall plant growth and physiology were reduced up to 80 % of the non-transgenic controls. Our results support the notion that the biosynthesis of a desired terpene can be dramatically improved by directing that metabolism to a non-native cellular compartment, thus avoiding regulatory mechanisms that might attenuate carbon flux within an engineered pathway. PMID:22729821

Effect of surface modifiers on an ectoenzyme: granulocyte 5'-nucleotidase.

PubMed

Smolen, J E; Karnovsky, M L

1980-05-01

Several agents that react with plasma membranes, namely the native lectins concanavalin A, Ricinus communis agglutinin, and wheat germ agglutinin, the modified lectin succinyl concanavalin A, and sodium meta-periodate, inhibited the ecto-5'-nucleotidase of intact guinea pig granulocytes. Stimulation of the enzyme was not observed at any lectin concentration. Inhibition by native lectins could be blocked or reversed by appropriate competing hapten sugars. In the case of concanavalin A, reversal could be achieved at 37 degrees C, but not at 5 degrees C. When lectins were used in combination with each other, the effects were found to be largely independent. However, when concanavalin A and R. communis agglutinin were applied together, complications arose because the former lectin binds to the latter as well as to the cell surface. To avoid some of the complexities inherent in studying intact cell 5'-nucleotidase and to gain additional information about the system, two broken cell enzyme preparations were also examined. The enzyme of plasma membrane-enriched fractions was inhibited by all five agents mentioned above. 5'-Nucleotidase solubilized in sodium deoxycholate was inhibited by the four lectins but stimulated by periodate. The effects of the surface modifiers on kinetic data for all three enzyme preparations are consistent with the hypothesis that direct interactions with the enzyme molecule give rise to changes in Vmax; interactions at membrane sites other than 5'-nucleotidase itself could cause increases in apparent Km values. Effects of interactions of ectoenzymes with plant lectins may serve as models for phenomena that result from cell-cell interactions or from interactions of animal cells with lectin-like components of the cellular environment.

A virus or more in (nearly) every cell: ubiquitous networks of virus-host interactions in extreme environments.

PubMed

Munson-McGee, Jacob H; Peng, Shengyun; Dewerff, Samantha; Stepanauskas, Ramunas; Whitaker, Rachel J; Weitz, Joshua S; Young, Mark J

2018-06-01

The application of viral and cellular metagenomics to natural environments has expanded our understanding of the structure, functioning, and diversity of microbial and viral communities. The high diversity of many communities, e.g., soils, surface ocean waters, and animal-associated microbiomes, make it difficult to establish virus-host associations at the single cell (rather than population) level, assign cellular hosts, or determine the extent of viral host range from metagenomics studies alone. Here, we combine single-cell sequencing with environmental metagenomics to characterize the structure of virus-host associations in a Yellowstone National Park (YNP) hot spring microbial community. Leveraging the relatively low diversity of the YNP environment, we are able to overlay evidence at the single-cell level with contextualized viral and cellular community structure. Combining evidence from hexanucelotide analysis, single cell read mapping, network-based analytics, and CRISPR-based inference, we conservatively estimate that >60% of cells contain at least one virus type and a majority of these cells contain two or more virus types. Of the detected virus types, nearly 50% were found in more than 2 cellular clades, indicative of a broad host range. The new lens provided by the combination of metaviromics and single-cell genomics reveals a network of virus-host interactions in extreme environments, provides evidence that extensive virus-host associations are common, and further expands the unseen impact of viruses on cellular life.

Novel approach to the diagnosis of fractures in an austere environment using a stethoscope and a cellular phone.

PubMed

Matzek, Brett A; Fivecoat, Phillip T; Ritz, Reis B

2014-03-01

Fracture diagnosis in the austere environment where radiographic tests are not available can be a challenge. In the past, a diagnostic technique has been described using a tuning fork and stethoscope to assess decreased sound conduction in the fractured extremity. In this study, we evaluate the use of a cellular phone's vibrate function and a stethoscope to limit equipment carried by expeditionary practitioners. The purpose of this study was to evaluate the accuracy of fracture diagnosis using a cellular phone and stethoscope. This is a pilot study to assess the usefulness of the above technique before clinical implementation. In 3 cadavers, we created fractures of the humerus and femur. Twenty-seven emergency medicine residents and an attending physician performed the diagnostic technique. Overall, the use of the cellular phone and stethoscope resulted in a sensitivity of 73% (95% confidence interval [CI]: 0.64 to 0.81) and a specificity of 83% (95% CI: 0.77 to 0.88), with a positive predicted value of 68% (95% CI: 0.59 to 0.77) and a negative predicted value of 86% (95% CI: 0.81 to 0.90). Positive likelihood ratio was 4.3, and negative likelihood ratio was 0.32. The use of a cellular phone and stethoscope may be a useful tool for the diagnosis of fractures in the austere environment. However, further study is needed to validate these findings in the clinical environment. Published by Wilderness Medical Society on behalf of Wilderness Medical Society.

Role of Mitochondrial Oxidative Stress in Spaceflight-Induced Tissue Degeneration

NASA Technical Reports Server (NTRS)

Torres, Samantha M.; Schreurs, Ann-Sofie; Truong, Tiffany A.; Tahimic, Candice; Globus, Ruth

2017-01-01

Microgravity and ionizing radiation in the spaceflight environment poses multiple challenges to homeostasis and may contribute to cellular stress. Effects may include increased generation of reactive oxygen species (ROS), DNA damage and repair error, cell cycle arrest, cell senescence or death. Our central hypothesis is that prolonged exposure to the spaceflight environment leads to the excess production of ROS and oxidative damage, culminating in accelerated tissue degeneration. The main goal of this project is to determine the importance of cellular redox defense for physiological adaptations and tissue degeneration in the space environment.

Can invasions occur without change? A comparison of G-matrices and selection in the peach-potato aphid, Myzus persicae

PubMed Central

Bacigalupe, Leonardo D; Barrientos, Karin; Beckerman, Andrew P; Carter, Mauricio J; Figueroa, Christian C; Foster, Stephen P; Moore, Allen J; Silva, Andrea X; Nespolo, Roberto F

2013-01-01

Most evolutionary research on biological invasions has focused on changes seen between the native and invaded range for a particular species. However, it is likely that species that live in human-modified habitats in their native range might have evolved specific adaptations to those environments, which increase the likelihood of establishment and spread in similar human-altered environments. From a quantitative genetic perspective, this hypothesis suggests that both native and introduced populations should reside at or near the same adaptive peak. Therefore, we should observe no overall changes in the G (genetic variance–covariance) matrices between native and introduced ranges, and stabilizing selection on fitness-related traits in all populations. We tested these predictions comparing three populations of the worldwide pest Myzus persicae from the Middle East (native range) and the UK and Chile (separately introduced ranges). In general, our results provide mixed support for this idea, but further comparisons of other species are needed. In particular, we found that there has been some limited evolution in the studied traits, with the Middle East population differing from the UK and Chilean populations. This was reflected in the structure of the G-matrices, in which Chile differed from both UK and Middle East populations. Furthermore, the amount of genetic variation was massively reduced in Chile in comparison with UK and Middle East populations. Finally, we found no detectable selection on any trait in the three populations, but clones from the introduced ranges started to reproduce later, were smaller, had smaller offspring, and had lower reproductive fitness than clones from the native range. PMID:24455140

Do low oxygen environments facilitate marine invasions? Relative tolerance of native and invasive species to low oxygen conditions.

PubMed

Lagos, Marcelo E; Barneche, Diego R; White, Craig R; Marshall, Dustin J

2017-06-01

Biological invasions are one of the biggest threats to global biodiversity. Marine artificial structures are proliferating worldwide and provide a haven for marine invasive species. Such structures disrupt local hydrodynamics, which can lead to the formation of oxygen-depleted microsites. The extent to which native fauna can cope with such low oxygen conditions, and whether invasive species, long associated with artificial structures in flow-restricted habitats, have adapted to these conditions remains unclear. We measured water flow and oxygen availability in marinas and piers at the scales relevant to sessile marine invertebrates (mm). We then measured the capacity of invasive and native marine invertebrates to maintain metabolic rates under decreasing levels of oxygen using standard laboratory assays. We found that marinas reduce water flow relative to piers, and that local oxygen levels can be zero in low flow conditions. We also found that for species with erect growth forms, invasive species can tolerate much lower levels of oxygen relative to native species. Integrating the field and laboratory data showed that up to 30% of available microhabitats within low flow environments are physiologically stressful for native species, while only 18% of the same habitat is physiologically stressful for invasive species. These results suggest that invasive species have adapted to low oxygen habitats associated with manmade habitats, and artificial structures may be creating niche opportunities for invasive species. © 2017 John Wiley & Sons Ltd.

ARSENIC MINERALS AS INDICATORS OF CONDITIONS OF GOLD DEPOSITION IN CARLIN-TYPE GOLD DEPOSITS.

USGS Publications Warehouse

Rytuba, James J.

1984-01-01

Arsenic minerals commonly occurring in Carlin-type gold deposits include orpiment and realgar and, more rarely, native arsenic and arsenopyrite. Other arsenic-bearing phases present include arsenian pyrite and stibnite and a number of thallium and mercury sulfides. Under conditions of constant temperature and pressure, the relative stability of arsenic minerals is a function of sulfur activity. At high sulfur activity, orpiment is the stable phase. As sulfur activity is decreased, more sulfur-deficient arsenic phases become stable with the progressive formation of realgar, native arsenic, arsenopyrite, and finally, loellingite at very low sulfur activity. Three univariant equilibrium assemblages: orpiment plus realgar, realgar plus native arsenic and native arsenic plus arsenopyrite are useful indicators of sulfur activity and commonly occur in the epithermal environment.

Protein quality control: the who’s who, the where’s and therapeutic escapes

PubMed Central

Yam, Gary Hin-Fai; Fan, Jingyu; Hirano, Kiyoko; Gaplovska-Kysela, Katarina; Le Fourn, Valerie; Guhl, Bruno; Santimaria, Roger; Torossi, Tania; Ziak, Martin

2007-01-01

In cells the quality of newly synthesized proteins is monitored in regard to proper folding and correct assembly in the early secretory pathway, the cytosol and the nucleoplasm. Proteins recognized as non-native in the ER will be removed and degraded by a process termed ERAD. ERAD of aberrant proteins is accompanied by various changes of cellular organelles and results in protein folding diseases. This review focuses on how the immunocytochemical labeling and electron microscopic analyses have helped to disclose the in situ subcellular distribution pattern of some of the key machinery proteins of the cellular protein quality control, the organelle changes due to the presence of misfolded proteins, and the efficiency of synthetic chaperones to rescue disease-causing trafficking defects of aberrant proteins. PMID:18075753

A tissue engineering approach to anterior cruciate ligament regeneration using novel shaped capillary channel polymer fibers

NASA Astrophysics Data System (ADS)

Sinclair, Kristofer D.

2009-12-01

Ruptures of the anterior cruciate ligament (ACL) are the most frequent of injuries to the knee due to its role in preventing anterior translation of the tibia. It is estimated that as many as 200,000 Americans per year will suffer from a ruptured ACL, resulting in management costs on the order of 5 billion dollars. Without treatment these patients are unable to return to normal activity, as a consequence of the joint instability found within the ACL deficient knee. Over the last thirty years, a variety of non-degradable, synthetic fibers have been evaluated for their use in ACL reconstruction; however, a widely accepted prosthesis has been unattainable due to differences in mechanical properties of the synthetic graft relative to the native tissue. Tissue engineering is an interdisciplinary field charged with the task of developing therapeutic solutions for tissue and organ failure by enhancing the natural wound healing process through the use of cellular transplants, biomaterials, and the delivery of bioactive molecules. The capillary channel polymer (CC-P) fibers used in this research were fabricated by melt extrusion from polyethylene terephthalate and polybutylene terephthalate. These fibers possess aligned micrometer scale surface channels that may serve as physical templates for tissue growth and regeneration. This inherent surface topography offers a unique and industrially viable approach for cellular contact guidance on three dimensional constructs. In this fundamental research the ability of these fiber channels to support the adhesion, alignment, and organization of fibroblasts was demonstrated and found to be superior to round fiber controls. The results demonstrated greater uniformity of seeding and accelerated formation of multi-layered three-dimensional biomass for the CC-P fibers relative to those with a circular cross-section. Furthermore, the CC-P geometry induced nuclear elongation consistent with that observed in native ACL tissue. Through the application of uniaxial cyclic strain the mechanical properties of the cell seeded CC-P fiber scaffold systems were shown to improve via the induction of increased cellular proliferation and extracellular matrix synthesis. Finally, unlike many studies examining the effects of cyclic strain on cellular behavior, the CC-P fiber geometry displayed the ability to maintain cellular alignment in the presence of an applied uniaxial cyclic strain.

Plant functional traits of dominant native and invasive species in mediterranean-climate ecosystems.

PubMed

Funk, Jennifer L; Standish, Rachel J; Stock, William D; Valladares, Fernando

2016-01-01

The idea that dominant invasive plant species outperform neighboring native species through higher rates of carbon assimilation and growth is supported by several analyses of global data sets. However, theory suggests that native and invasive species occurring in low-resource environments will be functionally similar, as environmental factors restrict the range of observed physiological and morphological trait values. We measured resource-use traits in native and invasive plant species across eight diverse vegetation communities distributed throughout the five mediterranean-climate regions, which are drought prone and increasingly threatened by human activities, including the introduction of exotic species. Traits differed strongly across the five regions. In regions with functional differences between native and invasive species groups, invasive species displayed traits consistent with high resource acquisition; however, these patterns were largely attributable to differences in life form. We found that species invading mediterranean-climate regions were more likely to be annual than perennial: three of the five regions were dominated by native woody species and invasive annuals. These results suggest that trait differences between native and invasive species are context dependent and will vary across vegetation communities. Native and invasive species within annual and perennial groups had similar patterns of carbon assimilation and resource use, which contradicts the widespread idea that invasive species optimize resource acquisition rather than resource conservation. .

Restoration of mangrove plantations and colonisation by native species in Leizhou bay, South China

USGS Publications Warehouse

Ren, H.; Jian, S.; Lu, H.; Zhang, Q.; Shen, W.; Han, W.; Yin, Z.; Guo, Q.

2008-01-01

To examine the natural colonisation of native mangrove species into remediated exotic mangrove stands in Leizhou Bay, South China, we compared soil physical-chemical properties, community structure and recruitments of barren mangrove areas, native mangrove species plantations, and exotic mangrove species-Sonneratia apetala Buch.Ham-between plantations and natural forest. We found that severely degraded mangrove stands could not regenerate naturally without human intervention due to severely altered local environments, whereas some native species had been recruited into the 4-10 year S. apetala plantations. In the first 10 years, the exotic species S. apetala grew better than native species such as Rhizophora stylosa Griff and Kandelia candel (Linn.) Druce. The mangrove plantation gradually affected soil physical and chemical properties during its recovery. The exotic S. apetala was more competitive than native species and its plantation was able to restore soil organic matter in about 14 years. Thus, S. apetala can be considered as a pioneer species to improve degraded habitats to facilitate recolonisation by native mangrove species. However, removal to control proliferation may be needed at late stages to facilitate growth of native species. To ensure sustainability of mangroves in South China, the existing mangrove wetlands must be managed as an ecosystem, with long-term scientific monitoring program in place. ?? 2007 The Ecological Society of Japan.

Durability of metals from archaeological objects, metal meteorites, and native metals

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

Johnson, A.B. Jr.; Francis, B.

1980-01-01

Metal durability is an important consideration in the multi-barrier nuclear waste storage concept. This study summarizes the ancient metals, the environments, and factors which appear to have contributed to metal longevity. Archaeological and radiochemical dating suggest that human use of metals began in the period 6000 to 7000 BC. Gold is clearly the most durable, but many objects fashioned from silver, copper, bronze, iron, lead, and tin have survived for several thousand years. Dry environments, such as tombs, appear to be optimum for metal preservation, but some metals have survived in shipwrecks for over a thousand years. The metal meteoritesmore » are Fe-base alloys with 5 to 60 wt% Ni and minor amounts of Co, I, and S. Some meteoritic masses with ages estimated to be 5,000 to 20,000 years have weathered very little, while other masses from the same meteorites are in advanced stages of weathering. Native metals are natural metallic ores. Approximately five million tonnes were mined from native copper deposits in Michigan. Copper masses from the Michigan deposits were transported by the Pleistocene glaciers. Areas on the copper surfaces which appear to represent glacial abrasion show minimal corrosion. Dry cooling tower technology has demonstrated that in pollution-free moist environments, metals fare better at temperatures above than below the dewpoint. Thus, in moderate temperature regimes, elevated temperatures may be useful rather than detrimental for exposures of metal to air. In liquid environments, relatively complex radiolysis reactions can occur, particularly where multiple species are present. A dry environment largely obviates radiolysis effects.« less

Holistic System of Care: a ten-year perspective.

PubMed

Nebelkopf, Ethan; Wright, Serena

2011-01-01

The Holistic System of Care for Native Americans in an Urban Environment is a community-focused intervention that provides behavioral health care, promotes health, and prevents disease. This approach is based on a community strategic planning process that honored Native American culture and relationships. Substance abuse, mental illness, homelessness, poverty, crime, physical illness, and violence are symptoms of historical trauma, family dysfunction, and spiritual imbalance. The holistic model links treatment, prevention, and recovery. The link between prevention and treatment is early intervention. Peer support is the link between treatment and recovery. Recovering individuals serve as role models linking recovery to prevention. Culture and spirituality build a strong and resilient foundation for recovery. This article documents the effectiveness of the holistic model over a ten-year period that it has been implemented at the Family & Child Guidance Clinic of the Native American Health Center in the San Francisco Bay Area. The holistic model has produced statistically significant reductions in substance abuse among adult Native American women, men, reentry, and homeless populations; reductions in substance abuse among Native American adolescents; reductions in HIV/AIDS high-risk behavior among Native American men, women, and adolescents; and decreases in acting out behavior among Native American severely emotionally disturbed children.

Alaska Natives assessing the health of their environment.

PubMed

Garza, D

2001-11-01

The changes in Alaska's ecosystems caused by pollution, contaminants and global climate change are negatively impacting Alaska Natives and rural residents who rely on natural resources for food, culture and community identity. While Alaska commerce has contributed little to these global changes and impacts, Alaska and its resources are nonetheless affected by the changes. While Alaska Natives have historically relied on Alaska's land, water and animals for survival and cultural identity, today their faith in the safety and quality of these resources has decreased. Alaska Natives no longer believe that these wild resources are the best and many are turning to alternative store-bought foods. Such a change in diet and activity may be contributing to a decline in traditional activities and a decline in general health. Contaminants are showing up in the animals, fish and waters that Alaska Natives use. Efforts need to be expanded to empower Alaska Native Tribes to collect and analyze local wild foods for various contaminants. In addition existing information on contaminants and pollution should be made readily available to Alaska residents. Armed with this type of information Alaska Native residents will be better prepared to make informed decisions on using wild foods and materials.

Hybridization and restricted gene flow between native and introduced stocks of Alpine whitefish (Coregonus sp.) across multiple environments

PubMed Central

Winkler, Kathrin A; Pamminger-Lahnsteiner, Barbara; Wanzenböck, Josef; Weiss, Steven

2011-01-01

Translocations of Baltic whitefish (Coregonus sp.) into Austrian Alpine lakes have created ‘artificial hybrid zones’, threatening the genetic integrity of native lineages. We evaluate the genetic structure of Coregonus in Austrian lakes and characterize hybridization and introgression between native and introduced lineages. Fifteen populations (N= 747) were assessed for allelic variation at eight microsatellite loci and a reduced set (N= 253) for variation across two mtDNA genes (cyt b and NADH-3). Bayesian approaches were used to estimate individual admixture proportions (q-values) and classify genotypes as native, introduced or hybrids. q-value distributions varied among populations highlighting differential hybridization and introgression histories. Many lakes revealed a clear distinction between native and introduced genotypes despite hybridization, whereas some locations revealed hybrid swarms. Genetic structure among lakes was congruent with morphological divergence and novelty raising speculation of multiple taxa, including a population south of the Alps, outside the putative native range of Coregonus. Although statistically congruent with inferences based on nuclear markers, mitochondrial haplotype data was not diagnostic with respect to native and non-native lineages, supporting that the Alpine region was colonized post-glacially by an admixture of mtDNA lineages, which coalesce >1 Ma. Mechanisms promoting or eroding lineage isolation are discussed, as well as a high potential to conserve native Alpine lineages despite the extensive historical use of introduced Baltic stocks. PMID:21199024

Differential use of temporal cues to the /s/-/z/ contrast by native and non-native speakers of English.

PubMed

Flege, J E; Hillenbrand, J

1986-02-01

This study examined the effect of linguistic experience on perception of the English /s/-/z/ contrast in word-final position. The durations of the periodic ("vowel") and aperiodic ("fricative") portions of stimuli, ranging from peas to peace, were varied in a 5 X 5 factorial design. Forced-choice identification judgments were elicited from two groups of native speakers of American English differing in dialect, and from two groups each of native speakers of French, Swedish, and Finnish differing in English-language experience. The results suggested that the non-native subjects used cues established for the perception of phonetic contrasts in their native language to identify fricatives as /s/ or /z/. Lengthening vowel duration increased /z/ judgments in all eight subject groups, although the effect was smaller for native speakers of French than for native speakers of the other languages. Shortening fricative duration, on the other hand, significantly decreased /z/ judgments only by the English and French subjects. It did not influence voicing judgments by the Swedish and Finnish subjects, even those who had lived for a year or more in an English-speaking environment. These findings raise the question of whether adults who learn a foreign language can acquire the ability to integrate multiple acoustic cues to a phonetic contrast which does not exist in their native language.

An Overview and Analysis of Mobile Internet Protocols in Cellular Environments.

ERIC Educational Resources Information Center

Chao, Han-Chieh

2001-01-01

Notes that cellular is the inevitable future architecture for the personal communication service system. Discusses the current cellular support based on Mobile Internet Protocol version 6 (Ipv6) and points out the shortfalls of using Mobile IP. Highlights protocols especially for mobile management schemes which can optimize a high-speed mobile…

Invasive Plants Rapidly Reshape Soil Properties in a Grassland Ecosystem.

PubMed

Gibbons, Sean M; Lekberg, Ylva; Mummey, Daniel L; Sangwan, Naseer; Ramsey, Philip W; Gilbert, Jack A

2017-01-01

Plant invasions often reduce native plant diversity and increase net primary productivity. Invaded soils appear to differ from surrounding soils in ways that impede restoration of diverse native plant communities. We hypothesize that invader-mediated shifts in edaphic properties reproducibly alter soil microbial community structure and function. Here, we take a holistic approach, characterizing plant, prokaryotic, and fungal communities and soil physicochemical properties in field sites, invasion gradients, and experimental plots for three invasive plant species that cooccur in the Rocky Mountain West. Each invader had a unique impact on soil physicochemical properties. We found that invasions drove shifts in the abundances of specific microbial taxa, while overall belowground community structure and functional potential were fairly constant. Forb invaders were generally enriched in copiotrophic bacteria with higher 16S rRNA gene copy numbers and showed greater microbial carbohydrate and nitrogen metabolic potential. Older invasions had stronger effects on abiotic soil properties, indicative of multiyear successions. Overall, we show that plant invasions are idiosyncratic in their impact on soils and are directly responsible for driving reproducible shifts in the soil environment over multiyear time scales. IMPORTANCE In this study, we show how invasive plant species drive rapid shifts in the soil environment from surrounding native communities. Each of the three plant invaders had different but consistent effects on soils. Thus, there does not appear to be a one-size-fits-all strategy for how plant invaders alter grassland soil environments. This work represents a crucial step toward understanding how invaders might be able to prevent or impair native reestablishment by changing soil biotic and abiotic properties.

Engineering of arteries in vitro

PubMed Central

Huang, Angela H.; Niklason, Laura E.

2014-01-01

This review will focus on two elements that are essential for functional arterial regeneration in vitro: the mechanical environment and the bioreactors used for tissue growth. The importance of the mechanical environment to embryological development, vascular functionality, and vascular graft regeneration will be discussed. Bioreactors generate mechanical stimuli to simulate the biomechanical environment of the arterial system. This system has been used to reconstruct arterial grafts with appropriate mechanical strength for implantation by controlling the chemical and mechanical environments in which the grafts are grown. Bioreactors are powerful tools to study the effect of mechanical stimuli on extracellular matrix (ECM) architecture and the mechanical properties of engineered vessels. Hence biomimetic systems enable us to optimize chemo-biomechanical culture conditions to regenerate engineered vessels with physiological properties similar to those of native arterial vessels. In addition, this review will introduce and examine various approaches and techniques that have been used to engineer biologically-based vascular grafts, including collagen-based grafts, fibrin-gel grafts, cell sheet engineering, biodegradable polymers, and decellularization of native vessels. PMID:24399290

Holistic risk-based environmental decision making: a Native perspective.

PubMed Central

Arquette, Mary; Cole, Maxine; Cook, Katsi; LaFrance, Brenda; Peters, Margaret; Ransom, James; Sargent, Elvera; Smoke, Vivian; Stairs, Arlene

2002-01-01

Native American Nations have become increasingly concerned about the impacts of toxic substances. Although risk assessment and risk management processes have been used by government agencies to help estimate and manage risks associated with exposure to toxicants, these tools have many inadequacies and as a result have not served Native people well. In addition, resources have not always been adequate to address the concerns of Native Nations, and involvement of Native decision makers on a government-to-government basis in discussions regarding risk has only recently become common. Finally, because the definitions of health used by Native people are strikingly different from that of risk assessors, there is also a need to expand current definitions and incorporate traditional knowledge into decision making. Examples are discussed from the First Environment Restoration Initiative, a project that is working to address toxicant issues facing the Mohawk territory of Akwesasne. This project is developing a community-defined model in which health is protected at the same time that traditional cultural practices, which have long been the key to individual and community health, are maintained and restored. PMID:11929736

Decellularization of Human Internal Mammary Artery: Biomechanical Properties and Histopathological Evaluation.

PubMed

Kajbafzadeh, Abdol-Mohammad; Khorramirouz, Reza; Kameli, Seyede Maryam; Hashemi, Javad; Bagheri, Amin

2017-01-01

This study undertook to create small-diameter vascular grafts and assess their structure and mechanical properties to withstand arterial implantation. Twenty samples of intact human internal mammary arteries (IMAs) were collected and decellularized using detergent-based methods. To evaluate residual cellular and extracellular matrix (ECM) components, histological analysis was performed. Moreover, collagen typing and ECM structure were analyzed by Picrosirius red and Movat's pentachrome staining. Scanning electron microscopy was also applied to assess microarchitecture of both endothelial and adventitial surfaces of native and decellularized arterial samples. Furthermore, mechanical tests were performed to evaluate the rigidity and suture strength of the arteries. Human IMAs were completely decellularized in all three segments (proximal, middle, and distal). ECM proteins such as collagen and elastic fibers were efficiently preserved and no structural distortion in intima, media, and adventitial surfaces was observed. The parameters of the mechanical tests revealed no significant differences in the mechanical properties of decellularized arteries in comparison to native arteries with considerable strength, suture retention, and stress relaxation (Young's modulus [MPa] = 0.22 ± 0.023 [native] and 0.22 ± 0.015 [acellular]; and suture strength 0.56 ± 0.19 [native] vs. 0.56 ± 0.12 [acellular], respectively). Decellularized IMA represents a potential arterial scaffold as an alternative to autologous grafts for future arterial bypass surgeries. By this technique, microarchitecture and mechanical integrity of decellularized arteries were considerably similar to native arteries. The goal of this study was to introduce an efficient method for complete decellularization of human IMA and evaluate the ECM and biomechanical properties.

Ecophysiology of native and alien-invasive clams in an ocean warming context.

PubMed

Anacleto, Patrícia; Maulvault, Ana Luísa; Lopes, Vanessa M; Repolho, Tiago; Diniz, Mário; Nunes, Maria Leonor; Marques, António; Rosa, Rui

2014-09-01

Both climate change and biological invasions are among the most serious global environmental threats. Yet mechanisms underlying these eventual interactions remain unclear. The aim of this study was to undertake a comprehensive examination of the physiological and biochemical responses of native (Ruditapes decussatus) and alien-invasive (Ruditapes philippinarum) clams to environmental warming. We evaluated thermal tolerance limits (CTMax), routine metabolic rates (RMRs) and respective thermal sensitivity (Q10 values), critical oxygen partial pressure (Pcrit), heat shock response (HSP70/HSC70 levels), lipid peroxidation (MDA build-up) and antioxidant enzyme [glutathione-S-transferase (GST), catalase (CAT) and superoxide dismutase (SOD)] activities. Contrary to most studies that show that invasive species have a higher thermal tolerance than native congeners, here we revealed that the alien-invasive and native species had similar CTMax values. However, warming had a stronger effect on metabolism and oxidative status of the native R. decussatus, as indicated by the higher RMRs and HSP70/HSC70 and MDA levels, as well as GST, CAT and SOD activities. Moreover, we argue that the alien-invasive clams, instead of up-regulating energetically expensive cellular responses, have evolved a less demanding strategy to cope with short-term environmental (oxidative) stress-pervasive valve closure. Although efficient during stressful short-term periods to ensure isolation and guarantee longer survival, such adaptive behavioural strategy entails metabolic arrest (and the enhancement of anaerobic pathways), which to some extent will not be advantageous under the chronically warming conditions predicted in the future. Copyright © 2014 Elsevier Inc. All rights reserved.

Post-secretion processing influences spider silk performance

PubMed Central

Blamires, Sean J.; Wu, Chung-Lin; Blackledge, Todd A.; Tso, I-Min

2012-01-01

Phenotypic variation facilitates adaptations to novel environments. Silk is an example of a highly variable biomaterial. The two-spidroin (MaSp) model suggests that spider major ampullate (MA) silk is composed of two proteins—MaSp1 predominately contains alanine and glycine and forms strength enhancing β-sheet crystals, while MaSp2 contains proline and forms elastic spirals. Nonetheless, mechanical properties can vary in spider silks without congruent amino acid compositional changes. We predicted that post-secretion processing causes variation in the mechanical performance of wild MA silk independent of protein composition or spinning speed across 10 species of spider. We used supercontraction to remove post-secretion effects and compared the mechanics of silk in this ‘ground state’ with wild native silks. Native silk mechanics varied less among species compared with ‘ground state’ silks. Variability in the mechanics of ‘ground state’ silks was associated with proline composition. However, variability in native silks did not. We attribute interspecific similarities in the mechanical properties of native silks, regardless of amino acid compositions, to glandular processes altering molecular alignment of the proteins prior to extrusion. Such post-secretion processing may enable MA silk to maintain functionality across environments, facilitating its function as a component of an insect-catching web. PMID:22628213

Astronomy and Geology Vocabulary, I.e. "NASA Words" in Native American Languages

NASA Astrophysics Data System (ADS)

Angrum, A.; Alexander, C. J.; Martin, M.

2014-12-01

The US Rosetta Project has developed a program in Native American communities in which contemporary STEM vocabulary is taught alongside the same vocabulary in Navajo. NASA images and science are used and described in the native language, alongside both lay English, and scientific English. Additionally, science curriculum (geology/chemistry/botany/physics) elements drawn from the reservation environment, including geomorphology, geochemistry, soil physics, are included and discussed in the native language as much as possible — with their analogs in other planetary environments (such as Mars). The program began with a student defining 30 Navajo words to describe what he called 'NASA' words, such as: cell phone, astronaut, space suit, computer, and planets not visible to the naked eye. The use of NASA material and imagery have a positive impact on the accessibility of the overall STEM material but community involvement, and buy-in, is criti! cal to the success of the program. The US Rosetta Project modified its goals, and curriculum, to accommodate the programmatic desires of teachers in the district, and the capabilities of the medicine men that agreed to participate. In this presentation we will report on lessons learned, as well as metrics and successes associated with our most recent Summer Science Academy [2014].

Multipotency of skeletal muscle stem cells on their native substrate and the expression of Connexin 43 during adoption of adipogenic and osteogenic fate.

PubMed

Elashry, Mohamed I; Heimann, Manuela; Wenisch, Sabine; Patel, Ketan; Arnhold, Stefan

2017-10-01

Muscle regeneration is performed by resident muscle stem cells called satellite cells (SC). However they are multipotent, being able to adopt adipogenic and osteogenic fate under the correct stimuli. Since SC behavior can be regulated by the extra-cellular matrix, we examined the robustness of the myogenic programme of SC on their native substrate-the surface of a myofiber. We show that the native substrate supports myogenic differentiation judged by the expression of members of the Myogenic Determination Factor (MRF) family. However SC even on their native substrate can be induced into adopting adipogenic or osteogenic fate. Furthermore conditions that support adipose or bone formation inhibit the proliferation of SC progeny as well as their migration. We show that Connexin43 (Cx43), a gap junction complex protein, is only expressed by activated and not quiescent SC. Furthermore, it is not expressed by SC that are in the process of changing their fate. Lastly we show that intact adult mouse muscle contains numerous cells expressing Cx43 and that the density of these cells seems to be related to capillary density. We suggest the Cx43 expression is localized to angioblasts and is more prominent in oxidative slow muscle compared to glycolytic fast muscle. Crown Copyright © 2017. Published by Elsevier GmbH. All rights reserved.

Comparison of root-associated communities of native and non-native ectomycorrhizal hosts in an urban landscape.

PubMed

Lothamer, K; Brown, S P; Mattox, J D; Jumpponen, A

2014-05-01

Non-native tree species are often used as ornamentals in urban landscapes. However, their root-associated fungal communities remain yet to be examined in detail. Here, we compared richness, diversity and community composition of ectomycorrhizosphere fungi in general and ectomycorrhizal (EcM) fungi in particular between a non-native Pinus nigra and a native Quercus macrocarpa across a growing season in urban parks using 454-pyrosequencing. Our data show that, while the ectomycorrhizosphere community richness and diversity did not differ between the two host, the EcM communities associated with the native host were often more species rich and included more exclusive members than those of the non-native hosts. In contrast, the ectomycorrhizosphere communities of the two hosts were compositionally clearly distinct in nonmetric multidimensional ordination analyses, whereas the EcM communities were only marginally so. Taken together, our data suggest EcM communities with broad host compatibilities and with a limited numbers of taxa with preference to the non-native host. Furthermore, many common fungi in the non-native Pinus were not EcM taxa, suggesting that the fungal communities of the non-native host may be enriched in non-mycorrhizal fungi at the cost of the EcM taxa. Finally, while our colonization estimates did not suggest a shortage in EcM inoculum for either host in urban parks, the differences in the fungi associated with the two hosts emphasize the importance of using native hosts in urban environments as a tool to conserve endemic fungal diversity and richness in man-made systems.

Role of local sequence in the folding of cellular retinoic abinding protein I: structural propensities of reverse turns.

PubMed

Rotondi, Kenneth S; Gierasch, Lila M

2003-07-08

The experiments described here explore the role of local sequence in the folding of cellular retinoic acid binding protein I (CRABP I). This is a 136-residue, 10-stranded, antiparallel beta-barrel protein with seven beta-hairpins and is a member of the intracellular lipid binding protein (iLBP) family. The relative roles of local and global sequence information in governing the folding of this class of proteins are not well-understood. In question is whether the beta-turns are locally defined by short-range interactions within their sequences, and are thus able to play an active role in reducing the conformational space available to the folding chain, or whether the turns are passive, relying upon global forces to form. Short (six- and seven-residue) peptides corresponding to the seven CRABP I turns were analyzed by circular dichroism and NMR for their tendencies to take up the conformations they adopt in the context of the native protein. The results indicate that two of the peptides, encompassing turns III and IV in CRABP I, have a strong intrinsic bias to form native turns. Intriguingly, these turns are on linked hairpins in CRABP I and represent the best-conserved turns in the iLBP family. These results suggest that local sequence may play an important role in narrowing the conformational ensemble of CRABP I during folding.

The Evolving Contribution of Mass Spectrometry to Integrative Structural Biology

NASA Astrophysics Data System (ADS)

Faini, Marco; Stengel, Florian; Aebersold, Ruedi

2016-06-01

Protein complexes are key catalysts and regulators for the majority of cellular processes. Unveiling their assembly and structure is essential to understanding their function and mechanism of action. Although conventional structural techniques such as X-ray crystallography and NMR have solved the structure of important protein complexes, they cannot consistently deal with dynamic and heterogeneous assemblies, limiting their applications to small scale experiments. A novel methodological paradigm, integrative structural biology, aims at overcoming such limitations by combining complementary data sources into a comprehensive structural model. Recent applications have shown that a range of mass spectrometry (MS) techniques are able to generate interaction and spatial restraints (cross-linking MS) information on native complexes or to study the stoichiometry and connectivity of entire assemblies (native MS) rapidly, reliably, and from small amounts of substrate. Although these techniques by themselves do not solve structures, they do provide invaluable structural information and are thus ideally suited to contribute to integrative modeling efforts. The group of Brian Chait has made seminal contributions in the use of mass spectrometric techniques to study protein complexes. In this perspective, we honor the contributions of the Chait group and discuss concepts and milestones of integrative structural biology. We also review recent examples of integration of structural MS techniques with an emphasis on cross-linking MS. We then speculate on future MS applications that would unravel the dynamic nature of protein complexes upon diverse cellular states.

Experimental studies of adaptation in Clarkia xantiana. II. Fitness variation across a subspecies border.

PubMed

Geber, Monica A; Eckhart, Vincent M

2005-03-01

Because the range boundary is the locale beyond which a taxon fails to persist, it provides a unique opportunity for studying the limits on adaptive evolution. Adaptive constraints on range expansion are perplexing in view of widespread ecotypic differentiation by habitat and region within a species' range (regional adaptation) and rapid evolutionary response to novel environments. In this study of two parapatric subspecies, Clarkia xantiana ssp. xantiana and C. x. ssp. parviflora, we compared the fitness of population transplants within their native region, in a non-native region within the native range, and in the non-native range to assess whether range expansion might be limited by a greater intensity of selection on colonists of a new range versus a new region within the range. The combined range of the two subspecies spans a west-to-east gradient of declining precipitation in the Sierra Nevada of California, with ssp. xantiana in the west being replaced by ssp. parviflora in the east. Both subspecies had significantly higher fitness in the native range (range adaptation), whereas regional adaptation was weak and was found only in the predominantly outcrossing ssp. xantiana but was absent in the inbreeding ssp. parvifilora. Because selection intensity on transplants was much stronger in the non-native range relative to non-native regions, there is a larger adaptive barrier to range versus regional expansion. Three of five sequential fitness components accounted for regional and range adaptation, but only one of them, survivorship from germination to flowering, contributed to both. Flower number contributed to regional adaptation in ssp. xantiana and fruit set (number of fruits per flower) to range adaptation. Differential survivorship of the two taxa or regional populations of ssp. xantiana in non-native environments was attributable, in part, to biotic interactions, including competition, herbivory, and pollination. For example, low fruit set in ssp. xantiana in the east was likely due to the absence of its principal specialist bee pollinators in ssp. parviflora's range. Thus, convergence on self-fertilization may be necessary for ssp. xantiana to invade ssp. parviflora's range, but the evolution of outcrossing would not be required for ssp. parviflora to invade ssp. xantiana's range.

Historical thermal regimes define limits to coral acclimatization.

PubMed

Howells, Emily J; Berkelmans, Ray; van Oppen, Madeleine J H; Willis, Bette L; Bay, Line K

2013-05-01

Knowledge of the degree to which corals undergo physiological acclimatization or genetic adaptation in response to changes in their thermal environment is crucial to the success of coral reef conservation strategies. The potential of corals to acclimatize to temperatures exceeding historical thermal regimes was investigated by reciprocal transplantation of Acropora millepora colonies between the warm central and cool southern regions of the Great Barrier Reef (GBR) for a duration of 14 months. Colony fragments retained at native sites remained healthy, whereas transplanted fragments, although healthy over initial months when temperatures remained within native thermal regimes, subsequently bleached and suffered mortality during seasonal temperature extremes. Corals hosting Symbiodinium D transplanted to the southern GBR bleached in winter and the majority suffered whole (40%; n=20 colonies) or partial (50%) mortality at temperatures 1.1 degrees C below their 15-year native minimum. In contrast, corals hosting Symbiodinium C2 transplanted to the central GBR bleached in summer and suffered whole (50%; n=10 colonies) or partial (42%) mortality at temperatures 2.5 degrees C above their 15-year native maximum. During summer bleaching, the dominant Symbiodinium type changed from C2 to D within corals transplanted to the central GBR. Corals transplanted to the cooler, southern GBR grew 74-80% slower than corals at their native site, and only 50% of surviving colonies reproduced, at least partially because of cold water bleaching of transplants. Despite the absence of any visual signs of stress, corals transplanted to the warmer, central GBR grew 52-59% more slowly than corals at their native site before the summer bleaching (i.e., from autumn to spring). Allocation of energy to initial acclimatization or reproduction may explain this pattern, as the majority (65%) of transplants reproduced one month earlier than portions of the same colonies retained at the southern native site. All parameters investigated (bleaching, mortality, Symbiodinium type fidelity, reproductive timing) demonstrated strong interactions between genotype and environment, indicating that the acclimatization potential of A. millepora populations may be limited by adaptation of the holobiont to native thermal regimes.

Anomalous droughts, not invasion, decrease persistence of native fishes in a desert river.

PubMed

Ruhí, Albert; Holmes, Elizabeth E; Rinne, John N; Sabo, John L

2015-04-01

Changing climate extremes and invasion by non-native species are two of the most prominent threats to native faunas. Predicting the relationships between global change and native faunas requires a quantitative toolkit that effectively links the timing and magnitude of extreme events to variation in species abundances. Here, we examine how discharge anomalies--unexpected floods and droughts--determine covariation in abundance of native and non-native fish species in a highly variable desert river in Arizona. We quantified stochastic variation in discharge using Fourier analyses on >15,000 daily observations. We subsequently coupled maximum annual spectral anomalies with a 15-year time series of fish abundances (1994-2008), using Multivariate Autoregressive State-Space (MARSS) models. Abiotic drivers (discharge anomalies) were paramount in determining long-term fish abundances, whereas biotic drivers (species interactions) played only a secondary role. As predicted, anomalous droughts reduced the abundances of native species, while floods increased them. However, in contrast to previous studies, we observed that the non-native assemblage was surprisingly unresponsive to extreme events. Biological trait analyses showed that functional uniqueness was higher in native than in non-native fishes. We also found that discharge anomalies influenced diversity patterns at the meta-community level, with nestedness increasing after anomalous droughts due to the differential impairment of native species. Overall, our results advance the notion that discharge variation is key in determining community trajectories in the long term, predicting the persistence of native fauna even in the face of invasion. We suggest this variation, rather than biotic interactions, may commonly underlie covariation between native and non-native faunas, especially in highly variable environments. If droughts become increasingly severe due to climate change, and floods increasingly muted due to regulation, fish assemblages in desert rivers may become taxonomically and functionally impoverished and dominated by non-native taxa. © 2014 John Wiley & Sons Ltd.

Super-Resolution Microscopy: Shedding Light on the Cellular Plasma Membrane.

PubMed

Stone, Matthew B; Shelby, Sarah A; Veatch, Sarah L

2017-06-14

Lipids and the membranes they form are fundamental building blocks of cellular life, and their geometry and chemical properties distinguish membranes from other cellular environments. Collective processes occurring within membranes strongly impact cellular behavior and biochemistry, and understanding these processes presents unique challenges due to the often complex and myriad interactions between membrane components. Super-resolution microscopy offers a significant gain in resolution over traditional optical microscopy, enabling the localization of individual molecules even in densely labeled samples and in cellular and tissue environments. These microscopy techniques have been used to examine the organization and dynamics of plasma membrane components, providing insight into the fundamental interactions that determine membrane functions. Here, we broadly introduce the structure and organization of the mammalian plasma membrane and review recent applications of super-resolution microscopy to the study of membranes. We then highlight some inherent challenges faced when using super-resolution microscopy to study membranes, and we discuss recent technical advancements that promise further improvements to super-resolution microscopy and its application to the plasma membrane.

Engineering tissue constructs to mimic native aortic and pulmonary valve leaflets' structures and mechanics

NASA Astrophysics Data System (ADS)

Masoumi, Nafiseh

There are several disadvantages correlated with current heart valve replacement, including anticoagulation therapy for patients with mechanical valves and the low durability of bioprosthetic valves. The non-viable nature of such devices is a critical drawback especially for pediatric cases due to the inability of the graft to grow in vivo with the patients. A tissue engineered heart valve (TEHV) with remodeling and growth ability, is conceptually appealing to use in the surgical repair and could serve as a permanent replacements when operating for pediatric valvular lesions. It is critical that scaffolds for functional heart valve tissue engineering, be capable of mimicking the native leaflet's structure and mechanical properties at the time of implantation. Meanwhile, the scaffolds should be able to support cellular proliferation and native-like tissue formation as the TEHV remodels toward a scaffold-free state. Our overall hypothesis is that an "ideal" engineered construct, designed based on native leaflet's structure and mechanics, will complement a native heart valve leaflet in providing benchmarks for use in the design of clinically-applicable TEHV. This hypothesis was addressed through several experiments conducted in the present study. To establish a functional biomimetic TEHV, we developed scaffolds capable of matching the anisotropic stiffness of native leaflet while promoting native-like cell and collagen content and supporting the ECM generation. Scaffolds with various polymer contents (e.g., poly (glycerol sebacate) (PGS) and poly (epsilon-caprolactone) (PCL)) and structural designs (e.g., microfabricated and microfibrous scaffolds), were fabricated based on native leaflet's structure and mechanics. It was found that the tri-layered scaffold, designed with assembly of microfabricated PGS and microfibrous PGS/PCL was a functional leaflet capable of promoting tissue formation. Furthermore, to investigate the effect of cyclic stress and flexure individually on the TEHV development, we designed a simple and novel stretch-flexure bioreactor in which samples were subjected to well-defined stimulations with a controlled strain-rate. The stretch and flexure was found to accelerate and increase tissue formation on the microfabricated PGS scaffolds cultivated in the bioreactors.

Propagation environments [Chapter 4

Treesearch

Douglass F. Jacobs; Thomas D. Landis; Tara Luna

2009-01-01

An understanding of all factors influencing plant growth in a nursery environment is needed for the successful growth and production of high-quality container plants. Propagation structures modify the atmospheric conditions of temperature, light, and relative humidity. Native plant nurseries are different from typical horticultural nurseries because plants must be...

A Second Home: Indigenous Considerations for Campus Housing

ERIC Educational Resources Information Center

Singson, Jamie M.; Tachine, Amanda R.; Davidson, Charlotte E.; Waterman, Stephanie J.

2016-01-01

The experiences of Native Students in campus housing has had limited attention in scholarship, which restricts cultural understanding and opportunities to create inclusive living environments. College and university housing is well positioned to create a positive living environment for students. We raise concerns on how higher education…

Cultural differences and similarities of environmental epistemology among Native American nations

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

Duplantier, S.

1997-08-01

A recent major effort of Xavier University`s Consortium for Environmental Risk Evaluation Project (CERE) has been to act as a facilitator for the convening of tribal forums on various environmental management decision making processes, especially the use of risk assessment. Two recent forums sponsored by the Shoshone-Bannock Nation of Ft. Hall, Idaho and the Nez Perce Nation of Lapwai, Idaho brought together tribal leaders, tribal professionals and tribal elders from around the nation to discuss tribal approaches to risk assessment. A statement in the brochure announcing the Nez Perce Forum said ``Our various cultural understandings of, and relationships to, themore » environment must play an essential role in determining how future risk assessment methods are determined and practiced.`` This paper will present and discuss the issue of differences in Native American epistemologies (ways of knowing) about the environment. Are these merely distinctions without differences? Do the differences in regional ecologies and cultures affect tribal views and tribal perceptions on risk assessment and risk communication? Must the tribes develop a single cultural risk model or can and must each one be unique? These and other topics will be discussed in this paper. This paper is an effort in understanding what Native Americans are saying about nature, the environment, and environmental risk and remediation.« less

Dissipation and enantioselective degradation of plant growth retardants paclobutrazol and uniconazole in open field, greenhouse, and laboratory soils.

PubMed

Wu, Chengwang; Sun, Jianqiang; Zhang, Anping; Liu, Weiping

2013-01-15

Greenhouses are increasingly important in human food supply. Pesticides used in greenhouses play important roles in horticulture; however, little is known about their behavior in greenhouse environments. This work investigates the dissipation and enantioselctive degradation of plant growth retardants including paclobutrazol and uniconazole in soils under three conditions (i.e., open field, greenhouse, and laboratory). The dissipation and enantioselective degradation of paclobutrazol and uniconazole in greenhouse were different from those in open field; they were more persistent in greenhouse than in open field soil. Leaching produced by rainfall is responsible for the difference in dissipation. Thus, local environmental impacts may occur more easily inside greenhouses, while groundwater may be more contaminated in open field. Spike concentrations of 5, 10, and 20 times the concentrations of native residues were tested for the enantioselective dissipation of the two pesticides; the most potent enantioselective degradation of paclobutrazol and uniconazole occurred at the 10 times that of the native residues in the greenhouse environments and at 20 times native residues in open field environments. The higher soil activity in greenhouses than in open fields was thought to be responsible for such a difference. The environmental risk and regulation of paclobutrazol and uniconazole should be considered at the enantiomeric level.

Nanodisc-Tm: Rapid functional assessment of nanodisc reconstituted membrane proteins by CPM assay.

PubMed

Ashok, Yashwanth; Jaakola, Veli-Pekka

2016-01-01

Membrane proteins are generally unstable in detergents. Therefore, biochemical and biophysical studies of membrane proteins in lipidic environments provides a near native-like environment suitable for membrane proteins. However, manipulation of proteins embedded in lipid bilayer has remained difficult. Methods such as nanodiscs and lipid cubic phase have been developed for easy manipulation of membrane proteins and have yielded significant insights into membrane proteins. Traditionally functional reconstitution of receptors in nanodiscs has been studied with radioligands. We present a simple and faster method for studying the functionality of reconstituted membrane proteins for routine characterization of protein batches after initial optimization of suitable conditions using radioligands. The benefits of the method are •Faster and generic method to assess functional reconstitution of membrane proteins.•Adaptable in high throughput format (≥96 well format).•Stability measurement in near-native lipid environment and lipid dependent melting temperatures.

Smoking-related knowledge, attitudes, and behaviors among Alaska Native people: a population-based study.

PubMed

Rohde, Kristen; Boles, Myde; Bushore, Chris J; Pizacani, Barbara A; Maher, Julie E; Peterson, Erin

2013-01-01

Several studies have shown that Alaska Native people have higher smoking prevalence than non-Natives. However, no population-based studies have explored whether smoking-related knowledge, attitudes, and behaviors also differ among Alaska Native people and non-Natives. We compared current smoking prevalence and smoking-related knowledge, attitudes, and behavior of Alaska Native adults living in the state of Alaska with non-Natives. We used Alaska Behavioral Risk Factor Surveillance System data for 1996 to 2010 to compare smoking prevalence, consumption, and cessation- and second-hand smoke-related knowledge, attitudes, and behaviors among self-identified Alaska Native people and non-Natives. Current smoking prevalence was 41% (95% CI: 37.9%-44.4%) among Alaska Native people compared with 17.1% (95% CI: 15.9%-18.4%) among non-Natives. Among current every day smokers, Alaska Natives were much more likely to smoke less than 10 cigarettes per day (OR = 5.0, 95% CI: 2.6-9.6) than non-Natives. Compared with non-Native smokers, Alaska Native smokers were as likely to have made a past year quit attempt (OR = 1.4, 95% CI: 0.9-2.1), but the attempt was less likely to be successful (OR = 0.5, 95% CI: 0.2-0.9). Among current smokers, Alaska Natives were more likely to believe second-hand smoke (SHS) was very harmful (OR = 4.5, 95% CI: 2.8-7.2), to believe that smoking should not be allowed in indoor work areas (OR = 1.9, 95% CI: 1.1-3.1) or in restaurants (OR = 4.2, 95% CI: 2.5-6.9), to have a home smoking ban (OR = 2.5, 95% CI: 1.6-3.9), and to have no home exposure to SHS in the past 30 days (OR = 2.3, 95% CI: 1.5-3.6) than non-Natives. Although a disparity in current smoking exists, Alaska Native people have smoking-related knowledge, attitudes, and behaviors that are encouraging for reducing the burden of smoking in this population. Programs should support efforts to promote cessation, prevent relapse, and establish smoke-free environments.

Tualang Honey Improves Human Corneal Epithelial Progenitor Cell Migration and Cellular Resistance to Oxidative Stress In Vitro

PubMed Central

Tan, Jun Jie; Azmi, Siti Maisura; Yong, Yoke Keong; Cheah, Hong Leong; Lim, Vuanghao; Sandai, Doblin; Shaharuddin, Bakiah

2014-01-01

Stem cells with enhanced resistance to oxidative stress after in vitro expansion have been shown to have improved engraftment and regenerative capacities. Such cells can be generated by preconditioning them with exposure to an antioxidant. In this study we evaluated the effects of Tualang honey (TH), an antioxidant-containing honey, on human corneal epithelial progenitor (HCEP) cells in culture. Cytotoxicity, gene expression, migration, and cellular resistance to oxidative stress were evaluated. Immunofluorescence staining revealed that HCEP cells were holoclonal and expressed epithelial stem cell marker p63 without corneal cytokeratin 3. Cell viability remained unchanged after cells were cultured with 0.004, 0.04, and 0.4% TH in the medium, but it was significantly reduced when the concentration was increased to 3.33%. Cell migration, tested using scratch migration assay, was significantly enhanced when cells were cultured with TH at 0.04% and 0.4%. We also found that TH has hydrogen peroxide (H2O2) scavenging ability, although a trace level of H2O2 was detected in the honey in its native form. Preconditioning HCEP cells with 0.4% TH for 48 h showed better survival following H2O2-induced oxidative stress at 50 µM than untreated group, with a significantly lower number of dead cells (15.3±0.4%) were observed compared to the untreated population (20.5±0.9%, p<0.01). Both TH and ascorbic acid improved HCEP viability following induction of 100 µM H2O2, but the benefit was greater with TH treatment than with ascorbic acid. However, no significant advantage was demonstrated using 5-hydroxymethyl-2-furancarboxaldehyde, a compound that was found abundant in TH using GC/MS analysis. This suggests that the cellular anti-oxidative capacity in HCEP cells was augmented by native TH and was attributed to its antioxidant properties. In conclusion, TH possesses antioxidant properties and can improve cell migration and cellular resistance to oxidative stress in HCEP cells in vitro. PMID:24802273

Reciprocal osmotic challenges reveal mechanisms of divergence in phenotypic plasticity in the killifish Fundulus heteroclitus.

PubMed

Brennan, Reid S; Galvez, Fernando; Whitehead, Andrew

2015-04-15

The killifish Fundulus heteroclitus is an estuarine species with broad physiological plasticity, enabling acclimation to diverse stressors. Previous work suggests that freshwater populations expanded their physiology to accommodate low salinity environments; however, it is unknown whether this compromises their tolerance to high salinity. We used a comparative approach to investigate the mechanisms of a derived freshwater phenotype and the fate of an ancestral euryhaline phenotype after invasion of a freshwater environment. We compared physiological and transcriptomic responses to high- and low-salinity stress in fresh and brackish water populations and found an enhanced plasticity to low salinity in the freshwater population coupled with a reduced ability to acclimate to high salinity. Transcriptomic data identified genes with a conserved common response, a conserved salinity-dependent response and responses associated with population divergence. Conserved common acclimation responses revealed stress responses and alterations in cell-cycle regulation as important mechanisms in the general osmotic response. Salinity-specific responses included the regulation of genes involved in ion transport, intracellular calcium, energetic processes and cellular remodeling. Genes diverged between populations were primarily those showing salinity-specific expression and included those regulating polyamine homeostasis and the cell cycle. Additionally, when populations were matched with their native salinity, expression patterns were consistent with the concept of 'transcriptomic resilience', suggesting local adaptation. These findings provide insight into the fate of a plastic phenotype after a shift in environmental salinity and help to reveal mechanisms allowing for euryhalinity. © 2015. Published by The Company of Biologists Ltd.

Performing Comparative Peptidomics Analyses of Salmonella from Different Growth Conditions

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

Adkins, Joshua N.; Mottaz, Heather; Metz, Thomas O.

2010-01-08

Host–pathogen interactions are complex competitions during which both the host and the pathogen adapt rapidly to each other in order for one or the other to survive. Salmonella enterica serovar Typhimurium is a pathogen with a broad host range that causes a typhoid fever-like disease in mice and severe food poisoning in humans. The murine typhoid fever is a systemic infection in which S.typhimurium evades part of the immune system by replicating inside macrophages and other cells. The transition from a foodborne contaminant to an intracellular pathogen must occur rapidly in multiple,ordered steps in order for S. typhimurium to thrivemore » within its host environment. Using S. typhimurium isolated from rich culture conditions and from conditions that mimic the hostile intracellular environment of the host cell, a native low molecular weight protein fraction, or peptidome, was enriched from cell lysates by precipitation with organic solvents. The enriched peptidome was analyzed by both LC–MS/MS and LC–MS-based methods, although several other methods are possible. Pre-fractionation of peptides allowed identification of small proteins and protein degradation products that would normally be overlooked. Comparison of peptides present in lysates prepared from Salmonella grown under different conditions provided a unique insight into cellular degradation processes as well as identification of novel peptides encoded in the genome but not annotated. The overall approach is detailed here as applied to Salmonella and is adaptable to a broad range of biological systems.« less

Nanofibers of Human Tropoelastin-inspired peptides: Structural characterization and biological properties.

PubMed

Secchi, Valeria; Franchi, Stefano; Fioramonti, Marco; Polzonetti, Giovanni; Iucci, Giovanna; Bochicchio, Brigida; Battocchio, Chiara

2017-08-01

Regenerative medicine is taking great advantage from the use of biomaterials in the treatments of a wide range of diseases and injuries. Among other biomaterials, self-assembling peptides are appealing systems due to their ability to spontaneously form nanostructured hydrogels that can be directly injected into lesions. Indeed, self-assembling peptide scaffolds are expected to behave as biomimetic matrices able to surround cells, to promote specific interactions, and to control and modify cell behavior by mimicking the native environment as well. We selected three pentadecapeptides inspired by Human Tropoelastin, a natural protein of the extracellular matrix, expected to show high biocompatibility. Moreover, the here proposed self-assembling peptides (SAPs) are able to spontaneously aggregate in nanofibers in biological environment, as revealed by AFM (Atomic Force Microscopy). Peptides were characterized by XPS (X-ray Photoelectron Spectroscopy) and IRRAS (Infrared Reflection Absorption Spectroscopy) both as lyophilized (not aggregated) and as aggregated (nanofibers) samples in order to investigate some potential differences in their chemical composition and intermolecular interactions, and to analyze the surface and interface of nanofibers. Finally, an accurate investigation of the biological properties of the SAPs and of their interaction with cells was performed by culturing for the first time human Mesenchymal Stem Cells (hMSCs) in presence of SAPs. The final aim of this work was to assess if Human Tropoelastin-inspired nanostructured fibers could exert a cytotoxic effect and to evaluate their biocompatibility, cellular adhesion and proliferation. Copyright © 2017 Elsevier B.V. All rights reserved.

Novel in vivo techniques to visualize kidney anatomy and function.

PubMed

Peti-Peterdi, János; Kidokoro, Kengo; Riquier-Brison, Anne

2015-07-01

Intravital imaging using multiphoton microscopy (MPM) has become an increasingly popular and widely used experimental technique in kidney research over the past few years. MPM allows deep optical sectioning of the intact, living kidney tissue with submicron resolution, which is unparalleled among intravital imaging approaches. MPM has solved a long-standing critical technical barrier in renal research to study several complex and inaccessible cell types and anatomical structures in vivo in their native environment. Comprehensive and quantitative kidney structure and function MPM studies helped our better understanding of the cellular and molecular mechanisms of the healthy and diseased kidney. This review summarizes recent in vivo MPM studies with a focus on the glomerulus and the filtration barrier, although select, glomerulus-related renal vascular and tubular functions are also mentioned. The latest applications of serial MPM of the same glomerulus in vivo, in the intact kidney over several days, during the progression of glomerular disease are discussed. This visual approach, in combination with genetically encoded fluorescent markers of cell lineage, has helped track the fate and function (e.g., cell calcium changes) of single podocytes during the development of glomerular pathologies, and provided visual proof for the highly dynamic, rather than static, nature of the glomerular environment. Future intravital imaging applications have the promise to further push the limits of optical microscopy, and to advance our understanding of the mechanisms of kidney injury. Also, MPM will help to study new mechanisms of tissue repair and regeneration, a cutting-edge area of kidney research.

Minimalist Model Systems Reveal Similarities and Differences between Membrane Interaction Modes of MCL1 and BAK*

PubMed Central

Landeta, Olatz; Landajuela, Ane; Garcia-Saez, Ana; Basañez, Gorka

2015-01-01

Proteins belonging to the BCL2 family are key modulators of apoptosis that establish a complex network of interactions among themselves and with other cellular factors to regulate cell fate. It is well established that mitochondrial membranes are the main locus of action of all BCL2 family proteins, but it is difficult to obtain a precise view of how BCL2 family members operate at the native mitochondrial membrane environment during apoptosis. Here, we used minimalist model systems and multiple fluorescence-based techniques to examine selected membrane activities of MCL1 and BAK under apoptotic-like conditions. We show that three distinct apoptosis-related factors (i.e. the BCL2 homology 3 ligand cBID, the mitochondrion-specific lipid cardiolipin, and membrane geometrical curvature) all promote membrane association of BCL2-like structural folds belonging to both MCL1 and BAK. However, at the same time, the two proteins exhibited distinguishing features in their membrane association modes under apoptotic-like conditions. In addition, scanning fluorescence cross-correlation spectroscopy and FRET measurements revealed that the BCL2-like structural fold of MCL1, but not that of BAK, forms stable heterodimeric complexes with cBID in a manner adjustable by membrane cardiolipin content and curvature degree. Our results add significantly to a growing body of evidence indicating that the mitochondrial membrane environment plays a complex and active role in the mode of action of BCL2 family proteins. PMID:25987560

In Cell Footprinting Coupled with Mass Spectrometry for the Structural Analysis of Proteins in Live Cells.

PubMed

Espino, Jessica A; Mali, Vishaal S; Jones, Lisa M

2015-08-04

Protein footprinting coupled with mass spectrometry has become a widely used tool for the study of protein-protein and protein-ligand interactions and protein conformational change. These methods provide residue-level analysis on protein interaction sites and have been successful in studying proteins in vitro. The extension of these methods for in cell footprinting would open an avenue to study proteins that are not amenable for in vitro studies and would probe proteins in their native environment. Here we describe the application of an oxidative-based footprinting approach inside cells in which hydroxyl radicals are used to oxidatively modify proteins. Mass spectrometry is used to detect modification sites and to calculate modification levels. The method is probing biologically relevant proteins in live cells, and proteins in various cellular compartments can be oxdiatively modified. Several different amino acid residues are modified making the method a general labeling strategy for the study of a variety of proteins. Further, comparison of the extent of oxidative modification with solvent accessible surface area reveals the method successfully probes solvent accessibility. This marks the first time protein footprinting has been performed in live cells.

High-level expression and purification of heparin-binding epidermal growth factor (HB-EGF) with SUMO fusion.

PubMed

Lu, Wuguang; Cao, Peng; Lei, Huangzong; Zhang, Shuangquan

2010-03-01

Heparin-binding epidermal growth factor (HB-EGF) can stimulate the division of various cell types and has potential clinical applications that stimulate growth and differentiation. HB-EGF has an EGF-like domain typical of all members of the EGF family. The high expression of active HB-EGF in Escherichia coli has not been successful as the protein contains three intra-molecular disulfide bonds, the same as other members of the EGF super family that are difficult to form correctly in the bacterial intracellular environment. This work fused the non-glycosylated HB-EGF gene with a small ubiquitin-related modifier gene (SUMO) by over-lap PCR. The resulting fusion gene SUMO-HBEGF was highly expressed in BL21(DE3) that the soluble SUMO-HBEGF was up to 30% of the total cellular protein. The fusion protein was purified by Ni-NTA affinity chromatography and cleaved by a SUMO-specific protease Ulp1 to obtain the native HB-EGF, which was further purified by Ni-NTA affinity chromatography. MTT assays indicated the purified HB-EGF, as well as SUMO-HBEGF, had mitogenic activity in a dose-dependent manner.

Native species behaviour mitigates the impact of habitat-forming invasive seaweed.

PubMed

Wright, Jeffrey T; Byers, James E; Koukoumaftsis, Loni P; Ralph, Peter J; Gribben, Paul E

2010-06-01

Habitat-forming invasive species cause large, novel changes to the abiotic environment. These changes may elicit important behavioural responses in native fauna, yet little is known about mechanisms driving this behaviour and how such trait-mediated responses influence the fitness of native species. Low dissolved oxygen is a key abiotic change created by the habitat-forming invasive seaweed, Caulerpa taxifolia, which influences an important behavioural response (burrowing depth) in the native infaunal bivalve Anadara trapezia. In Caulerpa-colonised areas, Anadara often emerged completely from the sediment, and we experimentally demonstrate that water column hypoxia beneath the Caulerpa canopy is the mechanism instigating this "pop-up" behaviour. Importantly, pop-up in Caulerpa allowed similar survivorship to that in unvegetated sediment; however, when we prevented Anadara from popping-up, they suffered >50% mortality in just 1 month. Our findings not only highlight the substantial environmental alteration by Caulerpa, but also an important role for the behaviour of native species in mitigating the effects of habitat-forming invasive species.

Assessment of awareness of connectedness as a culturally-based protective factor for Alaska native youth.

PubMed

Mohatt, Nathaniel V; Fok, Carlotta Ching Ting; Burket, Rebekah; Henry, David; Allen, James

2011-10-01

Research with Native Americans has identified connectedness as a culturally based protective factor against substance abuse and suicide. Connectedness refers to the interrelated welfare of the individual, one's family, one's community, and the natural environment. We developed an 18-item quantitative assessment of awareness of connectedness and tested it with 284 Alaska Native youth. Evaluation with confirmatory factor analysis and item response theory identified a 12-item subset that functions satisfactorily in a second-order four-factor model. The proposed Awareness of Connectedness Scale (ACS) displays good convergent and discriminant validity, and correlates positively with hypothesized protective factors such as reasons for living and communal mastery. The measure has utility in the study of culture-specific protective factors and as an outcomes measure for behavioral health programs with Native American youth.

Stepwise evolution of protein native structure with electrospray into the gas phase, 10−12 to 102 s

PubMed Central

Breuker, Kathrin; McLafferty, Fred W.

2008-01-01

Mass spectrometry (MS) has been revolutionized by electrospray ionization (ESI), which is sufficiently “gentle” to introduce nonvolatile biomolecules such as proteins and nucleic acids (RNA or DNA) into the gas phase without breaking covalent bonds. Although in some cases noncovalent bonding can be maintained sufficiently for ESI/MS characterization of the solution structure of large protein complexes and native enzyme/substrate binding, the new gaseous environment can ultimately cause dramatic structural alterations. The temporal (picoseconds to minutes) evolution of native protein structure during and after transfer into the gas phase, as proposed here based on a variety of studies, can involve side-chain collapse, unfolding, and refolding into new, non-native structures. Control of individual experimental factors allows optimization for specific research objectives. PMID:19033474

Assessment of Awareness of Connectedness as a Culturally-based Protective Factor for Alaska Native Youth

PubMed Central

Mohatt, Nathaniel V.; Fok, Carlotta Ching Ting; Burket, Rebekah; Henry, David; Allen, James

2011-01-01

Research with Native Americans has identified connectedness as a culturally-based protective factor against substance abuse and suicide. Connectedness refers to the interrelated welfare of the individual, one’s family, one’s community, and the natural environment. We developed an 18-item quantitative assessment of awareness of connectedness and tested it with 284 Alaska Native youth. Evaluation with confirmatory factor analysis and item response theory identified a 12-item subset that functions satisfactorily in a second-order, four-factor model. The proposed Awareness of Connectedness Scale displays good convergent and discriminant validity and correlates positively with hypothesized protective factors such as reasons for living and communal mastery. The measure has utility in the study of culture-specific protective factors and as an outcomes measure for behavioral health programs with Native American youth. PMID:21988583

Development of viral nanoparticles for efficient intracellular delivery

NASA Astrophysics Data System (ADS)

Wu, Zhuojun; Chen, Kevin; Yildiz, Ibrahim; Dirksen, Anouk; Fischer, Rainer; Dawson, Philip E.; Steinmetz, Nicole F.

2012-05-01

Viral nanoparticles (VNPs) based on plant viruses such as Cowpea mosaic virus (CPMV) can be used for a broad range of biomedical applications because they present a robust scaffold that allows functionalization by chemical conjugation and genetic modification, thereby offering an efficient drug delivery platform that can target specific cells and tissues. VNPs such as CPMV show natural affinity to cells; however, cellular uptake is inefficient. Here we show that chemical modification of the CPMV surface with a highly reactive, specific and UV-traceable hydrazone linker allows bioconjugation of polyarginine (R5) cell penetrating peptides (CPPs), which can overcome these limitations. The resulting CPMV-R5 particles were taken up into a human cervical cancer cell line (HeLa) more efficiently than native particles. Uptake efficiency was dependent on the density of R5 peptides on the surface of the VNP; particles displaying 40 R5 peptides per CPMV (denoted as CPMV-R5H) interact strongly with the plasma membrane and are taken up into the cells via an energy-dependent mechanism whereas particles displaying 10 R5 peptides per CPMV (CPMV-R5L) are only slowly taken up. The fate of CPMV-R5 versus native CPMV particles within cells was evaluated in a co-localization time course study. It was indicated that the intracellular localization of CPMV-R5 and CPMV differs; CPMV remains trapped in Lamp-1 positive endolysosomes over long time frames; in contrast, 30-50% of the CPMV-R5 particles transitioned from the endosome into other cellular vesicles or compartments. Our data provide the groundwork for the development of efficient drug delivery formulations based on CPMV-R5.Viral nanoparticles (VNPs) based on plant viruses such as Cowpea mosaic virus (CPMV) can be used for a broad range of biomedical applications because they present a robust scaffold that allows functionalization by chemical conjugation and genetic modification, thereby offering an efficient drug delivery platform that can target specific cells and tissues. VNPs such as CPMV show natural affinity to cells; however, cellular uptake is inefficient. Here we show that chemical modification of the CPMV surface with a highly reactive, specific and UV-traceable hydrazone linker allows bioconjugation of polyarginine (R5) cell penetrating peptides (CPPs), which can overcome these limitations. The resulting CPMV-R5 particles were taken up into a human cervical cancer cell line (HeLa) more efficiently than native particles. Uptake efficiency was dependent on the density of R5 peptides on the surface of the VNP; particles displaying 40 R5 peptides per CPMV (denoted as CPMV-R5H) interact strongly with the plasma membrane and are taken up into the cells via an energy-dependent mechanism whereas particles displaying 10 R5 peptides per CPMV (CPMV-R5L) are only slowly taken up. The fate of CPMV-R5 versus native CPMV particles within cells was evaluated in a co-localization time course study. It was indicated that the intracellular localization of CPMV-R5 and CPMV differs; CPMV remains trapped in Lamp-1 positive endolysosomes over long time frames; in contrast, 30-50% of the CPMV-R5 particles transitioned from the endosome into other cellular vesicles or compartments. Our data provide the groundwork for the development of efficient drug delivery formulations based on CPMV-R5. Electronic supplementary information (ESI) available: Experimental details and additional supporting data. See DOI: 10.1039/c2nr30366c

Path loss analysis in millimeter wave cellular systems for urban mobile communications

NASA Astrophysics Data System (ADS)

Rajagopalan, Ramesh; Hoffman, Mitchell

2016-09-01

The proliferation in the number of mobile devices and developments in cellular technology has led to an ever increasing demand for mobile data. The global bandwidth shortage facing wireless carriers today has motivated research for fifth generation (5G) cellular systems. In recent years, millimeter wave (mmW) frequencies between 30 and 300 GHz are being considered as a promising technology for 5G systems. Such systems can offer superior user experience by providing data rates that exceed one Gigabit per second and latencies lower than a millisecond. However, there is little research about cellular mmW propagation in densely populated urban environments. Understanding the radio channel is a primary requirement for optimal design of mmW systems. Radio propagation in mmW systems faces significant challenges due to rapidly varying channel conditions and intermittent connectivity. In this paper, we study the propagation of mmW spectrum in an urban environment. We use a statistical model to simulate an urban environment with diverse building distributions. We perform extensive simulations to analyze the path loss behavior for both line of sight (LOS) and non line of sight (NLOS) conditions for 28 GHZ and 73 GHZ mmW frequencies. We observe that the path loss approximates a logarithmic fit for both LOS and NLOS environments. Our simulations show that the omnidirectional free space path loss is approximately 30 dB higher for mmW systems compared to current 3G PP cellular systems. To address this challenge, we propose using highly directional horn antennas with beam forming for reducing the path loss.

40 CFR 158.80 - Use of other data.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Use of other data. 158.80 Section 158.80 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA... or a test material, such as a native soil, plant, or animal, that is not characteristic of the United...

24 CFR 1000.2 - What are the guiding principles in the implementation of NAHASDA?

Code of Federal Regulations, 2010 CFR

2010-04-01

... for their own economic condition. (5) Providing affordable homes in safe and healthy environments is... safe and healthy environments on Indian reservations, in Indian communities, and in Native Alaskan... Nation: (i) By using Federal resources to aid families and individuals seeking affordable homes in safe...

The emergence of extracellular matrix mechanics and cell traction forces as important regulators of cellular self-organization.

PubMed

Checa, Sara; Rausch, Manuel K; Petersen, Ansgar; Kuhl, Ellen; Duda, Georg N

2015-01-01

Physical cues play a fundamental role in a wide range of biological processes, such as embryogenesis, wound healing, tumour invasion and connective tissue morphogenesis. Although it is well known that during these processes, cells continuously interact with the local extracellular matrix (ECM) through cell traction forces, the role of these mechanical interactions on large scale cellular and matrix organization remains largely unknown. In this study, we use a simple theoretical model to investigate cellular and matrix organization as a result of mechanical feedback signals between cells and the surrounding ECM. The model includes bi-directional coupling through cellular traction forces to deform the ECM and through matrix deformation to trigger cellular migration. In addition, we incorporate the mechanical contribution of matrix fibres and their reorganization by the cells. We show that a group of contractile cells will self-polarize at a large scale, even in homogeneous environments. In addition, our simulations mimic the experimentally observed alignment of cells in the direction of maximum stiffness and the building up of tension as a consequence of cell and fibre reorganization. Moreover, we demonstrate that cellular organization is tightly linked to the mechanical feedback loop between cells and matrix. Cells with a preference for stiff environments have a tendency to form chains, while cells with a tendency for soft environments tend to form clusters. The model presented here illustrates the potential of simple physical cues and their impact on cellular self-organization. It can be used in applications where cell-matrix interactions play a key role, such as in the design of tissue engineering scaffolds and to gain a basic understanding of pattern formation in organogenesis or tissue regeneration.

24 CFR 1003.2 - Program objective.

Code of Federal Regulations, 2010 CFR

2010-04-01

... native communities, including decent housing, a suitable living environment, and economic opportunities... activities below the level of such support before the availability of this assistance. ...

24 CFR 1003.2 - Program objective.

Code of Federal Regulations, 2011 CFR

2011-04-01

... native communities, including decent housing, a suitable living environment, and economic opportunities... activities below the level of such support before the availability of this assistance. ...

Predicting patterns of non-native plant invasions in Yosemite National Park, California, USA

USGS Publications Warehouse

Underwood, E.C.; Klinger, R.; Moore, P.E.

2004-01-01

One of the major issues confronting management of parks and reserves is the invasion of non-native plant species. Yosemite National Park is one of the largest and best-known parks in the United States, harbouring significant cultural and ecological resources. Effective management of non-natives would be greatly assisted by information on their potential distribution that can be generated by predictive modelling techniques. Our goal was to identify key environmental factors that were correlated with the percent cover of non-native species and then develop a predictive model using the Genetic Algorithm for Rule-set Production technique. We performed a series of analyses using community-level data on species composition in 236 plots located throughout the park. A total of 41 non-native species were recorded which occurred in 23.7% of the plots. Plots with non-natives occurred most frequently at low- to mid-elevations, in flat areas with other herbaceous species. Based on the community-level results, we selected elevation, slope, and vegetation structure as inputs into the GARP model to predict the environmental niche of non-native species. Verification of results was performed using plot data reserved from the model, which calculated the correct prediction of non-native species occurrence as 76%. The majority of the western, lower-elevation portion of the park was predicted to have relatively low levels of non-native species occurrence, with highest concentrations predicted at the west and south entrances and in the Yosemite Valley. Distribution maps of predicted occurrences will be used by management to: efficiently target monitoring of non-native species, prioritize control efforts according to the likelihood of non-native occurrences, and inform decisions relating to the management of non-native species in postfire environments. Our approach provides a valuable tool for assisting decision makers to better manage non-native species, which can be readily adapted to target non-native species in other locations.

Older Age of Onset in Child L2 Acquisition Can Be Facilitative: Evidence from the Acquisition of English Passives by Spanish Natives

ERIC Educational Resources Information Center

Rothman, Jason; Long, Drew; Iverson, Michael; Judy, Tiffany; Lingwall, Anne; Chakravarty, Tushar

2016-01-01

We report a longitudinal comprehension study of (long) passive constructions in two native-Spanish child groups differing by age of initial exposure to L2 English (young group: 3;0-4;0; older group: 6;0-7;0), where amount of input, L2 exposure environment, and socioeconomic status are controlled. Data from a forced-choice task show that both…

Tracking of Short Distance Transport Pathways in Biological Tissues by Ultra-Small Nanoparticles

NASA Astrophysics Data System (ADS)

Segmehl, Jana S.; Lauria, Alessandro; Keplinger, Tobias; Berg, John K.; Burgert, Ingo

2018-03-01

In this work, ultra-small europium-doped HfO2 nanoparticles were infiltrated into native wood and used as trackers for studying penetrability and diffusion pathways in the hierarchical wood structure. The high electron density, laser induced luminescence, and crystallinity of these particles allowed for a complementary detection of the particles in the cellular tissue. Confocal Raman microscopy and high-resolution synchrotron scanning wide-angle X-ray scattering (WAXS) measurements were used to detect the infiltrated particles in the native wood cell walls. This approach allows for simultaneously obtaining chemical information of the probed biological tissue and the spatial distribution of the integrated particles. The in-depth information about particle distribution in the complex wood structure can be used for revealing transport pathways in plant tissues, but also for gaining better understanding of modification treatments of plant scaffolds aiming at novel functionalized materials.

Injectable Hydrogel Scaffold from Decellularized Human Lipoaspirate

PubMed Central

Young, D. Adam; Ibrahim, Dina O.; Hu, Diane; Christman, Karen L.

2010-01-01

Soft tissue fillers are rapidly gaining popularity for aesthetic improvements or repair of adipose tissue deficits. Several injectable biopolymers have been investigated for this purpose but often face rapid resorption or limited adipogenesis, and do not mimic the native adipose extracellular matrix (ECM). We have generated an injectable adipose matrix scaffold by efficiently removing both the cellular and lipid contents of human lipoaspirate. The decellularized material retained a complex composition of peptides and glycosaminoglycans found in native adipose ECM. This matrix can be further processed by solubilizing the extracted ECM to generate a thermally-responsive hydrogel that self-assembles upon subcutaneous injection. This hydrogel also supports the growth and survival of patient matched adipose - derived stem cells in vitro. The development of an injectable hydrogel from human lipoaspirate represents a minimally-invasive option for adipose tissue engineering in terms of both the collection of source material and delivery of the scaffold. PMID:20932943

Repositioning tolcapone as a potent inhibitor of transthyretin amyloidogenesis and associated cellular toxicity

PubMed Central

Sant'Anna, Ricardo; Gallego, Pablo; Robinson, Lei Z.; Pereira-Henriques, Alda; Ferreira, Nelson; Pinheiro, Francisca; Esperante, Sebastian; Pallares, Irantzu; Huertas, Oscar; Rosário Almeida, Maria; Reixach, Natàlia; Insa, Raul; Velazquez-Campoy, Adrian; Reverter, David; Reig, Núria; Ventura, Salvador

2016-01-01

Transthyretin (TTR) is a plasma homotetrameric protein implicated in fatal systemic amyloidoses. TTR tetramer dissociation precedes pathological TTR aggregation. Native state stabilizers are promising drugs to treat TTR amyloidoses. Here we repurpose tolcapone, an FDA-approved molecule for Parkinson's disease, as a potent TTR aggregation inhibitor. Tolcapone binds specifically to TTR in human plasma, stabilizes the native tetramer in vivo in mice and humans and inhibits TTR cytotoxicity. Crystal structures of tolcapone bound to wild-type TTR and to the V122I cardiomyopathy-associated variant show that it docks better into the TTR T4 pocket than tafamidis, so far the only drug on the market to treat TTR amyloidoses. These data indicate that tolcapone, already in clinical trials for familial amyloid polyneuropathy, is a strong candidate for therapeutic intervention in these diseases, including those affecting the central nervous system, for which no small-molecule therapy exists. PMID:26902880

Extracellular Matrix Scaffold Technology for Bioartificial Pancreas Engineering

PubMed Central

Salvatori, Marcus; Katari, Ravi; Patel, Timil; Peloso, Andrea; Mugweru, Jon; Owusu, Kofi

2014-01-01

Emergent technologies in regenerative medicine may soon overcome the limitations of conventional diabetes therapies. Collaborative efforts across the subfields of stem cell technology, islet encapsulation, and biomaterial carriers seek to produce a bioengineered pancreas capable of restoring endocrine function in patients with insulin-dependent diabetes. These technologies rely on a robust understanding of the extracellular matrix (ECM), the supportive 3-dimensional network of proteins necessary for cellular attachment, proliferation, and differentiation. Although these functions can be partially approximated by biosynthetic carriers, novel decellularization protocols have allowed researchers to discover the advantages afforded by the native pancreatic ECM. The native ECM has proven to be an optimal platform for recellularization and whole-organ pancreas bioengineering, an exciting new field with the potential to resolve the dire shortage of transplantable organs. This review seeks to contextualize recent findings, discuss current research goals, and identify future challenges of regenerative medicine as it applies to diabetes management. PMID:24876552

A molecular mechanism of chaperone-client recognition

PubMed Central

He, Lichun; Sharpe, Timothy; Mazur, Adam; Hiller, Sebastian

2016-01-01

Molecular chaperones are essential in aiding client proteins to fold into their native structure and in maintaining cellular protein homeostasis. However, mechanistic aspects of chaperone function are still not well understood at the atomic level. We use nuclear magnetic resonance spectroscopy to elucidate the mechanism underlying client recognition by the adenosine triphosphate-independent chaperone Spy at the atomic level and derive a structural model for the chaperone-client complex. Spy interacts with its partially folded client Im7 by selective recognition of flexible, locally frustrated regions in a dynamic fashion. The interaction with Spy destabilizes a partially folded client but spatially compacts an unfolded client conformational ensemble. By increasing client backbone dynamics, the chaperone facilitates the search for the native structure. A comparison of the interaction of Im7 with two other chaperones suggests that the underlying principle of recognizing frustrated segments is of a fundamental nature. PMID:28138538

How to Make a Heart Valve: From Embryonic Development to Bioengineering of Living Valve Substitutes

PubMed Central

MacGrogan, Donal; Luxán, Guillermo; Driessen-Mol, Anita; Bouten, Carlijn; Baaijens, Frank; de la Pompa, José Luis

2014-01-01

Cardiac valve disease is a significant cause of ill health and death worldwide, and valve replacement remains one of the most common cardiac interventions in high-income economies. Despite major advances in surgical treatment, long-term therapy remains inadequate because none of the current valve substitutes have the potential for remodeling, regeneration, and growth of native structures. Valve development is coordinated by a complex interplay of signaling pathways and environmental cues that cause disease when perturbed. Cardiac valves develop from endocardial cushions that become populated by valve precursor mesenchyme formed by an epithelial–mesenchymal transition (EMT). The mesenchymal precursors, subsequently, undergo directed growth, characterized by cellular compartmentalization and layering of a structured extracellular matrix (ECM). Knowledge gained from research into the development of cardiac valves is driving exploration into valve biomechanics and tissue engineering directed at creating novel valve substitutes endowed with native form and function. PMID:25368013

Enhanced nutrient transport improves the depth-dependent properties of tri-layered engineered cartilage constructs with zonal co-culture of chondrocytes and MSCs.

PubMed

Kim, Minwook; Farrell, Megan J; Steinberg, David R; Burdick, Jason A; Mauck, Robert L

2017-08-01

Biomimetic design in cartilage tissue engineering is a challenge given the complexity of the native tissue. While numerous studies have generated constructs with near-native bulk properties, recapitulating the depth-dependent features of native tissue remains a challenge. Furthermore, limitations in nutrient transport and matrix accumulation in engineered constructs hinders maturation within the central core of large constructs. To overcome these limitations, we fabricated tri-layered constructs that recapitulate the depth-dependent cellular organization and functional properties of native tissue using zonally derived chondrocytes co-cultured with MSCs. We also introduced porous hollow fibers (HFs) and HFs/cotton threads to enhance nutrient transport. Our results showed that tri-layered constructs with depth-dependent organization and properties could be fabricated. The addition of HFs or HFs/threads improved matrix accumulation in the central core region. With HF/threads, the local modulus in the deep region of tri-layered constructs nearly matched that of native tissue, though the properties in the central regions remained lower. These constructs reproduced the zonal organization and depth-dependent properties of native tissue, and demonstrate that a layer-by-layer fabrication scheme holds promise for the biomimetic repair of focal cartilage defects. Articular cartilage is a highly organized tissue driven by zonal heterogeneity of cells, extracellular matrix proteins and fibril orientations, resulting in depth-dependent mechanical properties. Therefore, the recapitulation of the functional properties of native cartilage in a tissue engineered construct requires such a biomimetic design of the morphological organization, and this has remained a challenge in cartilage tissue engineering. This study demonstrates that a layer-by-layer fabrication scheme, including co-cultures of zone-specific articular CHs and MSCs, can reproduce the depth-dependent characteristics and mechanical properties of native cartilage while minimizing the need for large numbers of chondrocytes. In addition, introduction of a porous hollow fiber (combined with a cotton thread) enhanced nutrient transport and depth-dependent properties of the tri-layered construct. Such a tri-layered construct may provide critical advantages for focal cartilage repair. These constructs hold promise for restoring native tissue structure and function, and may be beneficial in terms of zone-to-zone integration with adjacent host tissue and providing more appropriate strain transfer after implantation. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Co-introduction vs ecological fitting as pathways to the establishment of effective mutualisms during biological invasions.

PubMed

Le Roux, Johannes J; Hui, Cang; Keet, Jan-Hendrik; Ellis, Allan G

2017-09-01

Contents 1354 I. 1354 II. 1355 III. 1357 IV. 1357 V. 1359 1359 References 1359 SUMMARY: Interactions between non-native plants and their mutualists are often disrupted upon introduction to new environments. Using legume-rhizobium mutualistic interactions as an example, we discuss two pathways that can influence symbiotic associations in such situations: co-introduction of coevolved rhizobia; and utilization of, and adaptation to, resident rhizobia, hereafter referred to as 'ecological fitting'. Co-introduction and ecological fitting have distinct implications for successful legume invasions and their impacts. Under ecological fitting, initial impacts may be less severe and will accrue over longer periods as novel symbiotic associations and/or adaptations may require fine-tuning over time. Co-introduction will have more profound impacts that will accrue more rapidly as a result of positive feedbacks between densities of non-native rhizobia and their coevolved host plants, in turn enhancing competition between native and non-native rhizobia. Co-introduction can further impact invasion outcomes by the exchange of genetic material between native and non-native rhizobia, potentially resulting in decreased fitness of native legumes. A better understanding of the roles of these two pathways in the invasion dynamics of non-native legumes is much needed, and we highlight some of the exciting research avenues it presents. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

L'environnement institutionnel: occupations pour un bon usage des institutions (Institutional Environment: Activities to Make the Best Use of Institutions).

ERIC Educational Resources Information Center

Richterich, Rene

1982-01-01

Fifteen exploratory tasks are proposed to help the reader "invent" his or her solidarity with the environment. They are intended to make the person more aware of the influences of the environment on one's native and/or second language learning in order to take charge of them and increase one's independence. (AMH)

Spatial patterns and natural recruitment of native shrubs in a semi-arid sandy land.

PubMed

Wu, Bo; Yang, Hongxiao

2013-01-01

Passive restoration depending on native shrubs is an attractive approach for restoring desertified landscapes in semi-arid sandy regions. We sought to understand the relationships between spatial patterns of native shrubs and their survival ability in sandy environments. Furthermore, we applied our results to better understand whether passive restoration is feasible for desertified landscapes in semi-arid sandy regions. The study was conducted in the semi-arid Mu Us sandy land of northern China with the native shrub Artemisia ordosica. We analyzed population structures and patterns of A. ordosica at the edges and centers of land patches where sand was stabilized by A. ordosica-dominated vegetation. Saplings were more aggregated than adults, and both were more aggregated at the patch edges than at the patch centers. At the patch edges, spatial association of the saplings with the adults was mostly positive at distances 0.3-6.6 m, and turned from positive to neutral, and even negative, at other distances. At the patch centers, the saplings were spaced almost randomly around the adults, and their distances from the adults did not seem to affect their locations. A greater number of A. ordosica individuals emerged at the patch edges than at the patch centers. Such patterns may have resulted from their integrative adjustment to specific conditions of soil water supply and sand drift intensity. These findings suggest that in semi-arid sandy regions, native shrubs that are well-adapted to local environments may serve as low-cost and competent ecological engineers that can promote the passive restoration of surrounding patches of mobile sandy land.

Evolutionary Divergences in Root Exudate Composition among Ecologically-Contrasting Helianthus Species

PubMed Central

Bowsher, Alan W.; Ali, Rifhat; Harding, Scott A.; Tsai, Chung-Jui; Donovan, Lisa A.

2016-01-01

Plant roots exude numerous metabolites into the soil that influence nutrient availability. Although root exudate composition is hypothesized to be under selection in low fertility soils, few studies have tested this hypothesis in a phylogenetic framework. In this study, we examined root exudates of three pairs of Helianthus species chosen as phylogenetically-independent contrasts with respect to native soil nutrient availability. Under controlled environmental conditions, seedlings were grown to the three-leaf-pair stage, then transferred to either high or low nutrient treatments. After five days of nutrient treatments, we used gas chromatography-mass spectrometry for analysis of root exudates, and detected 37 metabolites across species. When compared in the high nutrient treatment, species native to low nutrient soils exhibited overall higher exudation than their sister species native to high nutrient soils in all three species pairs, providing support for repeated evolutionary shifts in response to native soil fertility. Species native to low nutrient soils and those native to high nutrient soils responded similarly to low nutrient treatments with increased exudation of organic acids (fumaric, citric, malic acids) and glucose, potentially as a mechanism to enhance nutrition acquisition. However, species native to low nutrient soils also responded to low nutrient treatments with a larger decrease in exudation of amino acids than species native to high nutrient soils in all three species pairs. This indicates that species native to low nutrient soils have evolved a unique sensitivity to changes in nutrient availability for some, but not all, root exudates. Overall, these repeated evolutionary divergences between species native to low nutrient soils and those native to high nutrient soils provide evidence for the adaptive value of root exudation, and its plasticity, in contrasting soil environments. PMID:26824236

Extended leaf phenology and the autumn niche in deciduous forest invasions.

PubMed

Fridley, Jason D

2012-05-17

The phenology of growth in temperate deciduous forests, including the timing of leaf emergence and senescence, has strong control over ecosystem properties such as productivity and nutrient cycling, and has an important role in the carbon economy of understory plants. Extended leaf phenology, whereby understory species assimilate carbon in early spring before canopy closure or in late autumn after canopy fall, has been identified as a key feature of many forest species invasions, but it remains unclear whether there are systematic differences in the growth phenology of native and invasive forest species or whether invaders are more responsive to warming trends that have lengthened the duration of spring or autumn growth. Here, in a 3-year monitoring study of 43 native and 30 non-native shrub and liana species common to deciduous forests in the eastern United States, I show that extended autumn leaf phenology is a common attribute of eastern US forest invasions, where non-native species are extending the autumn growing season by an average of 4 weeks compared with natives. In contrast, there was no consistent evidence that non-natives as a group show earlier spring growth phenology, and non-natives were not better able to track interannual variation in spring temperatures. Seasonal leaf production and photosynthetic data suggest that most non-native species capture a significant proportion of their annual carbon assimilate after canopy leaf fall, a behaviour that was virtually absent in natives and consistent across five phylogenetic groups. Pronounced differences in how native and non-native understory species use pre- and post-canopy environments suggest eastern US invaders are driving a seasonal redistribution of forest productivity that may rival climate change in its impact on forest processes.

Evaluating nurse plants for restoring native woody species to degraded subtropical woodlands.

PubMed

Yelenik, Stephanie G; DiManno, Nicole; D'Antonio, Carla M

2015-01-01

Harsh habitats dominated by invasive species are difficult to restore. Invasive grasses in arid environments slow succession toward more desired composition, yet grass removal exacerbates high light and temperature, making the use of "nurse plants" an appealing strategy. In this study of degraded subtropical woodlands dominated by alien grasses in Hawai'i, we evaluated whether individuals of two native (Dodonaea viscosa, Leptocophylla tameiameia) and one non-native (Morella faya) woody species (1) act as natural nodes of recruitment for native woody species and (2) can be used to enhance survivorship of outplanted native woody species. To address these questions, we quantified the presence and persistence of seedlings naturally recruiting beneath adult nurse shrubs and compared survival and growth of experimentally outplanted seedlings of seven native woody species under the nurse species compared to intact and cleared alien-grass plots. We found that the two native nurse shrubs recruit their own offspring, but do not act as establishment nodes for other species. Morella faya recruited even fewer seedlings than native shrubs. Thus, outplanting will be necessary to increase abundance and diversity of native woody species. Outplant survival was the highest under shrubs compared to away from them with few differences between nurse species. The worst habitat for native seedling survival and growth was within the unmanaged invasive grass matrix. Although the two native nurse species did not differentially affect outplant survival, D. viscosa is the most widespread and easily propagated and is thus more likely to be useful as an initial nurse species. The outplanted species showed variable responses to nurse habitats that we attribute to resource requirements resulting from their typical successional stage and nitrogen fixation capability.

Presence and abundance of non-native plant species associated with recent energy development in the Williston Basin

USGS Publications Warehouse

Preston, Todd M.

2015-01-01

The Williston Basin, located in the Northern Great Plains, is experiencing rapid energy development with North Dakota and Montana being the epicenter of current and projected development in the USA. The average single-bore well pad is 5 acres with an estimated 58,485 wells in North Dakota alone. This landscape-level disturbance may provide a pathway for the establishment of non-native plants. To evaluate potential influences of energy development on the presence and abundance of non-native species, vegetation surveys were conducted at 30 oil well sites (14 ten-year-old and 16 five-year-old wells) and 14 control sites in native prairie environments across the Williston Basin. Non-native species richness and cover were recorded in four quadrats, located at equal distances, along four transects for a total of 16 quadrats per site. Non-natives were recorded at all 44 sites and ranged from 5 to 13 species, 7 to 15 species, and 2 to 8 species at the 10-year, 5-year, and control sites, respectively. Respective non-native cover ranged from 1 to 69, 16 to 76, and 2 to 82 %. Total, forb, and graminoid non-native species richness and non-native forb cover were significantly greater at oil well sites compared to control sites. At oil well sites, non-native species richness and forb cover were significantly greater adjacent to the well pads and decreased with distance to values similar to control sites. Finally, non-native species whose presence and/or abundance were significantly greater at oil well sites relative to control sites were identified to aid management efforts.

Evaluating nurse plants for restoring native woody species to degraded subtropical woodlands

USGS Publications Warehouse

Yelenik, Stephanie G.; DiManno, Nicole; D’Antonio, Carla M.

2015-01-01

Harsh habitats dominated by invasive species are difficult to restore. Invasive grasses in arid environments slow succession toward more desired composition, yet grass removal exacerbates high light and temperature, making the use of “nurse plants” an appealing strategy. In this study of degraded subtropical woodlands dominated by alien grasses in Hawai'i, we evaluated whether individuals of two native (Dodonaea viscosa, Leptocophylla tameiameia) and one non-native (Morella faya) woody species (1) act as natural nodes of recruitment for native woody species and (2) can be used to enhance survivorship of outplanted native woody species. To address these questions, we quantified the presence and persistence of seedlings naturally recruiting beneath adult nurse shrubs and compared survival and growth of experimentally outplanted seedlings of seven native woody species under the nurse species compared to intact and cleared alien-grass plots. We found that the two native nurse shrubs recruit their own offspring, but do not act as establishment nodes for other species. Morella faya recruited even fewer seedlings than native shrubs. Thus, outplanting will be necessary to increase abundance and diversity of native woody species. Outplant survival was the highest under shrubs compared to away from them with few differences between nurse species. The worst habitat for native seedling survival and growth was within the unmanaged invasive grass matrix. Although the two native nurse species did not differentially affect outplant survival, D. viscosa is the most widespread and easily propagated and is thus more likely to be useful as an initial nurse species. The outplanted species showed variable responses to nurse habitats that we attribute to resource requirements resulting from their typical successional stage and nitrogen fixation capability.

Evolutionary Divergences in Root Exudate Composition among Ecologically-Contrasting Helianthus Species.

PubMed

Bowsher, Alan W; Ali, Rifhat; Harding, Scott A; Tsai, Chung-Jui; Donovan, Lisa A

2016-01-01

Plant roots exude numerous metabolites into the soil that influence nutrient availability. Although root exudate composition is hypothesized to be under selection in low fertility soils, few studies have tested this hypothesis in a phylogenetic framework. In this study, we examined root exudates of three pairs of Helianthus species chosen as phylogenetically-independent contrasts with respect to native soil nutrient availability. Under controlled environmental conditions, seedlings were grown to the three-leaf-pair stage, then transferred to either high or low nutrient treatments. After five days of nutrient treatments, we used gas chromatography-mass spectrometry for analysis of root exudates, and detected 37 metabolites across species. When compared in the high nutrient treatment, species native to low nutrient soils exhibited overall higher exudation than their sister species native to high nutrient soils in all three species pairs, providing support for repeated evolutionary shifts in response to native soil fertility. Species native to low nutrient soils and those native to high nutrient soils responded similarly to low nutrient treatments with increased exudation of organic acids (fumaric, citric, malic acids) and glucose, potentially as a mechanism to enhance nutrition acquisition. However, species native to low nutrient soils also responded to low nutrient treatments with a larger decrease in exudation of amino acids than species native to high nutrient soils in all three species pairs. This indicates that species native to low nutrient soils have evolved a unique sensitivity to changes in nutrient availability for some, but not all, root exudates. Overall, these repeated evolutionary divergences between species native to low nutrient soils and those native to high nutrient soils provide evidence for the adaptive value of root exudation, and its plasticity, in contrasting soil environments.

Microbial ecology of extreme environments: Antarctic yeasts and growth in substrate-limited habitats

NASA Technical Reports Server (NTRS)

Vishniac, H. S.

1984-01-01

An extreme environment is by definition one with a depauperate biota. While the Ross Desert is by no means homogeneous, the most exposed and arid habitats, soils in the unglaciated high valleys, do indeed contain a very sparse biota of low diversity. So sparse that the natives could easily be outnumbered by airborne exogenous microbes. Native biota must be capable of overwintering as well as growing in the high valley summer. Tourists may undergo a few divisions before contributing their enzymes and, ultimately, elements to the soil - or may die before landing. The simplest way to demonstrate the indigenicity of a particular microbe is therefore to establish unique distribution; occurrence only in the habitat in question precludes foreign origin.

Health effects of a subway environment in healthy volunteers.

PubMed

Klepczyńska Nyström, A; Svartengren, M; Grunewald, J; Pousette, C; Rödin, I; Lundin, A; Sköld, C M; Eklund, A; Larsson, B-M

2010-08-01

Environmental particle exposure, often estimated as the particulate mass of particles with a diameter <10 microm, <2.5 microm or <1 microm (PM(10), PM(2.5) or PM(1)), is known to have a negative impact on the health of the population. Little is known about how the size and origin of particles influence the effects. We have previously shown that exposure to a road tunnel environment causes a cellular inflammatory response in the airways of healthy individuals. In the present study, our aim was to investigate potential airway health effects from exposure to a subway environment. 20 healthy volunteers were exposed to a subway and a control environment for 2 h, followed by measurements of lung function and the inflammatory response in the lower airways (bronchoscopy) and in the peripheral blood. No cellular response was found in the airways after exposure to the subway environment. In the blood, we found a statistically significant increase in fibrinogen and regulatory T-cells expressing CD4/CD25/FOXP3. Subway and road tunnel environments have similar levels of PM(10) and PM(2.5), whilst the concentrations of ultrafine particles, nitrogen monoxide and dioxide are lower in the subway. Although no cellular response was detected, the findings indicate a biological response to the subway environment. Our studies show that using gravimetric estimates of ambient particulate air pollution alone may have clear limitations in health-risk assessment.

Local adaptation to osmotic environment in killifish, Fundulus heteroclitus, is supported by divergence in swimming performance but not by differences in excess post-exercise oxygen consumption or aerobic scope.

PubMed

Brennan, Reid S; Hwang, Ruth; Tse, Michelle; Fangue, Nann A; Whitehead, Andrew

2016-06-01

Regulation of internal ion homeostasis is essential for fishes inhabiting environments where salinities differ from their internal concentrations. It is hypothesized that selection will reduce energetic costs of osmoregulation in a population's native osmotic habitat, producing patterns of local adaptation. Killifish, Fundulus heteroclitus, occupy estuarine habitats where salinities range from fresh to seawater. Populations inhabiting an environmental salinity gradient differ in physiological traits associated with acclimation to acute salinity stress, consistent with local adaptation. Similarly, metabolic rates differ in populations adapted to different temperatures, but have not been studied in regard to salinity. We investigated evidence for local adaptation between populations of killifish native to fresh and brackish water habitats. Aerobic scope (the difference between minimum and maximum metabolic rates), excess post-exercise oxygen consumption, and swimming performance (time and distance to reach exhaustion) were used as proxies for fitness in fresh and brackish water treatments. Swimming performance results supported local adaptation; fish native to brackish water habitats performed significantly better than freshwater-native fish at high salinity while low salinity performance was similar between populations. However, results from metabolic measures did not support this conclusion; both populations showed an increase in resting metabolic rate and a decrease of aerobic scope in fresh water. Similarly, excess post-exercise oxygen consumption was higher for both populations in fresh than in brackish water. While swimming results suggest that environmentally dependent performance differences may be a result of selection in divergent osmotic environments, the differences between populations are not coupled with divergence in metabolic performance. Copyright © 2016 Elsevier Inc. All rights reserved.

Ionotropic AMPA-type glutamate and metabotropic GABAB receptors: determining cellular physiology by proteomes.

PubMed

Bettler, Bernhard; Fakler, Bernd

2017-08-01

Ionotropic AMPA-type glutamate receptors and G-protein-coupled metabotropic GABA B receptors are key elements of neurotransmission whose cellular functions are determined by their protein constituents. Over the past couple of years unbiased proteomic approaches identified comprehensive sets of protein building blocks of these two types of neurotransmitter receptors in the brain (termed receptor proteomes). This provided the opportunity to match receptor proteomes with receptor physiology and to study the structural organization, regulation and function of native receptor complexes in an unprecedented manner. In this review we discuss the principles of receptor architecture and regulation emerging from the functional characterization of the proteomes of AMPA and GABA B receptors. We also highlight progress in unraveling the role of unexpected protein components for receptor physiology. Copyright © 2017 Elsevier Ltd. All rights reserved.

Engineering Cellular Metabolism.

PubMed

Nielsen, Jens; Keasling, Jay D

2016-03-10

Metabolic engineering is the science of rewiring the metabolism of cells to enhance production of native metabolites or to endow cells with the ability to produce new products. The potential applications of such efforts are wide ranging, including the generation of fuels, chemicals, foods, feeds, and pharmaceuticals. However, making cells into efficient factories is challenging because cells have evolved robust metabolic networks with hard-wired, tightly regulated lines of communication between molecular pathways that resist efforts to divert resources. Here, we will review the current status and challenges of metabolic engineering and will discuss how new technologies can enable metabolic engineering to be scaled up to the industrial level, either by cutting off the lines of control for endogenous metabolism or by infiltrating the system with disruptive, heterologous pathways that overcome cellular regulation. Copyright © 2016 Elsevier Inc. All rights reserved.

Exploring public perception of non-native species from a visions of nature perspective.

PubMed

Verbrugge, Laura N H; Van den Born, Riyan J G; Lenders, H J Rob

2013-12-01

Not much is known about lay public perceptions of non-native species and their underlying values. Public awareness and engagement, however, are important aspects in invasive species management. In this study, we examined the relations between the lay public's visions of nature, their knowledge about non-native species, and their perceptions of non-native species and invasive species management with a survey administered in the Netherlands. Within this framework, we identified three measures for perception of non-native species: perceived risk, control and engagement. In general, respondents scored moderate values for perceived risk and personal engagement. However, in case of potential ecological or human health risks, control measures were supported. Respondents' images of the human-nature relationship proved to be relevant in engagement in problems caused by invasive species and in recognizing the need for control, while images of nature appeared to be most important in perceiving risks to the environment. We also found that eradication of non-native species was predominantly opposed for species with a high cuddliness factor such as mammals and bird species. We conclude that lay public perceptions of non-native species have to be put in a wider context of visions of nature, and we discuss the implications for public support for invasive species management.

Development of aquatic life criteria for triclosan and comparison of the sensitivity between native and non-native species.

PubMed

Wang, Xiao-Nan; Liu, Zheng-Tao; Yan, Zhen-Guang; Zhang, Cong; Wang, Wei-Li; Zhou, Jun-Li; Pei, Shu-Wei

2013-09-15

Triclosan (TCS) is an antimicrobial agent which is used as a broad-spectrum bacteriostatic and found in personal care products, and due to this it is widely spread in the aquatic environment. However, there is no paper dealing with the aquatic life criteria of TCS, mainly result from the shortage of toxicity data of different taxonomic levels. In the present study, toxicity data were obtained from 9 acute toxicity tests and 3 chronic toxicity tests using 9 Chinese native aquatic species from different taxonomic levels, and the aquatic life criteria was derived using 3 methods. Furthermore, differences of species sensitivity distributions (SSD) between native and non-native species were compared. Among the tested species, demersal fish Misgurnus anguillicaudatus was the most sensitive species, and the fishes were more sensitive than the aquatic invertebrates of Annelid and insect, and the insect was the least sensitive species. The comparison showed that there was no significant difference between SSDs constructed from native and non-native taxa. Finally, a criterion maximum concentration of 0.009 mg/L and a criterion continuous concentration of 0.002 mg/L were developed based on different taxa, according to the U.S. Environmental Protection Agency guidelines. Copyright © 2013 Elsevier B.V. All rights reserved.

21 CFR 5.1100 - Headquarters.

Code of Federal Regulations, 2011 CFR

2011-04-01

... Laboratories Complex Staff. Division of Engineering Services. Environment, Safety And Strategic Initiatives.... Office of Cellular, Tissue, and Gene Therapies. Regulatory Management Staff. Division of Cellular and Gene Therapies. Division of Clinical Evaluation and Pharmacology/Toxicology. Division of Human Tissues...

Tumor Heterogenity Research Interactive Visualization Environment (THRIVE) | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

A platform for quantitative evaluation of intratumoral spatial heterogeneity in multiplexed immunofluorescence images, via characterization of the spatial interactions between different cellular phenotypes and non-cellular constituents in the tumor microenvironment.

Cellular and Pharmacological Targets to Induce Coronary Arteriogenesis

PubMed Central

Hollander, Maurits R.; Horrevoets, Anton J.G.; van Royen, Niels

2014-01-01

The formation of collateral vessels (arteriogenesis) to sustain perfusion in ischemic tissue is native to the body and can compensate for coronary stenosis. However, arteriogenesis is a complex process and is dependent on many different factors. Although animal studies on collateral formation and stimulation show promising data, clinical trials have failed to replicate these results. Further research to the exact mechanisms is needed in order to develop a pharmalogical stimulant. This review gives an overview of recent data in the field of arteriogenesis. PMID:23638831

Self-organized perturbations enhance class IV behavior and 1/f power spectrum in elementary cellular automata.

PubMed

Nakajima, Kohei; Haruna, Taichi

2011-09-01

In this paper, we propose a new class of cellular automata based on the modification of its state space. It is introduced to model a computation which is exposed to an environment. We formalized the computation as extension and projection processes of its state space and resulting misidentifications of the state. This is motivated to embed the role of an environment into the system itself, which naturally induces self-organized internal perturbations rather than the usual external perturbations. Implementing this structure into the elementary cellular automata, we characterized its effect by means of input entropy and power spectral analysis. As a result, the cellular automata with this structure showed robust class IV behavior and a 1/f power spectrum in a wide range of rule space comparative to the notion of the edge of chaos. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Expression of phosphoinositide-specific phospholipase C isoforms in native endothelial cells.

PubMed

Béziau, Delphine M; Toussaint, Fanny; Blanchette, Alexandre; Dayeh, Nour R; Charbel, Chimène; Tardif, Jean-Claude; Dupuis, Jocelyn; Ledoux, Jonathan

2015-01-01

Phospholipase C (PLC) comprises a superfamily of enzymes that play a key role in a wide array of intracellular signalling pathways, including protein kinase C and intracellular calcium. Thirteen different mammalian PLC isoforms have been identified and classified into 6 families (PLC-β, γ, δ, ε, ζ and η) based on their biochemical properties. Although the expression of PLC isoforms is tissue-specific, concomitant expression of different PLC has been reported, suggesting that PLC family is involved in multiple cellular functions. Despite their critical role, the PLC isoforms expressed in native endothelial cells (ECs) remains undetermined. A conventional PCR approach was initially used to elucidate the mRNA expression pattern of PLC isoforms in 3 distinct murine vascular beds: mesenteric (MA), pulmonary (PA) and middle cerebral arteries (MCA). mRNA encoding for most PLC isoforms was detected in MA, MCA and PA with the exception of η2 and β2 (only expressed in PA), δ4 (only expressed in MCA), η1 (expressed in all but MA) and ζ (not detected in any vascular beds tested). The endothelial-specific PLC expression was then sought in freshly isolated ECs. Interestingly, the PLC expression profile appears to differ across the investigated arterial beds. While mRNA for 8 of the 13 PLC isoforms was detected in ECs from MA, two additional PLC isoforms were detected in ECs from PA and MCA. Co-expression of multiple PLC isoforms in ECs suggests an elaborate network of signalling pathways: PLC isoforms may contribute to the complexity or diversity of signalling by their selective localization in cellular microdomains. However in situ immunofluorescence revealed a homogeneous distribution for all PLC isoforms probed (β3, γ2 and δ1) in intact endothelium. Although PLC isoforms play a crucial role in endothelial signal transduction, subcellular localization alone does not appear to be sufficient to determine the role of PLC in the signalling microdomains found in the native endothelium.

High-molecular weight Aβ oligomers and protofibrils are the predominant Aβ species in the native soluble protein fraction of the AD brain.

PubMed

Upadhaya, Ajeet Rijal; Lungrin, Irina; Yamaguchi, Haruyasu; Fändrich, Marcus; Thal, Dietmar Rudolf

2012-02-01

Alzheimer's disease (AD) is characterized by the aggregation and deposition of amyloid β protein (Aβ) in the brain. Soluble Aβ oligomers are thought to be toxic. To investigate the predominant species of Aβ protein that may play a role in AD pathogenesis, we performed biochemical analysis of AD and control brains. Sucrose buffer-soluble brain lysates were characterized in native form using blue native (BN)-PAGE and also in denatured form using SDS-PAGE followed by Western blot analysis. BN-PAGE analysis revealed a high-molecular weight smear (>1000 kD) of Aβ(42) -positive material in the AD brain, whereas low-molecular weight and monomeric Aβ species were not detected. SDS-PAGE analysis, on the other hand, allowed the detection of prominent Aβ monomer and dimer bands in AD cases but not in controls. Immunoelectron microscopy of immunoprecipitated oligomers and protofibrils/fibrils showed spherical and protofibrillar Aβ-positive material, thereby confirming the presence of high-molecular weight Aβ (hiMWAβ) aggregates in the AD brain. In vitro analysis of synthetic Aβ(40) - and Aβ(42) preparations revealed Aβ fibrils, protofibrils, and hiMWAβ oligomers that were detectable at the electron microscopic level and after BN-PAGE. Further, BN-PAGE analysis exhibited a monomer band and less prominent low-molecular weight Aβ (loMWAβ) oligomers. In contrast, SDS-PAGE showed large amounts of loMWAβ but no hiMWAβ(40) and strikingly reduced levels of hiMWAβ(42) . These results indicate that hiMWAβ aggregates, particularly Aβ(42) species, are most prevalent in the soluble fraction of the AD brain. Thus, soluble hiMWAβ aggregates may play an important role in the pathogenesis of AD either independently or as a reservoir for release of loMWAβ oligomers. © 2011 The Authors Journal of Cellular and Molecular Medicine © 2011 Foundation for Cellular and Molecular Medicine/Blackwell Publishing Ltd.

Tibetans living at sea level have a hyporesponsive hypoxia-inducible factor system and blunted physiological responses to hypoxia

PubMed Central

Petousi, Nayia; Croft, Quentin P. P.; Cavalleri, Gianpiero L.; Cheng, Hung-Yuan; Formenti, Federico; Ishida, Koji; Lunn, Daniel; McCormack, Mark; Shianna, Kevin V.; Talbot, Nick P.; Ratcliffe, Peter J.

2013-01-01

Tibetan natives have lived on the Tibetan plateau (altitude ∼4,000 m) for at least 25,000 years, and as such they are adapted to life and reproduction in a hypoxic environment. Recent studies have identified two genetic loci, EGLN1 and EPAS1, that have undergone natural selection in Tibetans, and further demonstrated an association of EGLN1/EPAS1 genotype with hemoglobin concentration. Both genes encode major components of the hypoxia-inducible factor (HIF) transcriptional pathway, which coordinates an organism's response to hypoxia. Patients living at sea level with genetic disease of the HIF pathway have characteristic phenotypes at both the integrative-physiology and cellular level. We sought to test the hypothesis that natural selection to hypoxia within Tibetans results in related phenotypic differences. We compared Tibetans living at sea level with Han Chinese, who are Tibetans' most closely related major ethnic group. We found that Tibetans had a lower hemoglobin concentration, a higher pulmonary ventilation relative to metabolism, and blunted pulmonary vascular responses to both acute (minutes) and sustained (8 h) hypoxia. At the cellular level, the relative expression and hypoxic induction of HIF-regulated genes were significantly lower in peripheral blood lymphocytes from Tibetans compared with Han Chinese. Within the Tibetans, we found a significant correlation between both EPAS1 and EGLN1 genotype and the induction of erythropoietin by hypoxia. In conclusion, this study provides further evidence that Tibetans respond less vigorously to hypoxic challenge. This is evident at sea level and, at least in part, appears to arise from a hyporesponsive HIF transcriptional system. PMID:24030663

Surface Tension Guided Hanging-Drop: Producing Controllable 3D Spheroid of High-Passaged Human Dermal Papilla Cells and Forming Inductive Microtissues for Hair-Follicle Regeneration.

PubMed

Lin, Bojie; Miao, Yong; Wang, Jin; Fan, Zhexiang; Du, Lijuan; Su, Yongsheng; Liu, Bingcheng; Hu, Zhiqi; Xing, Malcolm

2016-03-09

Human dermal papilla (DP) cells have been studied extensively when grown in the conventional monolayer. However, because of great deviation from the real in vivo three-dimensional (3D) environment, these two-dimensional (2D) grown cells tend to lose the hair-inducible capability during passaging. Hence, these 2D caused concerns have motivated the development of novel 3D culture techniques to produce cellular microtissues with suitable mimics. The hanging-drop approach is based on surface tension-based technique and the interaction between surface tension and gravity field that makes a convergence of liquid drops. This study used this technique in a converged drop to form cellular spheroids of dermal papilla cells. It leads to a controllable 3Dspheroid model for scalable fabrication of inductive DP microtissues. The optimal conditions for culturing high-passaged (P8) DP spheroids were determined first. Then, the morphological, histological and functional studies were performed. In addition, expressions of hair-inductive markers including alkaline phosphatase, α-smooth muscle actin and neural cell adhesion molecule were also analyzed by quantitative RT-PCR, immunostaining and immunoblotting. Finally, P8-DP microtissues were coimplanted with newborn mouse epidermal cells (EPCs) into nude mice. Our results indicated that the formation of 3D microtissues not only endowed P8-DP microtissues many similarities to primary DP, but also confer these microtissues an enhanced ability to induce hair-follicle (HF) neogenesis in vivo. This model provides a potential to elucidate the native biology of human DP, and also shows the promising for the controllable and scalable production of inductive DP cells applied in future follicle regeneration.

Tracking the Spatial and Functional Gradient of Monocyte-To-Macrophage Differentiation in Inflamed Lung.

PubMed

Sen, Debasish; Jones, Stephen M; Oswald, Erin M; Pinkard, Henry; Corbin, Kaitlin; Krummel, Matthew F

2016-01-01

Myeloid-derived cells such as monocytes, dendritic cells (DCs), and macrophages are at the heart of the immune effector function in an inflammatory response. But because of the lack of an efficient imaging system to trace these cells live during their migration and maturation in their native environment at sub-cellular resolution, our knowledge is limited to data available from specific time-points analyzed by flow cytometry, histology, genomics and other immunological methods. Here, we have developed a ratiometric imaging method for measuring monocyte maturation in inflamed mouse lungs in situ using real-time using 2-photon imaging and complementary methods. We visualized that while undifferentiated monocytes were predominantly found only in the vasculature, a semi-differentiated monocyte/macrophage population could enter the tissue and resembled more mature and differentiated populations by morphology and surface phenotype. As these cells entered and differentiated, they were already selectively localized near inflamed airways and their entry was associated with changes in motility and morphology. We were able to visualize these during the act of differentiation, a process that can be demonstrated in this way to be faster on a per-cell basis under inflammatory conditions. Finally, our in situ analyses demonstrated increases, in the differentiating cells, for both antigen uptake and the ability to mediate interactions with T cells. This work, while largely confirming proposed models for in situ differentiation, provides important in situ data on the coordinated site-specific recruitment and differentiation of these cells and helps elaborate the predominance of immune pathology at the airways. Our novel imaging technology to trace immunogenic cell maturation in situ will complement existing information available on in situ differentiation deduced from other immunological methods, and assist better understanding of the spatio-temporal cellular behavior during an inflammatory response.

Yeast prions are useful for studying protein chaperones and protein quality control.

PubMed

Masison, Daniel C; Reidy, Michael

2015-01-01

Protein chaperones help proteins adopt and maintain native conformations and play vital roles in cellular processes where proteins are partially folded. They comprise a major part of the cellular protein quality control system that protects the integrity of the proteome. Many disorders are caused when proteins misfold despite this protection. Yeast prions are fibrous amyloid aggregates of misfolded proteins. The normal action of chaperones on yeast prions breaks the fibers into pieces, which results in prion replication. Because this process is necessary for propagation of yeast prions, even small differences in activity of many chaperones noticeably affect prion phenotypes. Several other factors involved in protein processing also influence formation, propagation or elimination of prions in yeast. Thus, in much the same way that the dependency of viruses on cellular functions has allowed us to learn much about cell biology, the dependency of yeast prions on chaperones presents a unique and sensitive way to monitor the functions and interactions of many components of the cell's protein quality control system. Our recent work illustrates the utility of this system for identifying and defining chaperone machinery interactions.

Draft De Novo Transcriptome of the Rat Kangaroo Potorous tridactylus as a Tool for Cell Biology

PubMed Central

Udy, Dylan B.; Voorhies, Mark; Chan, Patricia P.; Lowe, Todd M.; Dumont, Sophie

2015-01-01

The rat kangaroo (long-nosed potoroo, Potorous tridactylus) is a marsupial native to Australia. Cultured rat kangaroo kidney epithelial cells (PtK) are commonly used to study cell biological processes. These mammalian cells are large, adherent, and flat, and contain large and few chromosomes—and are thus ideal for imaging intra-cellular dynamics such as those of mitosis. Despite this, neither the rat kangaroo genome nor transcriptome have been sequenced, creating a challenge for probing the molecular basis of these cellular dynamics. Here, we present the sequencing, assembly and annotation of the draft rat kangaroo de novo transcriptome. We sequenced 679 million reads that mapped to 347,323 Trinity transcripts and 20,079 Unigenes. We present statistics emerging from transcriptome-wide analyses, and analyses suggesting that the transcriptome covers full-length sequences of most genes, many with multiple isoforms. We also validate our findings with a proof-of-concept gene knockdown experiment. We expect that this high quality transcriptome will make rat kangaroo cells a more tractable system for linking molecular-scale function and cellular-scale dynamics. PMID:26252667

Draft De Novo Transcriptome of the Rat Kangaroo Potorous tridactylus as a Tool for Cell Biology.

PubMed

Udy, Dylan B; Voorhies, Mark; Chan, Patricia P; Lowe, Todd M; Dumont, Sophie

2015-01-01

The rat kangaroo (long-nosed potoroo, Potorous tridactylus) is a marsupial native to Australia. Cultured rat kangaroo kidney epithelial cells (PtK) are commonly used to study cell biological processes. These mammalian cells are large, adherent, and flat, and contain large and few chromosomes-and are thus ideal for imaging intra-cellular dynamics such as those of mitosis. Despite this, neither the rat kangaroo genome nor transcriptome have been sequenced, creating a challenge for probing the molecular basis of these cellular dynamics. Here, we present the sequencing, assembly and annotation of the draft rat kangaroo de novo transcriptome. We sequenced 679 million reads that mapped to 347,323 Trinity transcripts and 20,079 Unigenes. We present statistics emerging from transcriptome-wide analyses, and analyses suggesting that the transcriptome covers full-length sequences of most genes, many with multiple isoforms. We also validate our findings with a proof-of-concept gene knockdown experiment. We expect that this high quality transcriptome will make rat kangaroo cells a more tractable system for linking molecular-scale function and cellular-scale dynamics.

Internal Disequilibria and Phenotypic Diversification during Replication of Hepatitis C Virus in a Noncoevolving Cellular Environment

PubMed Central

Moreno, Elena; Gallego, Isabel; Gregori, Josep; Lucía-Sanz, Adriana; Soria, María Eugenia; Castro, Victoria; Beach, Nathan M.; Manrubia, Susanna; Quer, Josep; Esteban, Juan Ignacio; Rice, Charles M.; Gómez, Jordi; Gastaminza, Pablo

2017-01-01

ABSTRACT Viral quasispecies evolution upon long-term virus replication in a noncoevolving cellular environment raises relevant general issues, such as the attainment of population equilibrium, compliance with the molecular-clock hypothesis, or stability of the phenotypic profile. Here, we evaluate the adaptation, mutant spectrum dynamics, and phenotypic diversification of hepatitis C virus (HCV) in the course of 200 passages in human hepatoma cells in an experimental design that precluded coevolution of the cells with the virus. Adaptation to the cells was evidenced by increase in progeny production. The rate of accumulation of mutations in the genomic consensus sequence deviated slightly from linearity, and mutant spectrum analyses revealed a complex dynamic of mutational waves, which was sustained beyond passage 100. The virus underwent several phenotypic changes, some of which impacted the virus-host relationship, such as enhanced cell killing, a shift toward higher virion density, and increased shutoff of host cell protein synthesis. Fluctuations in progeny production and failure to reach population equilibrium at the genomic level suggest internal instabilities that anticipate an unpredictable HCV evolution in the complex liver environment. IMPORTANCE Long-term virus evolution in an unperturbed cellular environment can reveal features of virus evolution that cannot be explained by comparing natural viral isolates. In the present study, we investigate genetic and phenotypic changes that occur upon prolonged passage of hepatitis C virus (HCV) in human hepatoma cells in an experimental design in which host cell evolutionary change is prevented. Despite replication in a noncoevolving cellular environment, the virus exhibited internal population disequilibria that did not decline with increased adaptation to the host cells. The diversification of phenotypic traits suggests that disequilibria inherent to viral populations may provide a selective advantage to viruses that can be fully exploited in changing environments. PMID:28275194

Diversity in times of adversity: probabilistic strategies in microbial survival games.

PubMed

Wolf, Denise M; Vazirani, Vijay V; Arkin, Adam P

2005-05-21

Population diversification strategies are ubiquitous among microbes, encompassing random phase-variation (RPV) of pathogenic bacteria, viral latency as observed in some bacteriophage and HIV, and the non-genetic diversity of bacterial stress responses. Precise conditions under which these diversification strategies confer an advantage have not been well defined. We develop a model of population growth conditioned on dynamical environmental and cellular states. Transitions among cellular states, in turn, may be biased by possibly noisy readings of the environment from cellular sensors. For various types of environmental dynamics and cellular sensor capability, we apply game-theoretic analysis to derive the evolutionarily stable strategy (ESS) for an organism and determine when that strategy is diversification. We find that: (1) RPV, effecting a sort of Parrondo paradox wherein random alternations between losing strategies produce a winning strategy, is selected when transitions between different selective environments cannot be sensed, (2) optimal RPV cell switching rates are a function of environmental lifecycle asymmetries and environmental autocorrelation, (3) probabilistic diversification upon entering a new environment is selected when sensors can detect environmental transitions but have poor precision in identifying new environments, and (4) in the presence of excess additive noise, low-pass filtering is required for evolutionary stability. We show that even when RPV is not the ESS, it may minimize growth rate variance and the risk of extinction due to 'unlucky' environmental dynamics.

Particle Trajectories in Rotating Wall Cell Culture Devices

NASA Technical Reports Server (NTRS)

Ramachandran N.; Downey, J. P.

1999-01-01

Cell cultures are extremely important to the medical community since such cultures provide an opportunity to perform research on human tissue without the concerns inherent in experiments on individual humans. Development of cells in cultures has been found to be greatly influenced by the conditions of the culture. Much work has focused on the effect of the motions of cells in the culture relative to the solution. Recently rotating wall vessels have been used with success in achieving improved cellular cultures. Speculation and limited research have focused on the low shear environment and the ability of rotating vessels to keep cells suspended in solution rather than floating or sedimenting as the primary reasons for the improved cellular cultures using these devices. It is widely believed that the cultures obtained using a rotating wall vessel simulates to some degree the effect of microgravity on cultures. It has also been speculated that the microgravity environment may provide the ideal acceleration environment for culturing of cellular tissues due to the nearly negligible levels of sedimentation and shear possible. This work predicts particle trajectories of cells in rotating wall vessels of cylindrical and annular design consistent with the estimated properties of typical cellular cultures. Estimates of the shear encountered by cells in solution and the interactions with walls are studied. Comparisons of potential experiments in ground and microgravity environments are performed.

Combinatorial contextualization of peptidic epitopes for enhanced cellular immunity.

PubMed

Ito, Masaki; Hayashi, Kazumi; Adachi, Eru; Minamisawa, Tamiko; Homma, Sadamu; Koido, Shigeo; Shiba, Kiyotaka

2014-01-01

Invocation of cellular immunity by epitopic peptides remains largely dependent on empirically developed protocols, such as interfusion of aluminum salts or emulsification using terpenoids and surfactants. To explore novel vaccine formulation, epitopic peptide motifs were co-programmed with structural motifs to produce artificial antigens using our "motif-programming" approach. As a proof of concept, we used an ovalbumin (OVA) system and prepared an artificial protein library by combinatorially polymerizing MHC class I and II sequences from OVA along with a sequence that tends to form secondary structures. The purified endotoxin-free proteins were then examined for their ability to activate OVA-specific T-cell hybridoma cells after being processed within dendritic cells. One clone, F37A (containing three MHC I and two MHC II OVA epitopes), possessed a greater ability to evoke cellular immunity than the native OVA or the other artificial antigens. The sensitivity profiles of drugs that interfered with the F37A uptake differed from those of the other artificial proteins and OVA, suggesting that alteration of the cross-presentation pathway is responsible for the enhanced immunogenicity. Moreover, F37A, but not an epitopic peptide, invoked cellular immunity when injected together with monophosphoryl lipid A (MPL), and retarded tumor growth in mice. Thus, an artificially synthesized protein antigen induced cellular immunity in vivo in the absence of incomplete Freund's adjuvant or aluminum salts. The method described here could be potentially used for developing vaccines for such intractable ailments as AIDS, malaria and cancer, ailments in which cellular immunity likely play a crucial role in prevention and treatment.

Non-Native Plant Invasion along Elevation and Canopy Closure Gradients in a Middle Rocky Mountain Ecosystem

PubMed Central

Averett, Joshua P.; McCune, Bruce; Parks, Catherine G.; Naylor, Bridgett J.; DelCurto, Tim; Mata-González, Ricardo

2016-01-01

Mountain environments are currently among the ecosystems least invaded by non-native species; however, mountains are increasingly under threat of non-native plant invasion. The slow pace of exotic plant invasions in mountain ecosystems is likely due to a combination of low anthropogenic disturbances, low propagule supply, and extreme/steep environmental gradients. The importance of any one of these factors is debated and likely ecosystem dependent. We evaluated the importance of various correlates of plant invasions in the Wallowa Mountain Range of northeastern Oregon and explored whether non-native species distributions differed from native species along an elevation gradient. Vascular plant communities were sampled in summer 2012 along three mountain roads. Transects (n = 20) were evenly stratified by elevation (~70 m intervals) along each road. Vascular plant species abundances and environmental parameters were measured. We used indicator species analysis to identify habitat affinities for non-native species. Plots were ordinated in species space, joint plots and non-parametric multiplicative regression were used to relate species and community variation to environmental variables. Non-native species richness decreased continuously with increasing elevation. In contrast, native species richness displayed a unimodal distribution with maximum richness occurring at mid–elevations. Species composition was strongly related to elevation and canopy openness. Overlays of trait and environmental factors onto non-metric multidimensional ordinations identified the montane-subalpine community transition and over-story canopy closure exceeding 60% as potential barriers to non-native species establishment. Unlike native species, non-native species showed little evidence for high-elevation or closed-canopy specialization. These data suggest that non-native plants currently found in the Wallowa Mountains are dependent on open canopies and disturbance for establishment in low and mid elevations. Current management objectives including restoration to more open canopies in dry Rocky Mountain forests, may increase immigration pressure of non-native plants from lower elevations into the montane and subalpine zones. PMID:26824750

Non-Native Plant Invasion along Elevation and Canopy Closure Gradients in a Middle Rocky Mountain Ecosystem.

PubMed

Averett, Joshua P; McCune, Bruce; Parks, Catherine G; Naylor, Bridgett J; DelCurto, Tim; Mata-González, Ricardo

2016-01-01

Mountain environments are currently among the ecosystems least invaded by non-native species; however, mountains are increasingly under threat of non-native plant invasion. The slow pace of exotic plant invasions in mountain ecosystems is likely due to a combination of low anthropogenic disturbances, low propagule supply, and extreme/steep environmental gradients. The importance of any one of these factors is debated and likely ecosystem dependent. We evaluated the importance of various correlates of plant invasions in the Wallowa Mountain Range of northeastern Oregon and explored whether non-native species distributions differed from native species along an elevation gradient. Vascular plant communities were sampled in summer 2012 along three mountain roads. Transects (n = 20) were evenly stratified by elevation (~70 m intervals) along each road. Vascular plant species abundances and environmental parameters were measured. We used indicator species analysis to identify habitat affinities for non-native species. Plots were ordinated in species space, joint plots and non-parametric multiplicative regression were used to relate species and community variation to environmental variables. Non-native species richness decreased continuously with increasing elevation. In contrast, native species richness displayed a unimodal distribution with maximum richness occurring at mid-elevations. Species composition was strongly related to elevation and canopy openness. Overlays of trait and environmental factors onto non-metric multidimensional ordinations identified the montane-subalpine community transition and over-story canopy closure exceeding 60% as potential barriers to non-native species establishment. Unlike native species, non-native species showed little evidence for high-elevation or closed-canopy specialization. These data suggest that non-native plants currently found in the Wallowa Mountains are dependent on open canopies and disturbance for establishment in low and mid elevations. Current management objectives including restoration to more open canopies in dry Rocky Mountain forests, may increase immigration pressure of non-native plants from lower elevations into the montane and subalpine zones.

Masking Release for Igbo and English.

PubMed

Ebem, Deborah U; Desloge, Joseph G; Reed, Charlotte M; Braida, Louis D; Uguru, Joy O

2013-09-01

In this research, we explored the effect of noise interruption rate on speech intelligibility. Specifically, we used the Hearing In Noise Test (HINT) procedure with the original HINT stimuli (English) and Igbo stimuli to assess speech reception ability in interrupted noise. For a given noise level, the HINT test provides an estimate of the signal-to-noise ratio (SNR) required for 50%-correct speech intelligibility. The SNR for 50%-correct intelligibility changes depending upon the interruption rate of the noise. This phenomenon (called Masking Release) has been studied extensively in English but not for Igbo - which is an African tonal language spoken predominantly in South Eastern Nigeria. This experiment explored and compared the phenomenon of Masking Release for (i) native English speakers listening to English, (ii) native Igbo speakers listening to English, and (iii) native Igbo speakers listening to Igbo. Since Igbo is a tonal language and English is a non-tonal language, this allowed us to compare Masking Release patterns on native speakers of tonal and non-tonal languages. Our results for native English speakers listening to English HINT show that the SNR and the masking release are orderly and consistent with other English HINT data for English speakers. Our result for Igbo speakers listening to English HINT sentences show that there is greater variability in results across the different Igbo listeners than across the English listeners. This result likely reflects different levels of ability in the English language across the Igbo listeners. The masking release values in dB are less than for English listeners. Our results for Igbo speakers listening to Igbo show that in general, the SNRs for Igbo sentences are lower than for English/English and Igbo/English. This means that the Igbo listeners could understand 50% of the Igbo sentences at SNRs less than those required for English sentences by either native or non-native listeners. This result can be explained by the fact that the perception of Igbo utterances by Igbo subjects may have been aided by the prediction of tonal and vowel harmony features existent in the Igbo language. In agreement with other studies, our results also show that in a noisy environment listeners are able to perceive their native language better than a second language. The ability of native language speakers to perceive their language better than a second language in a noisy environment may be attributed to the fact that: Native speakers are more familiar with the sounds of their language than second language speakers.One of the features of language is that it is predictable hence even in noise a native speaker may be able to predict a succeeding word that is scarcely audible. These contextual effects are facilitated by familiarity.

Differential Allocation to Photosynthetic and Non-Photosynthetic Nitrogen Fractions among Native and Invasive Species

PubMed Central

Funk, Jennifer L.; Glenwinkel, Lori A.; Sack, Lawren

2013-01-01

Invasive species are expected to cluster on the “high-return” end of the leaf economic spectrum, displaying leaf traits consistent with higher carbon assimilation relative to native species. Intra-leaf nitrogen (N) allocation should support these physiological differences; however, N biochemistry has not been examined in more than a few invasive species. We measured 34 leaf traits including seven leaf N pools for five native and five invasive species from Hawaii under low irradiance to mimic the forest understory environment. We found several trait differences between native and invasive species. In particular, invasive species showed preferential N allocation to metabolism (amino acids) rather than photosynthetic light reactions (membrane-bound protein) by comparison with native species. The soluble protein concentration did not vary between groups. Under these low irradiance conditions, native species had higher light-saturated photosynthetic rates, possibly as a consequence of a greater investment in membrane-bound protein. Invasive species may succeed by employing a wide range of N allocation mechanisms, including higher amino acid production for fast growth under high irradiance or storage of N in leaves as soluble protein or amino acids. PMID:23700483

Investigation of IGES for CAD/CAE data transfer

NASA Technical Reports Server (NTRS)

Zobrist, George W.

1989-01-01

In a CAD/CAE facility there is always the possibility that one may want to transfer the design graphics database from the native system to a non-native system. This may occur because of dissimilar systems within an organization or a new CAD/CAE system is to be purchased. The Initial Graphics Exchange Specification (IGES) was developed in an attempt to solve this scenario. IGES is a neutral database format into which the CAD/CAE native database format can be translated to and from. Translating the native design database format to IGES requires a pre-processor and transling from IGES to the native database format requires a post-processor. IGES is an artifice to represent CAD/CAE product data in a neutral environment to allow interfacing applications, archive the database, interchange of product data between dissimilar CAD/CAE systems, and other applications. The intent here is to present test data on translating design product data from a CAD/CAE system to itself and to translate data initially prepared in IGES format to various native design formats. This information can be utilized in planning potential procurement and developing a design discipline within the CAD/CAE community.

Bottom-up control of consumers leads to top-down indirect facilitation of invasive annual herbs in semiarid Chile.

PubMed

Madrigal, Jaime; Kelt, Douglas A; Meserve, Peter L; Gutierrez, Julio R; Squeo, Francisco A

2011-02-01

The abundance of exotic plants is thought to be limited by competition with resident species (including plants and generalist herbivores). In contrast, observations in semiarid Chile suggest that a native generalist rodent, the degu (Octodon degus), may be facilitating the expansion of exotic annual plants. We tested this hypothesis with a 20-year data set from a World Biosphere Reserve in mediterranean Chile. In this semiarid environment, rainfall varies annually and dramatically influences cover by both native and exotic annual plants; degu population density affects the composition and cover of exotic and native annual plants. In low-rainfall years, cover of both native and exotic herbs is extremely low. Higher levels of precipitation result in proportional increases in cover of all annual plants (exotic and native species), leading in turn to increases in degu population densities, at which point they impact native herbs in proportion to their greater cover, indirectly favoring the expansion of exotic plants. We propose that bottom-up control of consumers at our site results in top-down indirect facilitation of invasive annual herbs, and that this pattern may be general to other semiarid ecosystems.

integrating Solid State NMR and Computations in Membrane Protein Science

NASA Astrophysics Data System (ADS)

Cross, Timothy

2015-03-01

Helical membrane protein structures are influenced by their native environment. Therefore the characterization of their structure in an environment that models as closely as possible their native environment is critical for achieving not only structural but functional understanding of these proteins. Solid state NMR spectroscopy in liquid crystalline lipid bilayers provides an excellent tool for such characterizations. Two classes of restraints can be obtained - absolute restraints that constrain the structure to a laboratory frame of reference when using uniformly oriented samples (approximately 1° of mosaic spread) and relative restraints that restrain one part of the structure with respect to another part such as torsional and distance restraints. Here, I will discuss unique restraints derived from uniformly oriented samples and the characterization of initial structures utilizing both restraint types, followed by restrained molecular dynamics refinement in the same lipid bilayer environment as that used for the experimental restraint collection. Protein examples will be taken from Influenza virus and Mycobacterium tuberculosis. When available comparisons of structures to those obtained using different membrane mimetic environments will be shown and the causes for structural distortions explained based on an understanding of membrane biophysics and its sophisticated influence on membrane proteins.

Proteomic analysis highlights the molecular complexities of native Kv4 channel macromolecular complexes.

PubMed

Marionneau, Céline; Townsend, R Reid; Nerbonne, Jeanne M

2011-04-01

Voltage-gated K(+) (Kv) channels are key determinants of membrane excitability in the nervous and cardiovascular systems, functioning to control resting membrane potentials, shape action potential waveforms and influence the responses to neurotransmitters and neurohormones. Consistent with this functional diversity, multiple types of Kv currents, with distinct biophysical properties and cellular/subcellular distributions, have been identified. Rapidly activating and inactivating Kv currents, typically referred to as I(A) (A-type) in neurons, for example, regulate repetitive firing rates, action potential back-propagation (into dendrites) and modulate synaptic responses. Currents with similar properties, referred to as I(to,f) (fast transient outward), expressed in cardiomyocytes, control the early phase of myocardial action potential repolarization. A number of studies have demonstrated critical roles for pore-forming (α) subunits of the Kv4 subfamily in the generation of native neuronal I(A) and cardiac I(to,f) channels. Studies in heterologous cells have also suggested important roles for a number of Kv channel accessory and regulatory proteins in the generation of functional I(A) and I(to,f) channels. Quantitative mass spectrometry-based proteomic analysis is increasingly recognized as a rapid and, importantly, unbiased, approach to identify the components of native macromolecular protein complexes. The recent application of proteomic approaches to identify the components of native neuronal (and cardiac) Kv4 channel complexes has revealed even greater complexity than anticipated. The continued emphasis on development of improved biochemical and analytical proteomic methods seems certain to accelerate progress and to provide important new insights into the molecular determinants of native ion channel protein complexes. Copyright © 2010 Elsevier Ltd. All rights reserved.

L'environnement pedagogique: source de difficulte dans la maitrise des habiletes phonetiques en langue seconde (The Learning Environment: Source of Difficulty in the Mastery of Second Language Phonetic Skills).

ERIC Educational Resources Information Center

Champagne, Cecile

1984-01-01

Research is reported that showed phonetic and phonological training to be given peripheral attention or neglected in second language instruction in one geographic area. It is suggested this neglect stems from (1) low teacher and student expectation of success in attaining a native-like accent, and (2) assumptions that a non-native-like accent will…

We Shared the Same Chapter: Collaboration, Learning, and Transformation from the 2008 Subsistence, the Environment, and Community Well-Being Native Youth Exchange in Old Harbor, Alaska Project

ERIC Educational Resources Information Center

Richmond, Laurie; Di Piero, Daniela; Espinoza, Flowers; Simeonoff, Teacon; Faraday, Margaret

2010-01-01

On a small island belonging to the Alutiiq people of Old Harbor, 11 people sat around a campfire. Two community leaders, a nonprofit organizer, an academic scholar, a native filmmaker, and six young people from the Indian reservation of Taos Pueblo in New Mexico gathered after a day of interacting with Old Harbor residents--fishing, hunting and…

The Nuka System of Care: improving health through ownership and relationships.

PubMed

Gottlieb, Katherine

2013-01-01

Southcentral Foundation's Nuka System of Care, based in Anchorage, Alaska, is a result of a customer-driven overhaul of what was previously a bureaucratic system centrally controlled by the Indian Health Service. Alaska Native people are in control as the "customer-owners" of this health care system. The vision and mission focus on physical, mental, emotional, and spiritual wellness and working together as a Native Community. Coupled with operational principles based on relationships, core concepts and key points, this framework has fostered an environment for creativity, innovation and continuous quality improvement. Alaska Native people have received national and international recognition for their work and have set high standards for performance excellence, community engagement, and overall impact on population health. In this article, the health care transformation led by Alaska Native people is described and the benefits and results of customer ownership and the relationship-based Nuka System of Care are discussed.

The Nuka System of Care: improving health through ownership and relationships

PubMed Central

Gottlieb, Katherine

2013-01-01

Southcentral Foundation’s Nuka System of Care, based in Anchorage, Alaska, is a result of a customer-driven overhaul of what was previously a bureaucratic system centrally controlled by the Indian Health Service. Alaska Native people are in control as the “customer-owners” of this health care system. The vision and mission focus on physical, mental, emotional, and spiritual wellness and working together as a Native Community. Coupled with operational principles based on relationships, core concepts and key points, this framework has fostered an environment for creativity, innovation and continuous quality improvement. Alaska Native people have received national and international recognition for their work and have set high standards for performance excellence, community engagement, and overall impact on population health. In this article, the health care transformation led by Alaska Native people is described and the benefits and results of customer ownership and the relationship-based Nuka System of Care are discussed. PMID:23984269

A Unique Spatial Arrangement of the snRNPs within the Native Spliceosome Emerges from In-Silico Studies

PubMed Central

Frankenstein, Ziv; Sperling, Joseph; Sperling, Ruth; Eisenstein, Miriam

2012-01-01

Summary The spliceosome is a mega-Dalton ribonucleoprotein (RNP) assembly that processes primary RNA transcripts, producing functional mRNA. The electron microscopy structures of the native spliceosome and of several spliceosomal subcomplexes are available but the spatial arrangement of the latter within the native spliceosome is not known. We designed a new computational procedure to efficiently fit thousands of conformers into the spliceosome envelope. Despite the low resolution limitations, we obtained only one model that complies with the available biochemical data. Our model localizes the five small nuclear RNPs (snRNPs) mostly within the large subunit of the native spliceosome, requiring only minor conformation changes. The remaining free volume presumably accommodates additional spliceosomal components. The constituents of the active core of the spliceosome are juxtaposed, forming a continuous surface deep within the large spliceosomal cavity, which provides a sheltered environment for the splicing reaction. PMID:22578543

Environment and Urban Tourism: AN Emergent System in Rhetorical Place Identity Definitions

NASA Astrophysics Data System (ADS)

Mura, Marina

Within the systemic framework of Environmental Psychology (Bechtel and Churchman, 2002) and following Urry (2002) and Pearce's approaches (2005), the aim of this research is to investigate within the context of urban tourism which world views emerge from a Discourse Analysis (Edwards, Potter, 1993). of the speech of native and non-native Sardinian residents. It addresses the issue of how social-physical diversity might be preserved (the problem of tourism sustainability, Di Castri, Balaji, 2002). In this regard, forty in-depth narrative interviews of inhabitants with short- and long-term residential experience in Cagliari (Italy) were conducted and examined (Discourse Analysis). It was found that the native and non-native's rhetorical devices expressed similar representations of urban places, but in diverse relationship to social and place identity. Their environmental transitions were based on the tourist gaze, or the functional view and heritage pride. This displays some basic central dimensions of sustainable tourism.

Connecting culturally and spiritually to healthy eating: A community assessment with Native Hawaiians

PubMed Central

Oneha, Mary Frances; Dodgson, Joan E; DeCambra, Mabel Ho`oipo; Titcomb, Carol; Enos, Rachelle; Morimoto-Ching, Sandie

2017-01-01

Many of the chronic illnesses disproportionately experienced by Native Hawaiians are directly related to poor diets and long-standing obesity beginning in childhood. We report on the findings of in-depth key informant interviews (N=14) that took place in two Native Hawaiian communities as part of a larger, community-based participatory research study that included a community assessment through individual interviews and focused group discussions, and a pilot intervention targeting pregnant women, their infants, and families. Four categories emerged from the qualitative analysis of interview transcripts that described an understanding of “healthy eating”: family roles and responsibilities, aspects of community and physical environment, deeper spiritual meaning of food, and ways of operationalizing personal eating choices. The findings revealed previously undocumented intergenerational influences on healthy eating patterns and informed the design of the next study phases and are of significance in targeting nutritional interventions for Native Hawaiians. PMID:28239642

Is the isolated ligand binding domain a good model of the domain in the native receptor?

PubMed

Deming, Dustin; Cheng, Qing; Jayaraman, Vasanthi

2003-05-16

Numerous studies have used the atomic level structure of the isolated ligand binding domain of the glutamate receptor to elucidate the agonist-induced activation and desensitization processes in this group of proteins. However, no study has demonstrated the structural equivalence of the isolated ligand binding fragments and the protein in the native receptor. In this report, using visible absorption spectroscopy we show that the electronic environment of the antagonist 6-cyano-7-nitro-2,3-dihydroxyquinoxaline is identical for the isolated protein and the native glutamate receptors expressed in cells. Our results hence establish that the local structure of the ligand binding site is the same in the two proteins and validate the detailed structure-function relationships that have been developed based on a comparison of the structure of the isolated ligand binding domain and electrophysiological consequences in the native receptor.

Heavy metal contamination along the China coastline: A comprehensive study using Artificial Mussels and native mussels.

PubMed

Degger, Natalie; Chiu, Jill M Y; Po, Beverly H K; Tse, Anna C K; Zheng, Gene J; Zhao, Dong-Mei; Xu, Di; Cheng, Yu-Shan; Wang, Xin-Hong; Liu, Wen-Hua; Lau, T C; Wu, Rudolf S S

2016-09-15

A comprehensive study was carried out to assess metal contamination in five cities spanning from temperate to tropical environment along the coastal line of China with different hydrographical conditions. At each of the five cities, Artificial Mussels (AM) were deployed together with a native species of mussel at a control site and a polluted site. High levels of Cr, Cu and Hg were found in Qingdao, high level of Cd, Hg and Pb was found in Shanghai, and high level of Zn was found in Dalian. Furthermore, level of Cu contamination in all the five cities was consistently much higher than those reported in similar studies in other countries (e.g., Australia, Portugal, Scotland, Iceland, Korea, South Africa and Bangladesh). Levels of individual metal species in the AM showed a highly significant correlation with that in the native mussels (except for Zn in Mytilus edulis and Cd in Perna viridis), while no significant difference can be found between the regression relationships of metal in the AM and each of the two native mussel species. The results demonstrated that AM can provide a reliable time-integrated estimate of metal concentration in contrasting environments over large biogeographic areas and different hydrographic conditions, and overcome the shortcomings of monitoring metals in water, sediment and the use of biomonitors. Copyright © 2016 Elsevier Ltd. All rights reserved.

Marine bioinvasions: Differences in tropical copepod communities between inside and outside a port

NASA Astrophysics Data System (ADS)

Soares, Marcelo de Oliveira; Campos, Carolina Coelho; Santos, Nívia Maria Oliveira; Barroso, Hortência de Sousa; Mota, Erika Maria Targino; Menezes, Maria Ozilea Bezerra de; Rossi, Sergio; Garcia, Tatiane Martins

2018-04-01

The difficulty of detecting non-indigenous species (NIS) in marine environments is an "invisible problem" in areas where plankton monitoring does not occur. In this study, we investigated the dominance of the NIS Temora turbinata and copepod community structure in two tropical marine habitats: inside an offshore port, which had turbid and calm waters, and outside the port, which was more hydrodynamic. Our study area was on the northeast coast of Brazil. We found 17 taxa of Copepoda, which were dominated by T. turbinata and the congener, T. stylifera. The high average density of the NIS (21.03 ind./m3) was in stark contrast with that of the native copepods (0.01-3.27 ind./m3). The NIS density was negatively correlated with the species richness and evenness of the native community, was significantly higher inside the port than outside, and was positively correlated with phytoplankton density. A multivariate analysis revealed that there was a significant difference in copepod community structure between inside and outside the port; outside the port, the community was more diverse, and the native T. stylifera was more abundant. We found that tropical copepod communities inside an offshore port have low diversity, and probably have little biotic resistance against NIS invasions. Our results, combined with those previously obtained, highlight the need to study the spatial distributions of NIS and native species in pelagic environments.

Exploring the Complex Computer-Mediated Communication Needs of Learners in a Multilingual, Multicultural Online Learning Environment

ERIC Educational Resources Information Center

Burger, William Peter

2013-01-01

The purpose of this study was to understand student perceptions of social presence that resulted from communicating and collaborating via different forms of Internet-based communication technologies in a diverse, multicultural, multilingual online learning environment. In that it describes how non-native English speaking students from different…

MESA: An Interactive Modeling and Simulation Environment for Intelligent Systems Automation

NASA Technical Reports Server (NTRS)

Charest, Leonard

1994-01-01

This report describes MESA, a software environment for creating applications that automate NASA mission opterations. MESA enables intelligent automation by utilizing model-based reasoning techniques developed in the field of Artificial Intelligence. Model-based reasoning techniques are realized in Mesa through native support of causal modeling and discrete event simulation.

Invasive soil organisms and their effects on belowground processes

Treesearch

Erik Lilleskov; Jr. Mac A. Callaham; Richard Pouyat; Jane E. Smith; Michael Castellano; Grizelle Gonzalez; D. Jean Lodge; Rachel Arango; Frederick Green

2010-01-01

Invasive species have a wide range of effects on soils and their inhabitants. By altering soils, through their direct effects on native soil organisms (including plants), and by their interaction with the aboveground environment, invasive soil organisms can have dramatic effects on the environment, the economy and human health. The most widely recognized effects...

Estimating suitable environments for invasive plant species across large landscapes: A remote sensing strategy using Landsat 7 ETM+

USDA-ARS?s Scientific Manuscript database

The key to reducing ecological and economic damage caused by invasive plant species is to locate and eradicate new invasions before they threaten native biodiversity and ecological processes. We used Landsat Enhanced Thematic Mapper Plus imagery to estimate suitable environments for four invasive pl...

Language and EFL Teacher Preparation in Non-English-Speaking Environments.

ERIC Educational Resources Information Center

Peretz, Arna S.

Linguistic and paralinguistic problems faced by non-native-English speakers training to be teachers of English as a second or foreign language (ESL/EFL) in non-English-speaking environments are discussed. Relevant theories of second language learning and acquisition are reviewed, and the affective factors and sociocultural variables that appear to…

The Dynamics and Consequences of Occupational Deprivation on Displaced Individuals

ERIC Educational Resources Information Center

Kharma, Maher M.

2010-01-01

Following wars and natural disasters, individuals and their families face displacement from their native land and relocate to a new location where they become refugees. As occupational beings, people find meaning in their environment and build their identity through engaging in meaningful occupations. The environment plays a role in shaping the…

KSC-02pd0874

NASA Image and Video Library

2002-05-17

KENNEDY SPACE CENTER, FLA. - A wild pig is spotted near the KSC Press Site on its daily foraging rounds. Not a native in the environment, the pigs around KSC are believed to be descendants from those brought to Florida by the early Spanish explorers. Without many predators other than human, the pigs have flourished in the surrounding environs

High Efficient Expression, Purification, and Functional Characterization of Native Human Epidermal Growth Factor in Escherichia coli.

PubMed

Ma, Yi; Yu, Jieying; Lin, Jinglian; Wu, Shaomin; Li, Shan; Wang, Jufang

2016-01-01

Human epidermal growth factor (hEGF) is a small, mitotic growth polypeptide that promotes the proliferation of various cells and is widely applied in clinical practices. However, high efficient expression of native hEGF in Escherichia coli has not been successful, since three disulfide bonds in monomer hEGF made it unable to fold into correct 3D structure using in vivo system. To tackle this problem, we fused Mxe GyrA intein (Mxe) at the C-terminal of hEGF followed by small ubiquitin-related modifier (SUMO) and 10x His-tag to construct a chimeric protein hEGF-Mxe-SUMO-H 10 . The fusion protein was highly expressed at the concentration of 281 mg/L and up to 59.5% of the total cellular soluble proteins. The fusion protein was purified by affinity chromatography and 29.4 mg/L of native hEGF can be released by thiol induced N-terminal cleavage without any proteases. The mitotic activity in Balb/c 3T3 cells is proliferated by commercial and recombinant hEGF measured with methylthiazolyldiphenyl-tetrazolium bromide (MTT) assay which indicated that recombinant hEGF protein stimulates the cell proliferation similar to commercial protein. This study significantly improved the yield and reduced the cost of hEGF in the recombinant E. coli system and could be a better strategy to produce native hEGF for pharmaceutical development.

In vivo multiphoton tomography and fluorescence lifetime imaging of human brain tumor tissue.

PubMed

Kantelhardt, Sven R; Kalasauskas, Darius; König, Karsten; Kim, Ella; Weinigel, Martin; Uchugonova, Aisada; Giese, Alf

2016-05-01

High resolution multiphoton tomography and fluorescence lifetime imaging differentiates glioma from adjacent brain in native tissue samples ex vivo. Presently, multiphoton tomography is applied in clinical dermatology and experimentally. We here present the first application of multiphoton and fluorescence lifetime imaging for in vivo imaging on humans during a neurosurgical procedure. We used a MPTflex™ Multiphoton Laser Tomograph (JenLab, Germany). We examined cultured glioma cells in an orthotopic mouse tumor model and native human tissue samples. Finally the multiphoton tomograph was applied to provide optical biopsies during resection of a clinical case of glioblastoma. All tissues imaged by multiphoton tomography were sampled and processed for conventional histopathology. The multiphoton tomograph allowed fluorescence intensity- and fluorescence lifetime imaging with submicron spatial resolution and 200 picosecond temporal resolution. Morphological fluorescence intensity imaging and fluorescence lifetime imaging of tumor-bearing mouse brains and native human tissue samples clearly differentiated tumor and adjacent brain tissue. Intraoperative imaging was found to be technically feasible. Intraoperative image quality was comparable to ex vivo examinations. To our knowledge we here present the first intraoperative application of high resolution multiphoton tomography and fluorescence lifetime imaging of human brain tumors in situ. It allowed in vivo identification and determination of cell density of tumor tissue on a cellular and subcellular level within seconds. The technology shows the potential of rapid intraoperative identification of native glioma tissue without need for tissue processing or staining.

Method of physical vapor deposition of metal oxides on semiconductors

DOEpatents

Norton, David P.

2001-01-01

A process for growing a metal oxide thin film upon a semiconductor surface with a physical vapor deposition technique in a high-vacuum environment and a structure formed with the process involves the steps of heating the semiconductor surface and introducing hydrogen gas into the high-vacuum environment to develop conditions at the semiconductor surface which are favorable for growing the desired metal oxide upon the semiconductor surface yet is unfavorable for the formation of any native oxides upon the semiconductor. More specifically, the temperature of the semiconductor surface and the ratio of hydrogen partial pressure to water pressure within the vacuum environment are high enough to render the formation of native oxides on the semiconductor surface thermodynamically unstable yet are not so high that the formation of the desired metal oxide on the semiconductor surface is thermodynamically unstable. Having established these conditions, constituent atoms of the metal oxide to be deposited upon the semiconductor surface are directed toward the surface of the semiconductor by a physical vapor deposition technique so that the atoms come to rest upon the semiconductor surface as a thin film of metal oxide with no native oxide at the semiconductor surface/thin film interface. An example of a structure formed by this method includes an epitaxial thin film of (001)-oriented CeO.sub.2 overlying a substrate of (001) Ge.

Physical activity differences between children from migrant and native origin.

PubMed

Labree, Wim; Lötters, Freek; van de Mheen, Dike; Rutten, Frans; Rivera Chavarría, Ana; Neve, Madelon; Rodenburg, Gerda; Machielsen, Honorine; Koopmans, Gerrit; Foets, Marleen

2014-08-09

Children from migrant origin are at higher risk for overweight and obesity. As limited physical activity is a key factor in this overweight and obesity risk, in general, the aim of this study is to assess to what degree children from migrant and native Dutch origin differ with regard to levels of physical activity and to determine which home environment aspects contribute to these differences. A cross-sectional survey among primary caregivers of primary school children at the age of 8-9 years old (n = 1943) from 101 primary schools in two urban areas in The Netherlands. We used bivariate correlation and multivariate regression techniques to examine the relationship between physical and social environment aspects and the child's level of physical activity. All outcomes were reported by primary caregivers. Outcome measure was the physical activity level of the child. Main independent variables were migrant background, based on country of birth of the parents, and variables in the physical and social home environment which may enhance or restrict physical activity: the availability and the accessibility of toys and equipment, as well as sport club membership (physical environment), and both parental role modeling, and supportive parental policies (social environment). We controlled for age and sex of the child, and for socio-economic status, as indicated by educational level of the parents. In this sample, physical activity levels were significantly lower in migrant children, as compared to children in the native population. Less physical activity was most often seen in Turkish, Moroccan, and other non-western children (p < .05). Although traditional home characteristics in both the physical, and the social environment are often associated with child's physical activity, these characteristics provided only modest explanation of the differences in physical activity between migrant and non-migrant children in this study. The question arises whether interventions aimed at overweight and obesity should have to focus on home environmental characteristics with regard to physical activity.

An invasive clonal plant benefits from clonal integration more than a co-occurring native plant in nutrient-patchy and competitive environments.

PubMed

You, Wenhua; Fan, Shufeng; Yu, Dan; Xie, Dong; Liu, Chunhua

2014-01-01

Many notorious invasive plants are clonal, however, little is known about the different roles of clonal integration effects between invasive and native plants. Here, we hypothesize that clonal integration affect growth, photosynthetic performance, biomass allocation and thus competitive ability of invasive and native clonal plants, and invasive clonal plants benefit from clonal integration more than co-occurring native plants in heterogeneous habitats. To test these hypotheses, two stoloniferous clonal plants, Alternanthera philoxeroides (invasive), Jussiaea repens (native) were studied in China. The apical parts of both species were grown either with or without neighboring vegetation and the basal parts without competitors were in nutrient- rich or -poor habitats, with stolon connections were either severed or kept intact. Competition significantly reduced growth and photosynthetic performance of the apical ramets in both species, but not the biomass of neighboring vegetation. Without competition, clonal integration greatly improved the growth and photosynthetic performance of both species, especially when the basal parts were in nutrient-rich habitats. When grown with neighboring vegetation, growth of J. repens and photosynthetic performance of both species were significantly enhanced by clonal integration with the basal parts in both nutrient-rich and -poor habitats, while growth and relative neighbor effect (RNE) of A. philoxeroides were greatly improved by clonal integration only when the basal parts were in nutrient-rich habitats. Moreover, clonal integration increased A. philoxeroides's biomass allocation to roots without competition, but decreased it with competition, especially when the basal ramets were in nutrient-rich sections. Effects of clonal integration on biomass allocation of J. repens was similar to that of A. philoxeroides but with less significance. These results supported our hypothesis that invasive clonal plants A. philoxeroides benefits from clonal integration more than co-occurring native J. repens, suggesting that the invasiveness of A. philoxeroides may be closely related to clonal integration in heterogeneous environments.

Human land use promotes the abundance and diversity of exotic species on caribbean islands.

PubMed

Jesse, Wendy A M; Behm, Jocelyn E; Helmus, Matthew R; Ellers, Jacintha

2018-05-31

Human land use causes major changes in species abundance and composition, yet native and exotic species can exhibit different responses to land use change. Native populations generally decline in human-impacted habitats while exotic species often benefit. In this study, we assessed the effects of human land use on exotic and native reptile diversity, including functional diversity, which relates to the range of habitat use strategies in biotic communities. We surveyed 114 reptile communities from localities that varied in habitat structure and human impact level on two Caribbean islands, and calculated species richness, overall abundance and evenness for every plot. Functional diversity indices were calculated using published trait data, which enabled us to detect signs of trait filtering associated with impacted habitats. Our results show that environmental variation among sampling plots was explained by two PCA ordination axes related to habitat structure (i.e. forest or non-forest) and human impact level (i.e. addition of man-made constructions such as roads and buildings). Several diversity indices were significantly correlated with the two PCA axes, but exotic and native species showed opposing responses. Native species reached the highest abundance in forests, while exotic species were absent in this habitat. Human impact was associated with an increase in exotic abundance and species richness, while native species showed no significant associations. Functional diversity was highest in non-forested environments on both islands, and further increased on St. Martin with the establishment of functionally unique exotic species in non-forested habitat. Habitat structure, rather than human impact, proved to be an important agent for environmental filtering of traits, causing divergent functional trait values across forested and non-forested environments. Our results illustrate the importance of considering various elements of land use when studying its impact on species diversity and the establishment and spread of exotic species. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

An Invasive Clonal Plant Benefits from Clonal Integration More than a Co-Occurring Native Plant in Nutrient-Patchy and Competitive Environments

PubMed Central

You, Wenhua; Fan, Shufeng; Yu, Dan; Xie, Dong; Liu, Chunhua

2014-01-01

Many notorious invasive plants are clonal, however, little is known about the different roles of clonal integration effects between invasive and native plants. Here, we hypothesize that clonal integration affect growth, photosynthetic performance, biomass allocation and thus competitive ability of invasive and native clonal plants, and invasive clonal plants benefit from clonal integration more than co-occurring native plants in heterogeneous habitats. To test these hypotheses, two stoloniferous clonal plants, Alternanthera philoxeroides (invasive), Jussiaea repens (native) were studied in China. The apical parts of both species were grown either with or without neighboring vegetation and the basal parts without competitors were in nutrient- rich or -poor habitats, with stolon connections were either severed or kept intact. Competition significantly reduced growth and photosynthetic performance of the apical ramets in both species, but not the biomass of neighboring vegetation. Without competition, clonal integration greatly improved the growth and photosynthetic performance of both species, especially when the basal parts were in nutrient-rich habitats. When grown with neighboring vegetation, growth of J. repens and photosynthetic performance of both species were significantly enhanced by clonal integration with the basal parts in both nutrient-rich and -poor habitats, while growth and relative neighbor effect (RNE) of A. philoxeroides were greatly improved by clonal integration only when the basal parts were in nutrient-rich habitats. Moreover, clonal integration increased A. philoxeroides's biomass allocation to roots without competition, but decreased it with competition, especially when the basal ramets were in nutrient-rich sections. Effects of clonal integration on biomass allocation of J. repens was similar to that of A. philoxeroides but with less significance. These results supported our hypothesis that invasive clonal plants A. philoxeroides benefits from clonal integration more than co-occurring native J. repens, suggesting that the invasiveness of A. philoxeroides may be closely related to clonal integration in heterogeneous environments. PMID:24816849

Soil ecosystem function under native and exotic plant assemblages as alternative states of successional grasslands

NASA Astrophysics Data System (ADS)

Spirito, Florencia; Yahdjian, Laura; Tognetti, Pedro M.; Chaneton, Enrique J.

2014-01-01

Old fields often become dominated by exotic plants establishing persistent community states. Ecosystem functioning may differ widely between such novel communities and the native-dominated counterparts. We evaluated soil ecosystem attributes in native and exotic (synthetic) grass assemblages established on a newly abandoned field, and in remnants of native grassland in the Inland Pampa, Argentina. We asked whether exotic species alter soil functioning through the quality of the litter they shed or by changing the decomposition environment. Litter decomposition of the exotic dominant Festuca arundinacea in exotic assemblages was faster than that of the native dominant Paspalum quadrifarium in native assemblages and remnant grasslands. Decomposition of a standard litter (Triticum aestivum) was also faster in exotic assemblages than in native assemblages and remnant grasslands. In a common garden, F. arundinacea showed higher decay rates than P. quadrifarium, which reflected the higher N content and lower C:N of the exotic grass litter. Soil respiration rates were higher in the exotic than in the native assemblages and remnant grasslands. Yet there were no significant differences in soil N availability or net N mineralization between exotic and native assemblages. Our results suggest that exotic grass dominance affected ecosystem function by producing a more decomposable leaf litter and by increasing soil decomposer activity. These changes might contribute to the extended dominance of fast-growing exotic grasses during old-field succession. Further, increased organic matter turnover under novel, exotic communities could reduce the carbon storage capacity of the system in the long term.

Early biocompatibility of crosslinked and non-crosslinked biologic meshes in a porcine model of ventral hernia repair.

PubMed

Melman, L; Jenkins, E D; Hamilton, N A; Bender, L C; Brodt, M D; Deeken, C R; Greco, S C; Frisella, M M; Matthews, B D

2011-04-01

Biologic meshes have unique physical properties as a result of manufacturing techniques such as decellularization, crosslinking, and sterilization. The purpose of this study is to directly compare the biocompatibility profiles of five different biologic meshes, AlloDerm(®) (non-crosslinked human dermal matrix), PeriGuard(®) (crosslinked bovine pericardium), Permacol(®) (crosslinked porcine dermal matrix), Strattice(®) (non-crosslinked porcine dermal matrix), and Veritas(®) (non-crosslinked bovine pericardium), using a porcine model of ventral hernia repair. Full-thickness fascial defects were created in 20 Yucatan minipigs and repaired with the retromuscular placement of biologic mesh 3 weeks later. Animals were euthanized at 1 month and the repair sites were subjected to tensile testing and histologic analysis. Samples of unimplanted (de novo) meshes and native porcine abdominal wall were also analyzed for their mechanical properties. There were no significant differences in the biomechanical characteristics between any of the mesh-repaired sites at 1 month postimplantation or between the native porcine abdominal wall without implanted mesh and the mesh-repaired sites (P > 0.05 for all comparisons). Histologically, non-crosslinked materials exhibited greater cellular infiltration, extracellular matrix (ECM) deposition, and neovascularization compared to crosslinked meshes. While crosslinking differentiates biologic meshes with regard to cellular infiltration, ECM deposition, scaffold degradation, and neovascularization, the integrity and strength of the repair site at 1 month is not significantly impacted by crosslinking or by the de novo strength/stiffness of the mesh.

Ethnic differences in thermoregulatory responses during resting, passive and active heating: application of Werner's adaptation model.

PubMed

Lee, Joo-Young; Wakabayashi, Hitoshi; Wijayanto, Titis; Hashiguchi, Nobuko; Saat, Mohamed; Tochihara, Yutaka

2011-12-01

For the coherent understanding of heat acclimatization in tropical natives, we compared ethnic differences between tropical and temperate natives during resting, passive and active heating conditions. Experimental protocols included: (1) a resting condition (an air temperature of 28°C with 50% RH), (2) a passive heating condition (28°C with 50% RH; leg immersion in a hot tub at a water temperature of 42°C), and (3) an active heating condition (32°C with 70% RH; a bicycle exercise). Morphologically and physically matched tropical natives (ten Malaysian males, MY) and temperate natives (ten Japanese males, JP) participated in all three trials. The results saw that: tropical natives had a higher resting rectal temperature and lower hand and foot temperatures at rest, smaller rise of rectal temperature and greater temperature rise in bodily extremities, and a lower sensation of thirst during passive and active heating than the matched temperate natives. It is suggested that tropical natives' homeostasis during heating is effectively controlled with the improved stability in internal body temperature and the increased capability of vascular circulation in extremities, with a lower thirst sensation. The enhanced stability of internal body temperature and the extended thermoregulatory capability of vascular circulation in the extremities of tropical natives can be interpreted as an interactive change to accomplish a thermal dynamic equilibrium in hot environments. These heat adaptive traits were explained by Wilder's law of initial value and Werner's process and controller adaptation model.

Chemical-Biological Properties of Zinc Sensors TSQ and Zinquin: Formation of Sensor-Zn-Protein Adducts versus Zn(Sensor)2 Complexes.

PubMed

Nowakowski, Andrew B; Meeusen, Jeffrey W; Menden, Heather; Tomasiewicz, Henry; Petering, David H

2015-12-21

Fluorescent zinc sensors are the most commonly used tool to study the intracellular mobile zinc status within cellular systems. Previously, we have shown that the quinoline-based sensors Zinquin and 6-methoxy-8-p-toluenesulfonamido-quinoline (TSQ) predominantly form ternary adducts with members of the Zn-proteome. Here, the chemistries of these sensors are further characterized, including how Zn(sensor)2 complexes may react in an intracellular environment. We demonstrate that these sensors are typically used in higher concentrations than needed to obtain maximum signal. Exposing cells to either Zn(Zinquin)2 or Zn(TSQ)2 resulted in efficient cellular uptake and the formation of sensor-Zn-protein adducts as evidenced by both a fluorescence spectral shift toward that of ternary adducts and the localization of the fluorescence signal within the proteome after gel filtration of cellular lysates. Likewise, reacting Zn(sensor)2 with the Zn-proteome from LLC-PK1 cells resulted in the formation of sensor-Zn-protein ternary adducts that could be inhibited by first saturating the Zn- proteome with excess sensor. Further, a native SDS-PAGE analysis of the Zn-proteome reacted with either the sensor or the Zn(sensor)2 complex revealed that both reactions result in the formation of a similar set of sensor-Zn-protein fluorescent products. The results of this experiment also demonstrated that TSQ and Zinquin react with different members of the Zn-proteome. Reactions with the model apo-Zn-protein bovine serum albumin showed that both Zn(TSQ)2 and Zn(Zinquin)2 reacted to form ternary adducts with its apo-Zn-binding site. Moreover, incubating Zn(sensor)2 complexes with non-zinc binding proteins failed to elicit a spectral shift in the fluorescence spectrum, supporting the premise that blue-shifted emission spectra are due to sensor-Zn-protein ternary adducts. It was concluded that Zn(sensors)2 species do not play a significant role in the overall reaction between these sensors and intact cells. In turn, this study further supports the formation of sensor-Zn-protein adducts as the principal observed fluorescent product during experiments employing these two sensors.

Spatial Patterns and Natural Recruitment of Native Shrubs in a Semi-arid Sandy Land

PubMed Central

Wu, Bo; Yang, Hongxiao

2013-01-01

Passive restoration depending on native shrubs is an attractive approach for restoring desertified landscapes in semi-arid sandy regions. We sought to understand the relationships between spatial patterns of native shrubs and their survival ability in sandy environments. Furthermore, we applied our results to better understand whether passive restoration is feasible for desertified landscapes in semi-arid sandy regions. The study was conducted in the semi-arid Mu Us sandy land of northern China with the native shrub Artemisia ordosica. We analyzed population structures and patterns of A. ordosica at the edges and centers of land patches where sand was stabilized by A. ordosica-dominated vegetation. Saplings were more aggregated than adults, and both were more aggregated at the patch edges than at the patch centers. At the patch edges, spatial association of the saplings with the adults was mostly positive at distances 0.3–6.6 m, and turned from positive to neutral, and even negative, at other distances. At the patch centers, the saplings were spaced almost randomly around the adults, and their distances from the adults did not seem to affect their locations. A greater number of A. ordosica individuals emerged at the patch edges than at the patch centers. Such patterns may have resulted from their integrative adjustment to specific conditions of soil water supply and sand drift intensity. These findings suggest that in semi-arid sandy regions, native shrubs that are well-adapted to local environments may serve as low-cost and competent ecological engineers that can promote the passive restoration of surrounding patches of mobile sandy land. PMID:23505489

Three-dimensional neural cultures produce networks that mimic native brain activity.

PubMed

Bourke, Justin L; Quigley, Anita F; Duchi, Serena; O'Connell, Cathal D; Crook, Jeremy M; Wallace, Gordon G; Cook, Mark J; Kapsa, Robert M I

2018-02-01

Development of brain function is critically dependent on neuronal networks organized through three dimensions. Culture of central nervous system neurons has traditionally been limited to two dimensions, restricting growth patterns and network formation to a single plane. Here, with the use of multichannel extracellular microelectrode arrays, we demonstrate that neurons cultured in a true three-dimensional environment recapitulate native neuronal network formation and produce functional outcomes more akin to in vivo neuronal network activity. Copyright © 2017 John Wiley & Sons, Ltd.

Double-crested Cormorant Management Plan to Reduce Predation of Juvenile Salmonids in the Columbia River Estuary

DTIC Science & Technology

2015-01-01

Table ES-3): TABLE ES-3. Affected Environment. Affect ed Resource Summary Vegetation A mix of native a nd non-native plant species is fou nd on t...from British Columbia to California and east to the Continental Divide. Although the western population of double-crested cormorants composes a small ...no person shall be subject to a penalty for failing to comply with a collection of information if it does not display a currently valid OMB control

Alien plants confront expectations of climate change impacts.

PubMed

Hulme, Philip E

2014-09-01

The success of alien plants in novel environments questions basic assumptions about the fate of native species under climate change. Aliens generally spread faster than the velocity of climate change, display considerable phenotypic plasticity as well as adaptation to new selection pressures, and their ranges are often shaped by biotic rather than climatic factors. Given that many native species also exhibit these attributes, their risk of extinction as a result of climate change might be overestimated. Copyright © 2014 Elsevier Ltd. All rights reserved.

Do lichens have "memory" of their native nitrogen environment?

PubMed

Munzi, Silvana; Loppi, Stefano; Cruz, Cristina; Branquinho, Cristina

2011-02-01

This study aimed to deepen the knowledge about intraspecific mechanisms regulating nitrogen tolerance in lichens to wet nitrogen deposition. Thalli of the nitrophilous lichen Xanthoria parietina were collected from environments with different nitrogen availabilities and immersed in 80 mL of ammonium sulphate (NH₄)₂SO₄ solutions with distinct concentrations (0, 0.025, 0.05 and 0.25 M) for 5 h per day during 3 days in a week. After each soaking event, lichens were air dried. After each treatment, maximal PSII efficiency, localization of ammonium ions, concentrations of K+ and Mg²+ and thalli buffer capacity were determined. Our results show that lichens are marked by their native nitrogen environment, since there were important differences between the physiological responses of X. parietina thalli previously grown in an area with high nitrogen deposition (nitrogen emissions of ca. 13,000 t/year) and those previously grown in an unpolluted area (nitrogen emissions of ca. 500 t/year). Greater N availability seems to enable X. parietina to cope better with the effects of nitrogen pollution.

Enhancing Negotiation of Meaning through Task Familiarity Using Subtitled Videos in an Online TBLL Environment

ERIC Educational Resources Information Center

Arslanyilmaz, Abdurrahman; Pedersen, Susan

2010-01-01

This study examines the effects of task familiarity through the use of subtitled videos on negotiation of meaning in an online task-based language learning (TBLL) environment. It explores the amount of negotiation of meaning produced by non-native speakers (NNSs) aimed at improving input comprehension to enhance second language acquisition. Ten…

Apprentissage dans un Environnement Informatique: Possibilite, Nature, Transfert des Acquis (Learning within an Information Environment: Possibilities, Native, and Transfer of Ideas).

ERIC Educational Resources Information Center

Dagher, Antoine

1996-01-01

Examines possibilities for learning offered by a piece of software, Fonctuse, likely to encourage the linking of algebraic and graphical representations of functions. Studied the influence of prior algebraic knowledge on the cognitive processes and constructions of knowledge at play in this environment. (Author/MKR)

Perceived Affordances, Tensions, and Complementarities in the Physical and Digital Environments Frequented by Future Teachers

ERIC Educational Resources Information Center

Pruneau, Diane; Kerry, Jackie; Freiman, Viktor; Langis, Joanne; Bizid, Mohamed

2016-01-01

Is future teachers' contact with the physical environment significant enough for them to choose to educate their students about sustainability? These digital natives stand out from previous generations by their way of living. The research based on grounded theory was aimed at understanding future teachers' relationships with physical and…

Exploring the Effectiveness of Self-Regulated Learning in Massive Open Online Courses on Non-Native English Speakers

ERIC Educational Resources Information Center

Chung, Liang-Yi

2015-01-01

Massive Open Online Courses (MOOCs) are expanding the scope of online distance learning in the creation of a cross-country global learning environment. For learners worldwide, MOOCs offer a wealth of online learning resources. However, such a diversified environment makes the learning process complicated and challenging. To achieve their…

KSC-02pd0873

NASA Image and Video Library

2002-05-17

KENNEDY SPACE CENTER, FLA. - Wild pigs stop near the KSC Press Site in the Launch Complex 39 Area on their daily foraging rounds. Not a native in the environment, the pigs are believed to be descendants from those brought to Florida by the early Spanish explorers. Without many predators other than human, the pigs have flourished in the surrounding environs

Command & Control in Virtual Environments: Designing a Virtual Environment for Experimentation

DTIC Science & Technology

2010-06-01

proceed with the research: Second Life/ OpenSim A popular leader in the desktop virtual worlds revolution, for many Second Life has become...prototype environments and adapt them quickly within the world. OpenSim is an open-source community built around upon the Second Life platform...functionality natively present in Second Life and the Opensim platform. With the recent release of Second Life Viewer 2.0, which contains a complete

Microvascular Targets for Anti-Fibrotic Therapeutics

PubMed Central

Pu, Kai-Ming T.; Sava, Parid; Gonzalez, Anjelica L.

2013-01-01

Fibrosis is characterized by excessive extracellular matrix deposition and is the pathological outcome of repetitive tissue injury in many disorders. The accumulation of matrix disrupts the structure and function of the native tissue and can affect multiple organs including the lungs, heart, liver, and skin. Unfortunately, current therapies against the deadliest and most common fibrosis are ineffective. The pathogenesis of fibrosis is the result of aberrant wound healing, therefore, the microvasculature plays an important role, contributing through regulation of leukocyte recruitment, inflammation, and angiogenesis. Further exacerbating the condition, microvascular endothelial cells and pericytes can transdifferentiate into matrix depositing myofibroblasts. The contribution of the microvasculature to fibrotic progression makes its cellular components and acellular products attractive therapeutic targets. In this review, we examine many of the cytokine, matrix, and cellular microvascular components involved in fibrosis and discuss their potential as targets for fibrotic therapies with a particular focus on developing nanotechnologies. PMID:24348218

Single cell analysis in native tissue: Quantification of the retinoid content of hepatic stellate cells

NASA Astrophysics Data System (ADS)

Galler, Kerstin; Requardt, Robert Pascal; Glaser, Uwe; Markwart, Robby; Bocklitz, Thomas; Bauer, Michael; Popp, Jürgen; Neugebauer, Ute

2016-04-01

Hepatic stellate cells (HSCs) are retinoid storing cells in the liver: The retinoid content of those cells changes depending on nutrition and stress level. There are also differences with regard to a HSC’s anatomical position in the liver. Up to now, retinoid levels were only accessible from bulk measurements of tissue homogenates or cell extracts. Unfortunately, they do not account for the intercellular variability. Herein, Raman spectroscopy relying on excitation by the minimally destructive wavelength 785 nm is introduced for the assessment of the retinoid state of single HSCs in freshly isolated, unprocessed murine liver lobes. A quantitative estimation of the cellular retinoid content is derived. Implications of the retinoid content on hepatic health state are reported. The Raman-based results are integrated with histological assessments of the tissue samples. This spectroscopic approach enables single cell analysis regarding an important cellular feature in unharmed tissue.

The Structure of an Infectious Human Polyomavirus and Its Interactions with Cellular Receptors.

PubMed

Hurdiss, Daniel L; Frank, Martin; Snowden, Joseph S; Macdonald, Andrew; Ranson, Neil A

2018-06-05

BK polyomavirus (BKV) causes polyomavirus-associated nephropathy and hemorrhagic cystitis in immunosuppressed patients. These are diseases for which we currently have limited treatment options, but potential therapies could include pre-transplant vaccination with a multivalent BKV vaccine or therapeutics which inhibit capsid assembly or block attachment and entry into target cells. A useful tool in such efforts would be a high-resolution structure of the infectious BKV virion and how this interacts with its full repertoire of cellular receptors. We present the 3.4-Å cryoelectron microscopy structure of native, infectious BKV in complex with the receptor fragment of GT1b ganglioside. We also present structural evidence that BKV can utilize glycosaminoglycans as attachment receptors. This work highlights features that underpin capsid stability and provides a platform for rational design and development of urgently needed pharmacological interventions for BKV-associated diseases. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Reprogramming cellular functions with engineered membrane proteins.

PubMed

Arber, Caroline; Young, Melvin; Barth, Patrick

2017-10-01

Taking inspiration from Nature, synthetic biology utilizes and modifies biological components to expand the range of biological functions for engineering new practical devices and therapeutics. While early breakthroughs mainly concerned the design of gene circuits, recent efforts have focused on engineering signaling pathways to reprogram cellular functions. Since signal transduction across cell membranes initiates and controls intracellular signaling, membrane receptors have been targeted by diverse protein engineering approaches despite limited mechanistic understanding of their function. The modular architecture of several receptor families has enabled the empirical construction of chimeric receptors combining domains from distinct native receptors which have found successful immunotherapeutic applications. Meanwhile, progress in membrane protein structure determination, computational modeling and rational design promise to foster the engineering of a broader range of membrane receptor functions. Marrying empirical and rational membrane protein engineering approaches should enable the reprogramming of cells with widely diverse fine-tuned functions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Single cell analysis in native tissue: Quantification of the retinoid content of hepatic stellate cells

PubMed Central

Galler, Kerstin; Requardt, Robert Pascal; Glaser, Uwe; Markwart, Robby; Bocklitz, Thomas; Bauer, Michael; Popp, Jürgen; Neugebauer, Ute

2016-01-01

Hepatic stellate cells (HSCs) are retinoid storing cells in the liver: The retinoid content of those cells changes depending on nutrition and stress level. There are also differences with regard to a HSC’s anatomical position in the liver. Up to now, retinoid levels were only accessible from bulk measurements of tissue homogenates or cell extracts. Unfortunately, they do not account for the intercellular variability. Herein, Raman spectroscopy relying on excitation by the minimally destructive wavelength 785 nm is introduced for the assessment of the retinoid state of single HSCs in freshly isolated, unprocessed murine liver lobes. A quantitative estimation of the cellular retinoid content is derived. Implications of the retinoid content on hepatic health state are reported. The Raman-based results are integrated with histological assessments of the tissue samples. This spectroscopic approach enables single cell analysis regarding an important cellular feature in unharmed tissue. PMID:27063397

Self-interference 3D super-resolution microscopy for deep tissue investigations.

PubMed

Bon, Pierre; Linarès-Loyez, Jeanne; Feyeux, Maxime; Alessandri, Kevin; Lounis, Brahim; Nassoy, Pierre; Cognet, Laurent

2018-06-01

Fluorescence localization microscopy has achieved near-molecular resolution capable of revealing ultra-structures, with a broad range of applications, especially in cellular biology. However, it remains challenging to attain such resolution in three dimensions and inside biological tissues beyond the first cell layer. Here we introduce SELFI, a framework for 3D single-molecule localization within multicellular specimens and tissues. The approach relies on self-interference generated within the microscope's point spread function (PSF) to simultaneously encode equiphase and intensity fluorescence signals, which together provide the 3D position of an emitter. We combined SELFI with conventional localization microscopy to visualize F-actin 3D filament networks and reveal the spatial distribution of the transcription factor OCT4 in human induced pluripotent stem cells at depths up to 50 µm inside uncleared tissue spheroids. SELFI paves the way to nanoscale investigations of native cellular processes in intact tissues.

Membrane rupture generates single open membrane sheets during vaccinia virus assembly.

PubMed

Chlanda, Petr; Carbajal, Maria Alejandra; Cyrklaff, Marek; Griffiths, Gareth; Krijnse-Locker, Jacomine

2009-07-23

The biogenesis and dynamics of cellular membranes are governed by fusion and fission processes that ensure the maintenance of closed compartments. These principles also apply to viruses during acquisition of their envelope. Based on conventional electron microscopy (EM), however, it has been proposed that poxviruses assemble from membranes made de novo with "free" ends in the cytoplasm. Here, we analyze the origin and structure of poxvirus membranes in a close-to-native state and in three dimensions by using cryopreservation and electron tomography (ET). By cryo-EM, the precursor membrane of poxviruses appears as an open membrane sheet stabilized by a protein scaffold. ET shows that this membrane is derived from pre-existing cellular membranes that rupture to generate an open compartment, rather than being made de novo. Thus, poxvirus infection represents an excellent system to study how cytoplasmic membranes can form open sheets by a process distinct from well-defined mechanisms of membrane biogenesis.

Nanoscale monitoring of drug actions on cell membrane using atomic force microscopy

PubMed Central

Li, Mi; Liu, Lian-qing; Xi, Ning; Wang, Yue-chao

2015-01-01

Knowledge of the nanoscale changes that take place in individual cells in response to a drug is useful for understanding the drug action. However, due to the lack of adequate techniques, such knowledge was scarce until the advent of atomic force microscopy (AFM), which is a multifunctional tool for investigating cellular behavior with nanometer resolution under near-physiological conditions. In the past decade, researchers have applied AFM to monitor the morphological and mechanical dynamics of individual cells following drug stimulation, yielding considerable novel insight into how the drug molecules affect an individual cell at the nanoscale. In this article we summarize the representative applications of AFM in characterization of drug actions on cell membrane, including topographic imaging, elasticity measurements, molecular interaction quantification, native membrane protein imaging and manipulation, etc. The challenges that are hampering the further development of AFM for studies of cellular activities are aslo discussed. PMID:26027658

Advanced nanobiomaterial strategies for the development of organized tissue engineering constructs.

PubMed

An, Jia; Chua, Chee Kai; Yu, Ting; Li, Huaqiong; Tan, Lay Poh

2013-04-01

Nanobiomaterials, a field at the interface of biomaterials and nanotechnologies, when applied to tissue engineering applications, are usually perceived to resemble the cell microenvironment components or as a material strategy to instruct cells and alter cell behaviors. Therefore, they provide a clear understanding of the relationship between nanotechnologies and resulting cellular responses. This review will cover recent advances in nanobiomaterial research for applications in tissue engineering. In particular, recent developments in nanofibrous scaffolds, nanobiomaterial composites, hydrogel systems, laser-fabricated nanostructures and cell-based bioprinting methods to produce scaffolds with nanofeatures for tissue engineering are discussed. As in native niches of cells, where nanofeatures are constantly interacting and influencing cellular behavior, new generations of scaffolds will need to have these features to enable more desirable engineered tissues. Moving forward, tissue engineering will also have to address the issues of complexity and organization in tissues and organs.

Tribal Science Priorities - TEK

EPA Pesticide Factsheets

Traditional Ecological Knowledge (TEK) is the accumulated knowledge American Indians and Native Alaskans have about their environment. It's important for scientific research, but is threatened by environmental change. EPA should support its development.

Physically-Induced Cytoskeleton Remodeling of Cells in Three-Dimensional Culture

PubMed Central

Lee, Sheng-Lin; Nekouzadeh, Ali; Butler, Boyd; Pryse, Kenneth M.; McConnaughey, William B.; Nathan, Adam C.; Legant, Wesley R.; Schaefer, Pascal M.; Pless, Robert B.

2012-01-01

Characterizing how cells in three-dimensional (3D) environments or natural tissues respond to biophysical stimuli is a longstanding challenge in biology and tissue engineering. We demonstrate a strategy to monitor morphological and mechanical responses of contractile fibroblasts in a 3D environment. Cells responded to stretch through specific, cell-wide mechanisms involving staged retraction and reinforcement. Retraction responses occurred for all orientations of stress fibers and cellular protrusions relative to the stretch direction, while reinforcement responses, including extension of cellular processes and stress fiber formation, occurred predominantly in the stretch direction. A previously unreported role of F-actin clumps was observed, with clumps possibly acting as F-actin reservoirs for retraction and reinforcement responses during stretch. Responses were consistent with a model of cellular sensitivity to local physical cues. These findings suggest mechanisms for global actin cytoskeleton remodeling in non-muscle cells and provide insight into cellular responses important in pathologies such as fibrosis and hypertension. PMID:23300512

Structural and Binding Properties of Two Paralogous Fatty Acid Binding Proteins of Taenia solium Metacestode

PubMed Central

Yang, Hyun-Jong; Shin, Joo-Ho; Diaz-Camacho, Sylvia Paz; Nawa, Yukifumi; Kang, Insug; Kong, Yoon

2012-01-01

Background Fatty acid (FA) binding proteins (FABPs) of helminths are implicated in acquisition and utilization of host-derived hydrophobic substances, as well as in signaling and cellular interactions. We previously demonstrated that secretory hydrophobic ligand binding proteins (HLBPs) of Taenia solium metacestode (TsM), a causative agent of neurocysticercosis (NC), shuttle FAs in the surrounding host tissues and inwardly transport the FAs across the parasite syncytial membrane. However, the protein molecules responsible for the intracellular trafficking and assimilation of FAs have remained elusive. Methodology/Principal Findings We isolated two novel TsMFABP genes (TsMFABP1 and TsMFABP2), which encoded 133- and 136-amino acid polypeptides with predicted molecular masses of 14.3 and 14.8 kDa, respectively. They shared 45% sequence identity with each other and 15–95% with other related-members. Homology modeling demonstrated a characteristic β-barrel composed of 10 anti-parallel β-strands and two α-helices. TsMFABP2 harbored two additional loops between β-strands two and three, and β-strands six and seven, respectively. TsMFABP1 was secreted into cyst fluid and surrounding environments, whereas TsMFABP2 was intracellularly confined. Partially purified native proteins migrated to 15 kDa with different isoelectric points of 9.2 (TsMFABP1) and 8.4 (TsMFABP2). Both native and recombinant proteins bound to 11-([5-dimethylaminonaphthalene-1-sulfonyl]amino)undecannoic acid, dansyl-DL-α-amino-caprylic acid, cis-parinaric acid and retinol, which were competitively inhibited by oleic acid. TsMFABP1 exhibited high affinity toward FA analogs. TsMFABPs showed weak binding activity to retinol, but TsMFABP2 showed relatively high affinity. Isolation of two distinct genes from an individual genome strongly suggested their paralogous nature. Abundant expression of TsMFABP1 and TsMFABP2 in the canal region of worm matched well with the histological distributions of lipids and retinol. Conclusions/Significance The divergent biochemical properties, physiological roles and cellular distributions of the TsMFABPs might be one of the critical mechanisms compensating for inadequate de novo FA synthesis. These proteins might exert harmonized or independent roles on lipid assimilation and intracellular signaling. The specialized distribution of retinol in the canal region further implies that cells in this region might differentiate into diverse cell types during metamorphosis into an adult worm. Identification of bioactive systems pertinent to parasitic homeostasis may provide a valuable target for function-related drug design. PMID:23150743

PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways.

PubMed

Demir, E; Babur, O; Dogrusoz, U; Gursoy, A; Nisanci, G; Cetin-Atalay, R; Ozturk, M

2002-07-01

Availability of the sequences of entire genomes shifts the scientific curiosity towards the identification of function of the genomes in large scale as in genome studies. In the near future, data produced about cellular processes at molecular level will accumulate with an accelerating rate as a result of proteomics studies. In this regard, it is essential to develop tools for storing, integrating, accessing, and analyzing this data effectively. We define an ontology for a comprehensive representation of cellular events. The ontology presented here enables integration of fragmented or incomplete pathway information and supports manipulation and incorporation of the stored data, as well as multiple levels of abstraction. Based on this ontology, we present the architecture of an integrated environment named Patika (Pathway Analysis Tool for Integration and Knowledge Acquisition). Patika is composed of a server-side, scalable, object-oriented database and client-side editors to provide an integrated, multi-user environment for visualizing and manipulating network of cellular events. This tool features automated pathway layout, functional computation support, advanced querying and a user-friendly graphical interface. We expect that Patika will be a valuable tool for rapid knowledge acquisition, microarray generated large-scale data interpretation, disease gene identification, and drug development. A prototype of Patika is available upon request from the authors.

Effect of arginine methylation on the RNA recognition and cellular uptake of Tat-derived peptides.

PubMed

Li, Jhe-Hao; Chiu, Wen-Chieh; Yao, Yun-Chiao; Cheng, Richard P

2015-05-01

Arginine (Arg) methylation is a common post-translational modification that regulates gene expression and viral infection. The HIV-1 Tat protein is an essential regulatory protein for HIV proliferation, and is methylated in the cell. The basic region (residues 47-57) of the Tat protein contains six Arg residues, and is responsible for two biological functions: RNA recognition and cellular uptake. In this study, we explore the effect of three different methylation states at each Arg residue in Tat-derived peptides on the two biological functions. The Tat-derived peptides were synthesized by solid phase peptide synthesis. TAR RNA binding of the peptides was assessed by electrophoresis mobility shift assays. The cellular uptake of the peptides into Jurkat cells was determined by flow cytometry. Our results showed that RNA recognition was affected by both methylation state and position. In particular, asymmetric dimethylation at position 53 decreased TAR RNA binding affinity significantly, but unexpectedly less so upon asymmetric dimethylation at position 52. The RNA binding affinity even slightly increased upon methylation at some of the flanking Arg residues. Upon Arg methylation, the cellular uptake of Tat-derived peptides mostly decreased. Interestingly, cellular uptake of Tat-derived peptides with a single asymmetrically dimethylated Arg residue was similar to the native all Arg peptide (at 120 μM). Based on our results, TAR RNA binding apparently required both guanidinium terminal NH groups on Arg53, whereas cellular uptake apparently required guanidinium terminal NH₂ groups instead. These results should provide insight into how nature uses arginine methylation to regulate different biological functions, and should be useful for the development of functional molecules with methylated arginines. Copyright © 2015. Published by Elsevier Ltd.

Listening with a foreign-accent: The interlanguage speech intelligibility benefit in Mandarin speakers of English

PubMed Central

Xie, Xin; Fowler, Carol A.

2013-01-01

This study examined the intelligibility of native and Mandarin-accented English speech for native English and native Mandarin listeners. In the latter group, it also examined the role of the language environment and English proficiency. Three groups of listeners were tested: native English listeners (NE), Mandarin-speaking Chinese listeners in the US (M-US) and Mandarin listeners in Beijing, China (M-BJ). As a group, M-US and M-BJ listeners were matched on English proficiency and age of acquisition. A nonword transcription task was used. Identification accuracy for word-final stops in the nonwords established two independent interlanguage intelligibility effects. An interlanguage speech intelligibility benefit for listeners (ISIB-L) was manifest by both groups of Mandarin listeners outperforming native English listeners in identification of Mandarin-accented speech. In the benefit for talkers (ISIB-T), only M-BJ listeners were more accurate identifying Mandarin-accented speech than native English speech. Thus, both Mandarin groups demonstrated an ISIB-L while only the M-BJ group overall demonstrated an ISIB-T. The English proficiency of listeners was found to modulate the magnitude of the ISIB-T in both groups. Regression analyses also suggested that the listener groups differ in their use of acoustic information to identify voicing in stop consonants. PMID:24293741

Detergent-enzymatic decellularization of swine blood vessels: insight on mechanical properties for vascular tissue engineering.

PubMed

Pellegata, Alessandro F; Asnaghi, M Adelaide; Stefani, Ilaria; Maestroni, Anna; Maestroni, Silvia; Dominioni, Tommaso; Zonta, Sandro; Zerbini, Gianpaolo; Mantero, Sara

2013-01-01

Small caliber vessels substitutes still remain an unmet clinical need; few autologous substitutes are available, while synthetic grafts show insufficient patency in the long term. Decellularization is the complete removal of all cellular and nuclear matters from a tissue while leaving a preserved extracellular matrix representing a promising tool for the generation of acellular scaffolds for tissue engineering, already used for various tissues with positive outcomes. The aim of this work is to investigate the effect of a detergent-enzymatic decellularization protocol on swine arteries in terms of cell removal, extracellular matrix preservation, and mechanical properties. Furthermore, the effect of storage at -80°C on the mechanical properties of the tissue is evaluated. Swine arteries were harvested, frozen, and decellularized; histological analysis revealed complete cell removal and preserved extracellular matrix. Furthermore, the residual DNA content in decellularized tissues was far low compared to native one. Mechanical testings were performed on native, defrozen, and decellularized tissues; no statistically significant differences were reported for Young's modulus, ultimate stress, compliance, burst pressure, and suture retention strength, while ultimate strain and stress relaxation of decellularized vessels were significantly different from the native ones. Considering the overall results, the process was confirmed to be suitable for the generation of acellular scaffolds for vascular tissue engineering.

Clonal analysis of lineage fate in native haematopoiesis.

PubMed

Rodriguez-Fraticelli, Alejo E; Wolock, Samuel L; Weinreb, Caleb S; Panero, Riccardo; Patel, Sachin H; Jankovic, Maja; Sun, Jianlong; Calogero, Raffaele A; Klein, Allon M; Camargo, Fernando D

2018-01-11

Haematopoiesis, the process of mature blood and immune cell production, is functionally organized as a hierarchy, with self-renewing haematopoietic stem cells and multipotent progenitor cells sitting at the very top. Multiple models have been proposed as to what the earliest lineage choices are in these primitive haematopoietic compartments, the cellular intermediates, and the resulting lineage trees that emerge from them. Given that the bulk of studies addressing lineage outcomes have been performed in the context of haematopoietic transplantation, current models of lineage branching are more likely to represent roadmaps of lineage potential than native fate. Here we use transposon tagging to clonally trace the fates of progenitors and stem cells in unperturbed haematopoiesis. Our results describe a distinct clonal roadmap in which the megakaryocyte lineage arises largely independently of other haematopoietic fates. Our data, combined with single-cell RNA sequencing, identify a functional hierarchy of unilineage- and oligolineage-producing clones within the multipotent progenitor population. Finally, our results demonstrate that traditionally defined long-term haematopoietic stem cells are a significant source of megakaryocyte-restricted progenitors, suggesting that the megakaryocyte lineage is the predominant native fate of long-term haematopoietic stem cells. Our study provides evidence for a substantially revised roadmap for unperturbed haematopoiesis, and highlights unique properties of multipotent progenitors and haematopoietic stem cells in situ.

Biological and mechanical evaluation of a Bio-Hybrid scaffold for autologous valve tissue engineering.

PubMed

Jahnavi, S; Saravanan, U; Arthi, N; Bhuvaneshwar, G S; Kumary, T V; Rajan, S; Verma, R S

2017-04-01

Major challenge in heart valve tissue engineering for paediatric patients is the development of an autologous valve with regenerative capacity. Hybrid tissue engineering approach is recently gaining popularity to design scaffolds with desired biological and mechanical properties that can remodel post implantation. In this study, we fabricated aligned nanofibrous Bio-Hybrid scaffold made of decellularized bovine pericardium: polycaprolactone-chitosan with optimized polymer thickness to yield the desired biological and mechanical properties. CD44 + , αSMA + , Vimentin + and CD105 - human valve interstitial cells were isolated and seeded on these Bio-Hybrid scaffolds. Subsequent biological evaluation revealed interstitial cell proliferation with dense extra cellular matrix deposition that indicated the viability for growth and proliferation of seeded cells on the scaffolds. Uniaxial mechanical tests along axial direction showed that the Bio-Hybrid scaffolds has at least 20 times the strength of the native valves and its stiffness is nearly 3 times more than that of native valves. Biaxial and uniaxial mechanical studies on valve interstitial cells cultured Bio-Hybrid scaffolds revealed that the response along the axial and circumferential direction was different, similar to native valves. Overall, our findings suggest that Bio-Hybrid scaffold is a promising material for future development of regenerative heart valve constructs in children. Copyright © 2016 Elsevier B.V. All rights reserved.

Role of non-native electrostatic interactions in the coupled folding and binding of PUMA with Mcl-1

PubMed Central

Chu, Wen-Ting; Clarke, Jane; Shammas, Sarah L.; Wang, Jin

2017-01-01

PUMA, which belongs to the BH3-only protein family, is an intrinsically disordered protein (IDP). It binds to its cellular partner Mcl-1 through its BH3 motif, which folds upon binding into an α helix. We have applied a structure-based coarse-grained model, with an explicit Debye—Hückel charge model, to probe the importance of electrostatic interactions both in the early and the later stages of this model coupled folding and binding process. This model was carefully calibrated with the experimental data on helical content and affinity, and shown to be consistent with previously published experimental data on binding rate changes with respect to ionic strength. We find that intramolecular electrostatic interactions influence the unbound states of PUMA only marginally. Our results further suggest that intermolecular electrostatic interactions, and in particular non-native electrostatic interactions, are involved in formation of the initial encounter complex. We are able to reveal the binding mechanism in more detail than is possible using experimental data alone however, and in particular we uncover the role of non-native electrostatic interactions. We highlight the potential importance of such electrostatic interactions for describing the binding reactions of IDPs. Such approaches could be used to provide predictions for the results of mutational studies. PMID:28369057

Cytoprotective Mechanisms Mediated by Polyphenols from Chilean Native Berries against Free Radical-Induced Damage on AGS Cells

PubMed Central

Theoduloz, Cristina; López-Alarcón, Camilo; Dorta, Eva

2017-01-01

The prevalence of cytoprotective mechanisms induced by polyphenols such as activation of intracellular antioxidant responses (ICM) and direct free radical scavenging was investigated in native Chilean species of strawberries, raspberries, and currants. Human gastric epithelial cells were co- and preincubated with polyphenolic-enriched extracts (PEEs) from Chilean raspberries (Rubus geoides), strawberries (Fragaria chiloensis ssp. chiloensis f. chiloensis), and currants (Ribes magellanicum) and challenged with peroxyl and hydroxyl radicals. Cellular protection was determined in terms of cell viability, glyoxalase I and glutathione s-transferases activities, and carboxymethyl lysine (CML) and malondialdehyde levels. Our results indicate that cytoprotection induced by ICM was the prevalent mechanism for Rubus geoides and F. chiloensis. This agreed with increased levels of glyoxalase I and glutathione S-transferase activities in cells preincubated with PEEs. ORAC index indicated that F. chiloensis was the most efficient peroxyl radical scavenger. Moreover, ICM mediated by F. chiloensis was effective in protecting cells from CML accumulation in contrast to the protective effects induced by free radical scavenging. Our results indicate that although both polyphenol-mediated mechanisms can exert protective effects, ICM was the most prevalent in AGS cells. These results suggest a potential use of these native berries as functional food. PMID:28553436

Identification of potential novel interaction partners of the sodium-activated potassium channels Slick and Slack in mouse brain.

PubMed

Rizzi, Sandra; Schwarzer, Christoph; Kremser, Leopold; Lindner, Herbert H; Knaus, Hans-Günther

2015-12-01

The sodium-activated potassium channels Slick (Slo2.1, KCNT2) and Slack (Slo2.2, KCNT1) are paralogous channels of the Slo family of high-conductance potassium channels. Slick and Slack channels are widely distributed in the mammalian CNS and they play a role in slow afterhyperpolarization, generation of depolarizing afterpotentials and in setting and stabilizing the resting potential. In the present study we used a combined approach of (co)-immunoprecipitation studies, Western blot analysis, double immunofluorescence and mass spectrometric sequencing in order to investigate protein-protein interactions of the Slick and Slack channels. The data strongly suggest that Slick and Slack channels co-assemble into identical cellular complexes. Double immunofluorescence experiments revealed that Slick and Slack channels co-localize in distinct mouse brain regions. Moreover, we identified the small cytoplasmic protein beta-synuclein and the transmembrane protein 263 (TMEM 263) as novel interaction partners of both, native Slick and Slack channels. In addition, the inactive dipeptidyl-peptidase (DPP 10) and the synapse associated protein 102 (SAP 102) were identified as constituents of the native Slick and Slack channel complexes in the mouse brain. This study presents new insights into protein-protein interactions of native Slick and Slack channels in the mouse brain.