Induced Pluripotent Stem Cells Reveal Functional Differences Between Drugs Currently Investigated in Patients With Hutchinson-Gilford Progeria Syndrome

PubMed Central

Blondel, Sophie; Jaskowiak, Anne-Laure; Egesipe, Anne-Laure; Le Corf, Amelie; Navarro, Claire; Cordette, Véronique; Martinat, Cécile; Laabi, Yacine; Djabali, Karima; de Sandre-Giovannoli, Annachiara; Levy, Nicolas; Peschanski, Marc

2014-01-01

Hutchinson-Gilford progeria syndrome is a rare congenital disease characterized by premature aging in children. Identification of the mutation and related molecular mechanisms has rapidly led to independent clinical trials testing different marketed drugs with a preclinically documented impact on those mechanisms. However, the extensive functional effects of those drugs remain essentially unexplored. We have undertaken a systematic comparative study of the three main treatments currently administered or proposed to progeria-affected children, namely, a farnesyltransferase inhibitor, the combination of an aminobisphosphonate and a statin (zoledronate and pravastatin), and the macrolide antibiotic rapamycin. This work was based on the assumption that mesodermal stem cells, which are derived from Hutchinson-Gilford progeria syndrome-induced pluripotent stem cells expressing major defects associated with the disease, may be instrumental to revealing such effects. Whereas all three treatments significantly improved misshapen cell nuclei typically associated with progeria, differences were observed in terms of functional improvement in prelamin A farnesylation, progerin expression, defective cell proliferation, premature osteogenic differentiation, and ATP production. Finally, we have evaluated the effect of the different drug combinations on this cellular model. This study revealed no additional benefit compared with single-drug treatments, whereas a cytostatic effect equivalent to that of a farnesyltransferase inhibitor alone was systematically observed. Altogether, these results reveal the complexity of the modes of action of different drugs, even when they have been selected on the basis of a similar mechanistic hypothesis, and underscore the use of induced pluripotent stem cell derivatives as a critical and powerful tool for standardized, comparative pharmacological studies. PMID:24598781

Structural properties of prokaryotic promoter regions correlate with functional features.

PubMed

Meysman, Pieter; Collado-Vides, Julio; Morett, Enrique; Viola, Roberto; Engelen, Kristof; Laukens, Kris

2014-01-01

The structural properties of the DNA molecule are known to play a critical role in transcription. In this paper, the structural profiles of promoter regions were studied within the context of their diversity and their function for eleven prokaryotic species; Escherichia coli, Klebsiella pneumoniae, Salmonella Typhimurium, Pseudomonas auroginosa, Geobacter sulfurreducens Helicobacter pylori, Chlamydophila pneumoniae, Synechocystis sp., Synechoccocus elongates, Bacillus anthracis, and the archaea Sulfolobus solfataricus. The main anchor point for these promoter regions were transcription start sites identified through high-throughput experiments or collected within large curated databases. Prokaryotic promoter regions were found to be less stable and less flexible than the genomic mean across all studied species. However, direct comparison between species revealed differences in their structural profiles that can not solely be explained by the difference in genomic GC content. In addition, comparison with functional data revealed that there are patterns in the promoter structural profiles that can be linked to specific functional loci, such as sigma factor regulation or transcription factor binding. Interestingly, a novel structural element clearly visible near the transcription start site was found in genes associated with essential cellular functions and growth in several species. Our analyses reveals the great diversity in promoter structural profiles both between and within prokaryotic species. We observed relationships between structural diversity and functional features that are interesting prospects for further research to yet uncharacterized functional loci defined by DNA structural properties.

Outfielders playing in the infield: functions of aging-associated "nuclear" proteins in the mitochondria.

PubMed

Czypiorski, P; Altschmied, J; Rabanter, L L; Goy, C; Jakob, S; Haendeler, J

2014-01-01

Over the past few years it has become clear that mitochondria are not merely the powerhouses of cells. Proteome-analyses of mitochondria from different organisms and organs revealed that more than 1000 proteins are localized in and/or on mitochondria. This by far exceeds the number of proteins required for classical mitochondrial functions, e.g. the respiratory chain, the tricarboxylic acid cycle, fatty acid oxidation and apoptosis. This suggests that many of these proteins have other, as yet unknown functions. Several proteins with well-described nuclear functions, like the transcription factor FoxO3A or the Telomerase Reverse Transcriptase, have recently been shown to be localized also within the mitochondria. This mini-review will focus on the description of the functions of these two proteins in the nucleus and in the mitochondria - as two examples of many more proteins, which are yet to be uncovered. It will give insights into the role of these proteins within different organelles of the cell and will reveal that the functions of the proteins are probably not the same in the nucleus and the mitochondria. Therefore, these differences have to be considered when targeting proteins for therapeutic approaches.

Revealing common disease mechanisms shared by tumors of different tissues of origin through semantic representation of genomic alterations and topic modeling.

PubMed

Chen, Vicky; Paisley, John; Lu, Xinghua

2017-03-14

Cancer is a complex disease driven by somatic genomic alterations (SGAs) that perturb signaling pathways and consequently cellular function. Identifying patterns of pathway perturbations would provide insights into common disease mechanisms shared among tumors, which is important for guiding treatment and predicting outcome. However, identifying perturbed pathways is challenging, because different tumors can have the same perturbed pathways that are perturbed by different SGAs. Here, we designed novel semantic representations that capture the functional similarity of distinct SGAs perturbing a common pathway in different tumors. Combining this representation with topic modeling would allow us to identify patterns in altered signaling pathways. We represented each gene with a vector of words describing its function, and we represented the SGAs of a tumor as a text document by pooling the words representing individual SGAs. We applied the nested hierarchical Dirichlet process (nHDP) model to a collection of tumors of 5 cancer types from TCGA. We identified topics (consisting of co-occurring words) representing the common functional themes of different SGAs. Tumors were clustered based on their topic associations, such that each cluster consists of tumors sharing common functional themes. The resulting clusters contained mixtures of cancer types, which indicates that different cancer types can share disease mechanisms. Survival analysis based on the clusters revealed significant differences in survival among the tumors of the same cancer type that were assigned to different clusters. The results indicate that applying topic modeling to semantic representations of tumors identifies patterns in the combinations of altered functional pathways in cancer.

Deciphering life history transcriptomes in different environments

PubMed Central

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

2014-01-01

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

An Investigation of Dental Luting Cement Solubility as a Function of the Marginal Gap.

DTIC Science & Technology

1988-05-01

way ANOVA for the Phase 1 Diffusion Study revealed that there were statistically significant differences between the test groups. A Duncan’s Multiple...cement. The 25, 50, and 75 micron groups demonstrated no statistically significant differences in the amount of remaining luting cement. ( p< 0.05) A...one-way ANOVA was also performed on Phase 2 Dynamic Study. This test revealed that there were statistically significant differences among the test

A mechanism producing power law etc. distributions

NASA Astrophysics Data System (ADS)

Li, Heling; Shen, Hongjun; Yang, Bin

2017-07-01

Power law distribution is playing an increasingly important role in the complex system study. Based on the insolvability of complex systems, the idea of incomplete statistics is utilized and expanded, three different exponential factors are introduced in equations about the normalization condition, statistical average and Shannon entropy, with probability distribution function deduced about exponential function, power function and the product form between power function and exponential function derived from Shannon entropy and maximal entropy principle. So it is shown that maximum entropy principle can totally replace equal probability hypothesis. Owing to the fact that power and probability distribution in the product form between power function and exponential function, which cannot be derived via equal probability hypothesis, can be derived by the aid of maximal entropy principle, it also can be concluded that maximal entropy principle is a basic principle which embodies concepts more extensively and reveals basic principles on motion laws of objects more fundamentally. At the same time, this principle also reveals the intrinsic link between Nature and different objects in human society and principles complied by all.

Neurodegenerative disease mutations in TREM2 reveal a functional surface and distinct loss-of-function mechanisms

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

Kober, Daniel L.; Alexander-Brett, Jennifer M.; Karch, Celeste M.

Genetic variations in the myeloid immune receptor TREM2 are linked to several neurodegenerative diseases. To determine how TREM2 variants contribute to these diseases, we performed structural and functional studies of wild-type and variant proteins. Our 3.1 Å TREM2 crystal structure revealed that mutations found in Nasu-Hakola disease are buried whereas Alzheimer’s disease risk variants are found on the surface, suggesting that these mutations have distinct effects on TREM2 function. Biophysical and cellular methods indicate that Nasu-Hakola mutations impact protein stability and decrease folded TREM2 surface expression, whereas Alzheimer’s risk variants impact binding to a TREM2 ligand. Additionally, the Alzheimer’s riskmore » variants appear to epitope map a functional surface on TREM2 that is unique within the larger TREM family. These findings provide a guide to structural and functional differences among genetic variants of TREM2, indicating that therapies targeting the TREM2 pathway should be tailored to these genetic and functional differences with patient-specific medicine approaches for neurodegenerative disorders.« less

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

PubMed

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

2017-01-09

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

Comparative Metabolomics of Mycoplasma bovis and Mycoplasma gallisepticum Reveals Fundamental Differences in Active Metabolic Pathways and Suggests Novel Gene Annotations.

PubMed

Masukagami, Y; De Souza, D P; Dayalan, S; Bowen, C; O'Callaghan, S; Kouremenos, K; Nijagal, B; Tull, D; Tivendale, K A; Markham, P F; McConville, M J; Browning, G F; Sansom, F M

2017-01-01

Mycoplasmas are simple, but successful parasites that have the smallest genome of any free-living cell and are thought to have a highly streamlined cellular metabolism. Here, we have undertaken a detailed metabolomic analysis of two species, Mycoplasma bovis and Mycoplasma gallisepticum , which cause economically important diseases in cattle and poultry, respectively. Untargeted gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry analyses of mycoplasma metabolite extracts revealed significant differences in the steady-state levels of many metabolites in central carbon metabolism, while 13 C stable isotope labeling studies revealed marked differences in carbon source utilization. These data were mapped onto in silico metabolic networks predicted from genome wide annotations. The analyses elucidated distinct differences, including a clear difference in glucose utilization, with a marked decrease in glucose uptake and glycolysis in M. bovis compared to M. gallisepticum , which may reflect differing host nutrient availabilities. The 13 C-labeling patterns also revealed several functional metabolic pathways that were previously unannotated in these species, allowing us to assign putative enzyme functions to the products of a number of genes of unknown function, especially in M. bovis . This study demonstrates the considerable potential of metabolomic analyses to assist in characterizing significant differences in the metabolism of different bacterial species and in improving genome annotation. IMPORTANCE Mycoplasmas are pathogenic bacteria that cause serious chronic infections in production animals, resulting in considerable losses worldwide, as well as causing disease in humans. These bacteria have extremely reduced genomes and are thought to have limited metabolic flexibility, even though they are highly successful persistent parasites in a diverse number of species. The extent to which different Mycoplasma species are capable of catabolizing host carbon sources and nutrients, or synthesizing essential metabolites, remains poorly defined. We have used advanced metabolomic techniques to identify metabolic pathways that are active in two species of Mycoplasma that infect distinct hosts (poultry and cattle). We show that these species exhibit marked differences in metabolite steady-state levels and carbon source utilization. This information has been used to functionally characterize previously unknown genes in the genomes of these pathogens. These species-specific differences are likely to reflect important differences in host nutrient levels and pathogenic mechanisms.

Master stability functions reveal diffusion-driven pattern formation in networks

NASA Astrophysics Data System (ADS)

Brechtel, Andreas; Gramlich, Philipp; Ritterskamp, Daniel; Drossel, Barbara; Gross, Thilo

2018-03-01

We study diffusion-driven pattern formation in networks of networks, a class of multilayer systems, where different layers have the same topology, but different internal dynamics. Agents are assumed to disperse within a layer by undergoing random walks, while they can be created or destroyed by reactions between or within a layer. We show that the stability of homogeneous steady states can be analyzed with a master stability function approach that reveals a deep analogy between pattern formation in networks and pattern formation in continuous space. For illustration, we consider a generalized model of ecological meta-food webs. This fairly complex model describes the dispersal of many different species across a region consisting of a network of individual habitats while subject to realistic, nonlinear predator-prey interactions. In this example, the method reveals the intricate dependence of the dynamics on the spatial structure. The ability of the proposed approach to deal with this fairly complex system highlights it as a promising tool for ecology and other applications.

Screening of the chemical reactivity of three different graphite sources using the formation of reductively alkylated graphene as a model reaction.

PubMed

Knirsch, Kathrin C; Englert, Jan M; Dotzer, Christoph; Hauke, Frank; Hirsch, Andreas

2013-11-28

Reductive alkylation of three graphite starting materials G(flake), G(powder), and G(spherical) reveals pronounced differences in the obtained covalently functionalized graphene with respect to the degree of functionalization, exfoliation efficiency and product homogeneity, as demonstrated by statistical Raman microscopy (SRM), TGA/MS, IR-spectroscopy and solubility behavior.

Dynamic functional connectivity analysis reveals transient states of dysconnectivity in schizophrenia.

PubMed

Damaraju, E; Allen, E A; Belger, A; Ford, J M; McEwen, S; Mathalon, D H; Mueller, B A; Pearlson, G D; Potkin, S G; Preda, A; Turner, J A; Vaidya, J G; van Erp, T G; Calhoun, V D

2014-01-01

Schizophrenia is a psychotic disorder characterized by functional dysconnectivity or abnormal integration between distant brain regions. Recent functional imaging studies have implicated large-scale thalamo-cortical connectivity as being disrupted in patients. However, observed connectivity differences in schizophrenia have been inconsistent between studies, with reports of hyperconnectivity and hypoconnectivity between the same brain regions. Using resting state eyes-closed functional imaging and independent component analysis on a multi-site data that included 151 schizophrenia patients and 163 age- and gender matched healthy controls, we decomposed the functional brain data into 100 components and identified 47 as functionally relevant intrinsic connectivity networks. We subsequently evaluated group differences in functional network connectivity, both in a static sense, computed as the pairwise Pearson correlations between the full network time courses (5.4 minutes in length), and a dynamic sense, computed using sliding windows (44 s in length) and k-means clustering to characterize five discrete functional connectivity states. Static connectivity analysis revealed that compared to healthy controls, patients show significantly stronger connectivity, i.e., hyperconnectivity, between the thalamus and sensory networks (auditory, motor and visual), as well as reduced connectivity (hypoconnectivity) between sensory networks from all modalities. Dynamic analysis suggests that (1), on average, schizophrenia patients spend much less time than healthy controls in states typified by strong, large-scale connectivity, and (2), that abnormal connectivity patterns are more pronounced during these connectivity states. In particular, states exhibiting cortical-subcortical antagonism (anti-correlations) and strong positive connectivity between sensory networks are those that show the group differences of thalamic hyperconnectivity and sensory hypoconnectivity. Group differences are weak or absent during other connectivity states. Dynamic analysis also revealed hypoconnectivity between the putamen and sensory networks during the same states of thalamic hyperconnectivity; notably, this finding cannot be observed in the static connectivity analysis. Finally, in post-hoc analyses we observed that the relationships between sub-cortical low frequency power and connectivity with sensory networks is altered in patients, suggesting different functional interactions between sub-cortical nuclei and sensorimotor cortex during specific connectivity states. While important differences between patients with schizophrenia and healthy controls have been identified, one should interpret the results with caution given the history of medication in patients. Taken together, our results support and expand current knowledge regarding dysconnectivity in schizophrenia, and strongly advocate the use of dynamic analyses to better account for and understand functional connectivity differences.

Dynamic functional connectivity analysis reveals transient states of dysconnectivity in schizophrenia

PubMed Central

Damaraju, E.; Allen, E.A.; Belger, A.; Ford, J.M.; McEwen, S.; Mathalon, D.H.; Mueller, B.A.; Pearlson, G.D.; Potkin, S.G.; Preda, A.; Turner, J.A.; Vaidya, J.G.; van Erp, T.G.; Calhoun, V.D.

2014-01-01

Schizophrenia is a psychotic disorder characterized by functional dysconnectivity or abnormal integration between distant brain regions. Recent functional imaging studies have implicated large-scale thalamo-cortical connectivity as being disrupted in patients. However, observed connectivity differences in schizophrenia have been inconsistent between studies, with reports of hyperconnectivity and hypoconnectivity between the same brain regions. Using resting state eyes-closed functional imaging and independent component analysis on a multi-site data that included 151 schizophrenia patients and 163 age- and gender matched healthy controls, we decomposed the functional brain data into 100 components and identified 47 as functionally relevant intrinsic connectivity networks. We subsequently evaluated group differences in functional network connectivity, both in a static sense, computed as the pairwise Pearson correlations between the full network time courses (5.4 minutes in length), and a dynamic sense, computed using sliding windows (44 s in length) and k-means clustering to characterize five discrete functional connectivity states. Static connectivity analysis revealed that compared to healthy controls, patients show significantly stronger connectivity, i.e., hyperconnectivity, between the thalamus and sensory networks (auditory, motor and visual), as well as reduced connectivity (hypoconnectivity) between sensory networks from all modalities. Dynamic analysis suggests that (1), on average, schizophrenia patients spend much less time than healthy controls in states typified by strong, large-scale connectivity, and (2), that abnormal connectivity patterns are more pronounced during these connectivity states. In particular, states exhibiting cortical–subcortical antagonism (anti-correlations) and strong positive connectivity between sensory networks are those that show the group differences of thalamic hyperconnectivity and sensory hypoconnectivity. Group differences are weak or absent during other connectivity states. Dynamic analysis also revealed hypoconnectivity between the putamen and sensory networks during the same states of thalamic hyperconnectivity; notably, this finding cannot be observed in the static connectivity analysis. Finally, in post-hoc analyses we observed that the relationships between sub-cortical low frequency power and connectivity with sensory networks is altered in patients, suggesting different functional interactions between sub-cortical nuclei and sensorimotor cortex during specific connectivity states. While important differences between patients with schizophrenia and healthy controls have been identified, one should interpret the results with caution given the history of medication in patients. Taken together, our results support and expand current knowledge regarding dysconnectivity in schizophrenia, and strongly advocate the use of dynamic analyses to better account for and understand functional connectivity differences. PMID:25161896

Functional Assays and Metagenomic Analyses Reveals Differences between the Microbial Communities Inhabiting the Soil Horizons of a Norway Spruce Plantation

PubMed Central

Uroz, Stéphane; Ioannidis, Panos; Lengelle, Juliette; Cébron, Aurélie; Morin, Emmanuelle; Buée, Marc; Martin, Francis

2013-01-01

In temperate ecosystems, acidic forest soils are among the most nutrient-poor terrestrial environments. In this context, the long-term differentiation of the forest soils into horizons may impact the assembly and the functions of the soil microbial communities. To gain a more comprehensive understanding of the ecology and functional potentials of these microbial communities, a suite of analyses including comparative metagenomics was applied on independent soil samples from a spruce plantation (Breuil-Chenue, France). The objectives were to assess whether the decreasing nutrient bioavailability and pH variations that naturally occurs between the organic and mineral horizons affects the soil microbial functional biodiversity. The 14 Gbp of pyrosequencing and Illumina sequences generated in this study revealed complex microbial communities dominated by bacteria. Detailed analyses showed that the organic soil horizon was significantly enriched in sequences related to Bacteria, Chordata, Arthropoda and Ascomycota. On the contrary the mineral horizon was significantly enriched in sequences related to Archaea. Our analyses also highlighted that the microbial communities inhabiting the two soil horizons differed significantly in their functional potentials according to functional assays and MG-RAST analyses, suggesting a functional specialisation of these microbial communities. Consistent with this specialisation, our shotgun metagenomic approach revealed a significant increase in the relative abundance of sequences related glycoside hydrolases in the organic horizon compared to the mineral horizon that was significantly enriched in glycoside transferases. This functional stratification according to the soil horizon was also confirmed by a significant correlation between the functional assays performed in this study and the functional metagenomic analyses. Together, our results suggest that the soil stratification and particularly the soil resource availability impact the functional diversity and to a lesser extent the taxonomic diversity of the bacterial communities. PMID:23418476

[NUCLEAR STRUCTURE IN THE SECRETORY CELLS OF MAMMARY GLANDS IN LACTATING AND NON-LACTATING RATS].

PubMed

Tyutina, K V; Skopichev, V G; Bogolyubov, D S; Bogolyubova, I O

2016-01-01

The features of structural and functional organization of the main nuclear compartments and distribution of their key molecular components (chromatin-remodeling protein ATRX, RNA polymerase I and II, and the splicing factor SC35) has been studied in the nuclei of mammary gland cells at different functional states. No significant differences between the nuclei of the cells in the lactating and non-lactating mammary glands have been revealed at the ultrastructural level. At the same time, photometric analysis has revealed higher intensity of nucleoplasmic immunofluorescent staining of mammary glands in the lactating animals when antibodies against the proteins ATRX and SC35 were used. Apparently, this observation reflects the changes of the structural and functional status of chromatin as well as the redistribution of splicing factors between the sites of their deposition and transcription.

Temporal Dynamics Assessment of Spatial Overlap Pattern of Functional Brain Networks Reveals Novel Functional Architecture of Cerebral Cortex.

PubMed

Jiang, Xi; Li, Xiang; Lv, Jinglei; Zhao, Shijie; Zhang, Shu; Zhang, Wei; Zhang, Tuo; Han, Junwei; Guo, Lei; Liu, Tianming

2018-06-01

Various studies in the brain mapping field have demonstrated that there exist multiple concurrent functional networks that are spatially overlapped and interacting with each other during specific task performance to jointly realize the total brain function. Assessing such spatial overlap patterns of functional networks (SOPFNs) based on functional magnetic resonance imaging (fMRI) has thus received increasing interest for brain function studies. However, there are still two crucial issues to be addressed. First, the SOPFNs are assessed over the entire fMRI scan assuming the temporal stationarity, while possibly time-dependent dynamics of the SOPFNs is not sufficiently explored. Second, the SOPFNs are assessed within individual subjects, while group-wise consistency of the SOPFNs is largely unknown. To address the two issues, we propose a novel computational framework of group-wise sparse representation of whole-brain fMRI temporal segments to assess the temporal dynamic spatial patterns of SOPFNs that are consistent across different subjects. Experimental results based on the recently publicly released Human Connectome Project grayordinate task fMRI data demonstrate that meaningful SOPFNs exhibiting dynamic spatial patterns across different time periods are effectively and robustly identified based on the reconstructed concurrent functional networks via the proposed framework. Specifically, those SOPFNs locate significantly more on gyral regions than on sulcal regions across different time periods. These results reveal novel functional architecture of cortical gyri and sulci. Moreover, these results help better understand functional dynamics mechanisms of cerebral cortex in the future.

Within-Cohort Age-Related Differences in Cognitive Functioning

PubMed Central

Salthouse, Timothy A.

2013-01-01

It is widely accepted that the level of cognitive functioning can be influenced by characteristics of the environment that change over time. Many developmental researchers have referred to these influences as cohort effects, and have used year of birth as the basis for determining cohort membership. Furthermore, age-related differences in cognitive functioning are sometimes assumed to be primarily attributable to cohort differences, which implies that differences between birth cohorts should be much larger than differences within birth cohorts. Comparisons of composite scores for five cognitive abilities in different people tested at different ages in different years revealed that within-cohort differences across ages were often as large as between-cohort differences across ages. These results lead to questions about the practice of relying on birth cohort to represent influences on cognitive functioning associated with temporal shifts in characteristics of the environment. PMID:23319401

The Powdering Process with a Set of Ceramic Mills for Green Tea Promoted Catechin Extraction and the ROS Inhibition Effect.

PubMed

Fujioka, Kouki; Iwamoto, Takeo; Shima, Hidekazu; Tomaru, Keiko; Saito, Hideki; Ohtsuka, Masaki; Yoshidome, Akihiro; Kawamura, Yuri; Manome, Yoshinobu

2016-04-11

For serving green tea, there are two prominent methods: steeping the leaf or the powdered leaf (matcha style) in hot water. The purpose of the present study was to reveal chemical and functional differences before and after the powdering process of green tea leaf, since powdered green tea may contribute to expanding the functionality because of the different ingesting style. In this study, we revealed that the powdering process with a ceramic mill and stirring in hot water increased the average extracted concentration of epigallocatechin gallate (EGCG) by more than three times compared with that in leaf tea using high-performance liquid chromatography (HPLC) and liquid chromatography-tandem mass Spectrometry (LC-MS/MS) analyses. Moreover, powdered green tea has a higher inhibition effect of reactive oxygen species (ROS) production in vitro compared with the same amount of leaf tea. Our data suggest that powdered green tea might have a different function from leaf tea due to the higher catechin contents and particles.

Differential Adjustment Among Rural Adolescents Exposed to Family Violence

PubMed Central

Sianko, Natallia; Hedge, Jasmine M.; McDonell, James R.

2016-01-01

This study examines differences in psychological adjustment in a sample of rural adolescents who have been exposed to family violence. Self-report questionnaires were administered to 580 adolescents and their primary caregivers. The results revealed that over two thirds of the study participants (68.8%) had been exposed to violence in their families. As hypothesized, cluster analysis identified several profiles among adolescents, distinguished by their psychological and emotional functioning: well adjusted (46.2%), moderately adjusted (44.3%), and struggling (9.5%). Discriminant function analysis confirmed the groupings and revealed that family functioning was among the most influential factors explaining adjustment differences. Multivariate analyses of variance (MANOVAs) further showed that adolescents from each of the three adjustment profiles reported significantly different levels of family social support, parental involvement, and perceived neighborhood safety. Overall, the results confirm heterogeneity of adolescent adaptation in the aftermath of family violence and provide insights into family and neighborhood factors that account for variability in adolescents’ reactions to violence. Implications for future research and practical interventions are discussed. PMID:27106255

Adaptation to High Ethanol Reveals Complex Evolutionary Pathways

PubMed Central

Das, Anupam; Espinosa-Cantú, Adriana; De Maeyer, Dries; Arslan, Ahmed; Van Pee, Michiel; van der Zande, Elisa; Meert, Wim; Yang, Yudi; Zhu, Bo; Marchal, Kathleen; DeLuna, Alexander; Van Noort, Vera; Jelier, Rob; Verstrepen, Kevin J.

2015-01-01

Tolerance to high levels of ethanol is an ecologically and industrially relevant phenotype of microbes, but the molecular mechanisms underlying this complex trait remain largely unknown. Here, we use long-term experimental evolution of isogenic yeast populations of different initial ploidy to study adaptation to increasing levels of ethanol. Whole-genome sequencing of more than 30 evolved populations and over 100 adapted clones isolated throughout this two-year evolution experiment revealed how a complex interplay of de novo single nucleotide mutations, copy number variation, ploidy changes, mutator phenotypes, and clonal interference led to a significant increase in ethanol tolerance. Although the specific mutations differ between different evolved lineages, application of a novel computational pipeline, PheNetic, revealed that many mutations target functional modules involved in stress response, cell cycle regulation, DNA repair and respiration. Measuring the fitness effects of selected mutations introduced in non-evolved ethanol-sensitive cells revealed several adaptive mutations that had previously not been implicated in ethanol tolerance, including mutations in PRT1, VPS70 and MEX67. Interestingly, variation in VPS70 was recently identified as a QTL for ethanol tolerance in an industrial bio-ethanol strain. Taken together, our results show how, in contrast to adaptation to some other stresses, adaptation to a continuous complex and severe stress involves interplay of different evolutionary mechanisms. In addition, our study reveals functional modules involved in ethanol resistance and identifies several mutations that could help to improve the ethanol tolerance of industrial yeasts. PMID:26545090

Unique and shared roles of the posterior parietal and dorsolateral prefrontal cortex in cognitive functions

PubMed Central

Katsuki, Fumi; Constantinidis, Christos

2012-01-01

The dorsolateral prefrontal cortex (PFC) and posterior parietal cortex (PPC) are two parts of a broader brain network involved in the control of cognitive functions such as working-memory, spatial attention, and decision-making. The two areas share many functional properties and exhibit similar patterns of activation during the execution of mental operations. However, neurophysiological experiments in non-human primates have also documented subtle differences, revealing functional specialization within the fronto-parietal network. These differences include the ability of the PFC to influence memory performance, attention allocation, and motor responses to a greater extent, and to resist interference by distracting stimuli. In recent years, distinct cellular and anatomical differences have been identified, offering insights into how functional specialization is achieved. This article reviews the common functions and functional differences between the PFC and PPC, and their underlying mechanisms. PMID:22563310

Conservation of tubulin-binding sequences in TRPV1 throughout evolution.

PubMed

Sardar, Puspendu; Kumar, Abhishek; Bhandari, Anita; Goswami, Chandan

2012-01-01

Transient Receptor Potential Vanilloid sub type 1 (TRPV1), commonly known as capsaicin receptor can detect multiple stimuli ranging from noxious compounds, low pH, temperature as well as electromagnetic wave at different ranges. In addition, this receptor is involved in multiple physiological and sensory processes. Therefore, functions of TRPV1 have direct influences on adaptation and further evolution also. Availability of various eukaryotic genomic sequences in public domain facilitates us in studying the molecular evolution of TRPV1 protein and the respective conservation of certain domains, motifs and interacting regions that are functionally important. Using statistical and bioinformatics tools, our analysis reveals that TRPV1 has evolved about ∼420 million years ago (MYA). Our analysis reveals that specific regions, domains and motifs of TRPV1 has gone through different selection pressure and thus have different levels of conservation. We found that among all, TRP box is the most conserved and thus have functional significance. Our results also indicate that the tubulin binding sequences (TBS) have evolutionary significance as these stretch sequences are more conserved than many other essential regions of TRPV1. The overall distribution of positively charged residues within the TBS motifs is conserved throughout evolution. In silico analysis reveals that the TBS-1 and TBS-2 of TRPV1 can form helical structures and may play important role in TRPV1 function. Our analysis identifies the regions of TRPV1, which are important for structure-function relationship. This analysis indicates that tubulin binding sequence-1 (TBS-1) near the TRP-box forms a potential helix and the tubulin interactions with TRPV1 via TBS-1 have evolutionary significance. This interaction may be required for the proper channel function and regulation and may also have significance in the context of Taxol®-induced neuropathy.

Exploring the Phenotype of Phonological Reading Disability as a Function of the Phonological Deficit Severity: Evidence from the Error Analysis Paradigm in Arabic

ERIC Educational Resources Information Center

Taha, Haitham; Ibrahim, Raphiq; Khateb, Asaid

2014-01-01

The dominant error types were investigated as a function of phonological processing (PP) deficit severity in four groups of impaired readers. For this aim, an error analysis paradigm distinguishing between four error types was used. The findings revealed that the different types of impaired readers were characterized by differing predominant error…

Life in Oligotropic Desert Environments: Contrasting Taxonomic and Functional Diversity of Two Microbial Mats with Metagenomics

NASA Astrophysics Data System (ADS)

Bonilla-Rosso, G.; Peimbert, M.; Olmedo, G.; Alcaraz, L. D.; Eguiarte, L. E.; Souza, V.

2010-04-01

The metagenomic analysis of two microbial mats from the oligotrophic waters in the Cuatrociéngas basin reveals large differences both at taxonomic and functional level. These are explained in terms of environmental stability and nutrient availability.

Trait-based Modeling Reveals How Plankton Biodiversity-Ecosystem Function (BEF) Relationships Depend on Environmental Variability

NASA Astrophysics Data System (ADS)

Smith, S. L.; Chen, B.; Vallina, S. M.

2017-12-01

Biodiversity-Ecosystem Function (BEF) relationships, which are most commonly quantified in terms of productivity or total biomass yield, are known to depend on the timescale of the experiment or field study, both for terrestrial plants and phytoplankton, which have each been widely studied as model ecosystems. Although many BEF relationships are positive (i.e., increasing biodiversity enhances function), in some cases there is an optimal intermediate diversity level (i.e., a uni-modal relationship), and in other cases productivity decreases with certain measures of biodiversity. These differences in BEF relationships cannot be reconciled merely by differences in the timescale of experiments. We will present results from simulation experiments applying recently developed trait-based models of phytoplankton communities and ecosystems, using the `adaptive dynamics' framework to represent continuous distributions of size and other key functional traits. Controlled simulation experiments were conducted with different levels of phytoplankton size-diversity, which through trait-size correlations implicitly represents functional-diversity. One recent study applied a theoretical box model for idealized simulations at different frequencies of disturbance. This revealed how the shapes of BEF relationships depend systematically on the frequency of disturbance and associated nutrient supply. We will also present more recent results obtained using a trait-based plankton ecosystem model embedded in a three-dimensional ocean model applied to the North Pacific. This reveals essentially the same pattern in a spatially explicit model with more realistic environmental forcing. In the relatively more variable subarctic, productivity tends to increase with the size (and hence functional) diversity of phytoplankton, whereas productivity tends to decrease slightly with increasing size-diversity in the relatively calm subtropics. Continuous trait-based models can capture essential features of BEF relationships, while requiring far fewer calculations compared to typical plankton diversity models that explicitly simulate a great many idealized species.

Functional connectivity change as shared signal dynamics

PubMed Central

Cole, Michael W.; Yang, Genevieve J.; Murray, John D.; Repovš, Grega; Anticevic, Alan

2015-01-01

Background An increasing number of neuroscientific studies gain insights by focusing on differences in functional connectivity – between groups, individuals, temporal windows, or task conditions. We found using simulations that additional insights into such differences can be gained by forgoing variance normalization, a procedure used by most functional connectivity measures. Simulations indicated that these functional connectivity measures are sensitive to increases in independent fluctuations (unshared signal) in time series, consistently reducing functional connectivity estimates (e.g., correlations) even though such changes are unrelated to corresponding fluctuations (shared signal) between those time series. This is inconsistent with the common notion of functional connectivity as the amount of inter-region interaction. New Method Simulations revealed that a version of correlation without variance normalization – covariance – was able to isolate differences in shared signal, increasing interpretability of observed functional connectivity change. Simulations also revealed cases problematic for non-normalized methods, leading to a “covariance conjunction” method combining the benefits of both normalized and non-normalized approaches. Results We found that covariance and covariance conjunction methods can detect functional connectivity changes across a variety of tasks and rest in both clinical and non-clinical functional MRI datasets. Comparison with Existing Method(s) We verified using a variety of tasks and rest in both clinical and non-clinical functional MRI datasets that it matters in practice whether correlation, covariance, or covariance conjunction methods are used. Conclusions These results demonstrate the practical and theoretical utility of isolating changes in shared signal, improving the ability to interpret observed functional connectivity change. PMID:26642966

Temporal trend and source apportionment of water pollution in different functional zones of Qiantang River, China.

PubMed

Su, Shiliang; Li, Dan; Zhang, Qi; Xiao, Rui; Huang, Fang; Wu, Jiaping

2011-02-01

The increasingly serious river water pollution in developing countries poses great threat to environmental health and human welfare. The assignment of river function to specific uses, known as zoning, is a useful tool to reveal variations of water environmental adaptability to human impact. Therefore, characterizing the temporal trend and identifying responsible pollution sources in different functional zones could greatly improve our knowledge about human impacts on the river water environment. The aim of this study is to obtain a deeper understanding of temporal trends and sources of water pollution in different functional zones with a case study of the Qiantang River, China. Measurement data were obtained and pretreated for 13 variables from 41 monitoring sites in four categories of functional zones during the period 1996-2004. An exploratory approach, which combines smoothing and non-parametric statistical tests, was applied to characterize trends of four significant parameters (permanganate index, ammonia nitrogen, total cadmium and fluoride) accounting for differences among different functional zones identified by discriminant analysis. Aided by GIS, yearly pollution index (PI) for each monitoring site was further mapped to compare the within-group variations in temporal dynamics for different functional zones. Rotated principal component analysis and receptor model (absolute principle component score-multiple linear regression, APCS-MLR) revealed that potential pollution sources and their corresponding contributions varied among the four functional zones. Variations of APCS values for each site of one functional zone as well as their annual average values highlighted the uncertainties associated with cross space-time effects in source apportionment. All these results reinforce the notion that the concept of zoning should be taken seriously in water pollution control. Being applicable to other rivers, the framework of management-oriented source apportionment is thus believed to have potentials to offer new insights into water management and advance the source apportionment framework as an operational basis for national and local governments. © 2010 Elsevier Ltd. All rights reserved.

The Interaction Properties of the Human Rab GTPase Family – A Comparative Analysis Reveals Determinants of Molecular Binding Selectivity

PubMed Central

Stein, Matthias; Pilli, Manohar; Bernauer, Sabine; Habermann, Bianca H.; Zerial, Marino; Wade, Rebecca C.

2012-01-01

Background Rab GTPases constitute the largest subfamily of the Ras protein superfamily. Rab proteins regulate organelle biogenesis and transport, and display distinct binding preferences for effector and activator proteins, many of which have not been elucidated yet. The underlying molecular recognition motifs, binding partner preferences and selectivities are not well understood. Methodology/Principal Findings Comparative analysis of the amino acid sequences and the three-dimensional electrostatic and hydrophobic molecular interaction fields of 62 human Rab proteins revealed a wide range of binding properties with large differences between some Rab proteins. This analysis assists the functional annotation of Rab proteins 12, 14, 26, 37 and 41 and provided an explanation for the shared function of Rab3 and 27. Rab7a and 7b have very different electrostatic potentials, indicating that they may bind to different effector proteins and thus, exert different functions. The subfamily V Rab GTPases which are associated with endosome differ subtly in the interaction properties of their switch regions, and this may explain exchange factor specificity and exchange kinetics. Conclusions/Significance We have analysed conservation of sequence and of molecular interaction fields to cluster and annotate the human Rab proteins. The analysis of three dimensional molecular interaction fields provides detailed insight that is not available from a sequence-based approach alone. Based on our results, we predict novel functions for some Rab proteins and provide insights into their divergent functions and the determinants of their binding partner selectivity. PMID:22523562

Dynamic Changes in Amygdala Psychophysiological Connectivity Reveal Distinct Neural Networks for Facial Expressions of Basic Emotions.

PubMed

Diano, Matteo; Tamietto, Marco; Celeghin, Alessia; Weiskrantz, Lawrence; Tatu, Mona-Karina; Bagnis, Arianna; Duca, Sergio; Geminiani, Giuliano; Cauda, Franco; Costa, Tommaso

2017-03-27

The quest to characterize the neural signature distinctive of different basic emotions has recently come under renewed scrutiny. Here we investigated whether facial expressions of different basic emotions modulate the functional connectivity of the amygdala with the rest of the brain. To this end, we presented seventeen healthy participants (8 females) with facial expressions of anger, disgust, fear, happiness, sadness and emotional neutrality and analyzed amygdala's psychophysiological interaction (PPI). In fact, PPI can reveal how inter-regional amygdala communications change dynamically depending on perception of various emotional expressions to recruit different brain networks, compared to the functional interactions it entertains during perception of neutral expressions. We found that for each emotion the amygdala recruited a distinctive and spatially distributed set of structures to interact with. These changes in amygdala connectional patters characterize the dynamic signature prototypical of individual emotion processing, and seemingly represent a neural mechanism that serves to implement the distinctive influence that each emotion exerts on perceptual, cognitive, and motor responses. Besides these differences, all emotions enhanced amygdala functional integration with premotor cortices compared to neutral faces. The present findings thus concur to reconceptualise the structure-function relation between brain-emotion from the traditional one-to-one mapping toward a network-based and dynamic perspective.

Voxel-based morphometry of auditory and speech-related cortex in stutterers.

PubMed

Beal, Deryk S; Gracco, Vincent L; Lafaille, Sophie J; De Nil, Luc F

2007-08-06

Stutterers demonstrate unique functional neural activation patterns during speech production, including reduced auditory activation, relative to nonstutterers. The extent to which these functional differences are accompanied by abnormal morphology of the brain in stutterers is unclear. This study examined the neuroanatomical differences in speech-related cortex between stutterers and nonstutterers using voxel-based morphometry. Results revealed significant differences in localized grey matter and white matter densities of left and right hemisphere regions involved in auditory processing and speech production.

Cluster analysis differentiates high and low community functioning in schizophrenia: Subgroups differ on working memory but not other neurocognitive domains.

PubMed

Alden, Eva C; Cobia, Derin J; Reilly, James L; Smith, Matthew J

2015-10-01

Schizophrenia is characterized by impairment in multiple aspects of community functioning. Available literature suggests that community functioning may be enhanced through cognitive remediation, however, evidence is limited regarding whether specific neurocognitive domains may be treatment targets. We characterized schizophrenia subjects based on their level of community functioning through cluster analysis in an effort to identify whether specific neurocognitive domains were associated with variation in functioning. Schizophrenia (SCZ, n=60) and control (CON, n=45) subjects completed a functional capacity task, social competence role-play, functional attainment interview, and a neuropsychological battery. Multiple cluster analytic techniques were used on the measures of functioning in the schizophrenia subjects to generate functionally-defined subgroups. MANOVA evaluated between-group differences in neurocognition. The cluster analysis revealed two distinct groups, consisting of 36 SCZ characterized by high levels of community functioning (HF-SCZ) and 24 SCZ with low levels of community functioning (LF-SCZ). There was a main group effect for neurocognitive performance (p<0.001) with CON outperforming both SCZ groups in all neurocognitive domains. Post-hoc tests revealed that HF-SCZ had higher verbal working memory compared to LF-SCZ (p≤0.05, Cohen's d=0.78) but the two groups did not differ in remaining domains. The cluster analysis classified schizophrenia subjects in HF-SCZ and LF-SCZ using a multidimensional assessment of community functioning. Moreover, HF-SCZ demonstrated rather preserved verbal working memory relative to LF-SCZ. The results suggest that verbal working memory may play a critical role in community functioning, and is a potential cognitive treatment target for schizophrenia subjects. Copyright © 2015 Elsevier B.V. All rights reserved.

Sex differences in the functional connectivity of the amygdalae in association with cortisol.

PubMed

Kogler, Lydia; Müller, Veronika I; Seidel, Eva-Maria; Boubela, Roland; Kalcher, Klaudius; Moser, Ewald; Habel, Ute; Gur, Ruben C; Eickhoff, Simon B; Derntl, Birgit

2016-07-01

Human amygdalae are involved in various behavioral functions such as affective and stress processing. For these behavioral functions, as well as for psychophysiological arousal including cortisol release, sex differences are reported. Here, we assessed cortisol levels and resting-state functional connectivity (rsFC) of left and right amygdalae in 81 healthy participants (42 women) to investigate potential modulation of amygdala rsFC by sex and cortisol concentration. Our analyses revealed that rsFC of the left amygdala significantly differed between women and men: Women showed stronger rsFC than men between the left amygdala and left middle temporal gyrus, inferior frontal gyrus, postcentral gyrus and hippocampus, regions involved in face processing, inner-speech, fear and pain processing. No stronger connections were detected for men and no sex difference emerged for right amygdala rsFC. Also, an interaction of sex and cortisol appeared: In women, cortisol was negatively associated with rsFC of the amygdalae with striatal regions, mid-orbital frontal gyrus, anterior cingulate gyrus, middle and superior frontal gyri, supplementary motor area and the parietal-occipital sulcus. Contrarily in men, positive associations of cortisol with rsFC of the left amygdala and these structures were observed. Functional decoding analyses revealed an association of the amygdalae and these regions with emotion, reward and memory processing, as well as action execution. Our results suggest that functional connectivity of the amygdalae as well as the regulatory effect of cortisol on brain networks differs between women and men. These sex-differences and the mediating and sex-dependent effect of cortisol on brain communication systems should be taken into account in affective and stress-related neuroimaging research. Thus, more studies including both sexes are required. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

An exemplar-based approach to individualized parcellation reveals the need for sex specific functional networks

PubMed Central

Salehi, Mehraveh; Karbasi, Amin; Shen, Xilin; Scheinost, Dustin; Constable, R. Todd

2018-01-01

Recent work with functional connectivity data has led to significant progress in understanding the functional organization of the brain. While the majority of the literature has focused on group-level parcellation approaches, there is ample evidence that the brain varies in both structure and function across individuals. In this work, we introduce a parcellation technique that incorporates delineation of functional networks both at the individual- and group-level. The proposed technique deploys the notion of “submodularity” to jointly parcellate the cerebral cortex while establishing an inclusive correspondence between the individualized functional networks. Using this parcellation technique, we successfully established a cross-validated predictive model that predicts individuals’ sex, solely based on the parcellation schemes (i.e. the node-to-network assignment vectors). The sex prediction finding illustrates that individualized parcellation of functional networks can reveal subgroups in a population and suggests that the use of a global network parcellation may overlook fundamental differences in network organization. This is a particularly important point to consider in studies comparing patients versus controls or even patient subgroups. Network organization may differ between individuals and global configurations should not be assumed. This approach to the individualized study of functional organization in the brain has many implications for both neuroscience and clinical applications. PMID:28882628

Genome-Wide Identification and Structural Analysis of bZIP Transcription Factor Genes in Brassica napus.

PubMed

Zhou, Yan; Xu, Daixiang; Jia, Ledong; Huang, Xiaohu; Ma, Guoqiang; Wang, Shuxian; Zhu, Meichen; Zhang, Aoxiang; Guan, Mingwei; Lu, Kun; Xu, Xinfu; Wang, Rui; Li, Jiana; Qu, Cunmin

2017-10-24

The basic region/leucine zipper motif (bZIP) transcription factor family is one of the largest families of transcriptional regulators in plants. bZIP genes have been systematically characterized in some plants, but not in rapeseed ( Brassica napus ). In this study, we identified 247 BnbZIP genes in the rapeseed genome, which we classified into 10 subfamilies based on phylogenetic analysis of their deduced protein sequences. The BnbZIP genes were grouped into functional clades with Arabidopsis genes with similar putative functions, indicating functional conservation. Genome mapping analysis revealed that the BnbZIPs are distributed unevenly across all 19 chromosomes, and that some of these genes arose through whole-genome duplication and dispersed duplication events. All expression profiles of 247 bZIP genes were extracted from RNA-sequencing data obtained from 17 different B . napus ZS11 tissues with 42 various developmental stages. These genes exhibited different expression patterns in various tissues, revealing that these genes are differentially regulated. Our results provide a valuable foundation for functional dissection of the different BnbZIP homologs in B . napus and its parental lines and for molecular breeding studies of bZIP genes in B . napus .

Genome-Wide Identification and Structural Analysis of bZIP Transcription Factor Genes in Brassica napus

PubMed Central

Zhou, Yan; Xu, Daixiang; Jia, Ledong; Huang, Xiaohu; Ma, Guoqiang; Wang, Shuxian; Zhu, Meichen; Zhang, Aoxiang; Guan, Mingwei; Xu, Xinfu; Wang, Rui; Li, Jiana

2017-01-01

The basic region/leucine zipper motif (bZIP) transcription factor family is one of the largest families of transcriptional regulators in plants. bZIP genes have been systematically characterized in some plants, but not in rapeseed (Brassica napus). In this study, we identified 247 BnbZIP genes in the rapeseed genome, which we classified into 10 subfamilies based on phylogenetic analysis of their deduced protein sequences. The BnbZIP genes were grouped into functional clades with Arabidopsis genes with similar putative functions, indicating functional conservation. Genome mapping analysis revealed that the BnbZIPs are distributed unevenly across all 19 chromosomes, and that some of these genes arose through whole-genome duplication and dispersed duplication events. All expression profiles of 247 bZIP genes were extracted from RNA-sequencing data obtained from 17 different B. napus ZS11 tissues with 42 various developmental stages. These genes exhibited different expression patterns in various tissues, revealing that these genes are differentially regulated. Our results provide a valuable foundation for functional dissection of the different BnbZIP homologs in B. napus and its parental lines and for molecular breeding studies of bZIP genes in B. napus. PMID:29064393

Differential expression pattern of UBX family genes in Caenorhabditis elegans

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

Yamauchi, Seiji; Sasagawa, Yohei; Ogura, Teru

2007-06-29

UBX (ubiquitin regulatory X)-containing proteins belong to an evolutionary conserved protein family and determine the specificity of p97/VCP/Cdc48p function by binding as its adaptors. Caenorhabditis elegans was found to possess six UBX-containing proteins, named UBXN-1 to -6. However, no general or specific function of them has been revealed. During the course of understanding not only their function but also specified function of p97, we investigated spatial and temporal expression patterns of six ubxn genes in this study. Transcript analyses showed that the expression pattern of each ubxn gene was different throughout worm's development and may show potential developmental dynamics inmore » their function, especially ubxn-5 was expressed specifically in the spermatogenic germline, suggesting a crucial role in spermatogenesis. In addition, as ubxn-4 expression was induced by ER stress, it would function as an ERAD factor in C. elegans. In vivo expression analysis by using GFP translational fusion constructs revealed that six ubxn genes show distinct expression patterns. These results altogether demonstrate that the expression of all six ubxn genes of C. elegans is differently regulated.« less

PyramidalExplorer: A New Interactive Tool to Explore Morpho-Functional Relations of Human Pyramidal Neurons.

PubMed

Toharia, Pablo; Robles, Oscar D; Fernaud-Espinosa, Isabel; Makarova, Julia; Galindo, Sergio E; Rodriguez, Angel; Pastor, Luis; Herreras, Oscar; DeFelipe, Javier; Benavides-Piccione, Ruth

2015-01-01

This work presents PyramidalExplorer, a new tool to interactively explore and reveal the detailed organization of the microanatomy of pyramidal neurons with functionally related models. It consists of a set of functionalities that allow possible regional differences in the pyramidal cell architecture to be interactively discovered by combining quantitative morphological information about the structure of the cell with implemented functional models. The key contribution of this tool is the morpho-functional oriented design that allows the user to navigate within the 3D dataset, filter and perform Content-Based Retrieval operations. As a case study, we present a human pyramidal neuron with over 9000 dendritic spines in its apical and basal dendritic trees. Using PyramidalExplorer, we were able to find unexpected differential morphological attributes of dendritic spines in particular compartments of the neuron, revealing new aspects of the morpho-functional organization of the pyramidal neuron.

PyramidalExplorer: A New Interactive Tool to Explore Morpho-Functional Relations of Human Pyramidal Neurons

PubMed Central

Toharia, Pablo; Robles, Oscar D.; Fernaud-Espinosa, Isabel; Makarova, Julia; Galindo, Sergio E.; Rodriguez, Angel; Pastor, Luis; Herreras, Oscar; DeFelipe, Javier; Benavides-Piccione, Ruth

2016-01-01

This work presents PyramidalExplorer, a new tool to interactively explore and reveal the detailed organization of the microanatomy of pyramidal neurons with functionally related models. It consists of a set of functionalities that allow possible regional differences in the pyramidal cell architecture to be interactively discovered by combining quantitative morphological information about the structure of the cell with implemented functional models. The key contribution of this tool is the morpho-functional oriented design that allows the user to navigate within the 3D dataset, filter and perform Content-Based Retrieval operations. As a case study, we present a human pyramidal neuron with over 9000 dendritic spines in its apical and basal dendritic trees. Using PyramidalExplorer, we were able to find unexpected differential morphological attributes of dendritic spines in particular compartments of the neuron, revealing new aspects of the morpho-functional organization of the pyramidal neuron. PMID:26778972

Alterations in the coupling functions between cortical and cardio-respiratory oscillations due to anaesthesia with propofol and sevoflurane

NASA Astrophysics Data System (ADS)

Stankovski, Tomislav; Petkoski, Spase; Raeder, Johan; Smith, Andrew F.; McClintock, Peter V. E.; Stefanovska, Aneta

2016-05-01

The precise mechanisms underlying general anaesthesia pose important and still open questions. To address them, we have studied anaesthesia induced by the widely used (intravenous) propofol and (inhalational) sevoflurane anaesthetics, computing cross-frequency coupling functions between neuronal, cardiac and respiratory oscillations in order to determine their mutual interactions. The phase domain coupling function reveals the form of the function defining the mechanism of an interaction, as well as its coupling strength. Using a method based on dynamical Bayesian inference, we have thus identified and analysed the coupling functions for six relationships. By quantitative assessment of the forms and strengths of the couplings, we have revealed how these relationships are altered by anaesthesia, also showing that some of them are differently affected by propofol and sevoflurane. These findings, together with the novel coupling function analysis, offer a new direction in the assessment of general anaesthesia and neurophysiological interactions, in general.

Social Maturity and Executive Function among Deaf Learners

ERIC Educational Resources Information Center

Marschark, Marc; Kronenberger, William G.; Rosica, Mark; Borgna, Georgianna; Convertino, Carol; Durkin, Andreana; Machmer, Elizabeth; Schmitz, Kathryn L.

2017-01-01

Two experiments examined relations among social maturity, executive function, language, and cochlear implant (CI) use among deaf high school and college students. Experiment 1 revealed no differences between deaf CI users, deaf nonusers, and hearing college students in measures of social maturity. However, deaf students (both CI users and…

Exploratory graphical models of functional and structural connectivity patterns for Alzheimer's Disease diagnosis.

PubMed

Ortiz, Andrés; Munilla, Jorge; Álvarez-Illán, Ignacio; Górriz, Juan M; Ramírez, Javier

2015-01-01

Alzheimer's Disease (AD) is the most common neurodegenerative disease in elderly people. Its development has been shown to be closely related to changes in the brain connectivity network and in the brain activation patterns along with structural changes caused by the neurodegenerative process. Methods to infer dependence between brain regions are usually derived from the analysis of covariance between activation levels in the different areas. However, these covariance-based methods are not able to estimate conditional independence between variables to factor out the influence of other regions. Conversely, models based on the inverse covariance, or precision matrix, such as Sparse Gaussian Graphical Models allow revealing conditional independence between regions by estimating the covariance between two variables given the rest as constant. This paper uses Sparse Inverse Covariance Estimation (SICE) methods to learn undirected graphs in order to derive functional and structural connectivity patterns from Fludeoxyglucose (18F-FDG) Position Emission Tomography (PET) data and segmented Magnetic Resonance images (MRI), drawn from the ADNI database, for Control, MCI (Mild Cognitive Impairment Subjects), and AD subjects. Sparse computation fits perfectly here as brain regions usually only interact with a few other areas. The models clearly show different metabolic covariation patters between subject groups, revealing the loss of strong connections in AD and MCI subjects when compared to Controls. Similarly, the variance between GM (Gray Matter) densities of different regions reveals different structural covariation patterns between the different groups. Thus, the different connectivity patterns for controls and AD are used in this paper to select regions of interest in PET and GM images with discriminative power for early AD diagnosis. Finally, functional an structural models are combined to leverage the classification accuracy. The results obtained in this work show the usefulness of the Sparse Gaussian Graphical models to reveal functional and structural connectivity patterns. This information provided by the sparse inverse covariance matrices is not only used in an exploratory way but we also propose a method to use it in a discriminative way. Regression coefficients are used to compute reconstruction errors for the different classes that are then introduced in a SVM for classification. Classification experiments performed using 68 Controls, 70 AD, and 111 MCI images and assessed by cross-validation show the effectiveness of the proposed method.

New aspects of grassland recovery in old-fields revealed by trait-based analyses of perennial-crop-mediated succession.

PubMed

Kelemen, András; Tóthmérész, Béla; Valkó, Orsolya; Miglécz, Tamás; Deák, Balázs; Török, Péter

2017-04-01

Classical old-field succession studies focused on vegetation changes after the abandonment of annual croplands or on succession after the elimination of cultivated crops. Perennial-crop-mediated succession, where fields are initially covered by perennial crops, reveals alternative aspects of old-field succession theories. We tested the validity of classical theories of old-field succession for perennial-crop-mediated succession. We formulated the following hypotheses: (1) functional diversity increases with increasing field age; (2) resource acquisition versus conservation trade-off shifts toward conservation at community level during the succession; (3) the importance of spatial and temporal seed dispersal decreases during the succession; and (4) competitiveness and stress-tolerance increases and ruderality decreases at community level during the succession. We studied functional diversity, trait distributions and plant strategies in differently aged old-fields using chronosequence method. We found increasing functional richness and functional divergence, but also unchanged or decreasing functional evenness. We detected a shift from resource acquisition to resource conservation strategy of communities during the succession. The role of spatial and temporal seed dispersal was found to be important not only at the initial but also at latter successional stages. We found an increasing stress-tolerance and a decreasing ruderality during succession, while the competitiveness remained unchanged at the community level. Despite the markedly different starting conditions, we found that classical and perennial-crop-mediated old-field successions have some similarities regarding the changes of functional diversity, resource acquisition versus conservation trade-off, and seed dispersal strategies. However, we revealed also the subsequent differences. The competitive character of communities remained stable during the succession; hence, the initial stages of perennial-crop-mediated succession can be similar to the middle stages of classical old-field succession. Moreover, the occupied functional niche space and differentiation were larger in the older stages, but resources were not effectively utilized within this space, suggesting that the stabilization of the vegetation requires more time.

Correspondent Functional Topography of the Human Left Inferior Parietal Lobule at Rest and Under Task Revealed Using Resting-State fMRI and Coactivation Based Parcellation.

PubMed

Wang, Jiaojian; Xie, Sangma; Guo, Xin; Becker, Benjamin; Fox, Peter T; Eickhoff, Simon B; Jiang, Tianzi

2017-03-01

The human left inferior parietal lobule (LIPL) plays a pivotal role in many cognitive functions and is an important node in the default mode network (DMN). Although many previous studies have proposed different parcellation schemes for the LIPL, the detailed functional organization of the LIPL and the exact correspondence between the DMN and LIPL subregions remain unclear. Mounting evidence indicates that spontaneous fluctuations in the brain are strongly associated with cognitive performance at the behavioral level. However, whether a consistent functional topographic organization of the LIPL during rest and under task can be revealed remains unknown. Here, they used resting-state functional connectivity (RSFC) and task-related coactivation patterns separately to parcellate the LIPL and identified seven subregions. Four subregions were located in the supramarginal gyrus (SMG) and three subregions were located in the angular gyrus (AG). The subregion-specific networks and functional characterization revealed that the four anterior subregions were found to be primarily involved in sensorimotor processing, movement imagination and inhibitory control, audition perception and speech processing, and social cognition, whereas the three posterior subregions were mainly involved in episodic memory, semantic processing, and spatial cognition. The results revealed a detailed functional organization of the LIPL and suggested that the LIPL is a functionally heterogeneous area. In addition, the present study demonstrated that the functional architecture of the LIPL during rest corresponds with that found in task processing. Hum Brain Mapp 38:1659-1675, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Cerebral responses to innocuous somatic pressure stimulation following aerobic exercise rehabilitation in chronic pain patients: a functional magnetic resonance imaging study

PubMed Central

Micalos, Peter S; Korgaonkar, Mayuresh S; Drinkwater, Eric J; Cannon, Jack; Marino, Frank E

2014-01-01

Objective The purpose of this research was to assess the functional brain activity and perceptual rating of innocuous somatic pressure stimulation before and after exercise rehabilitation in patients with chronic pain. Materials and methods Eleven chronic pain patients and eight healthy pain-free controls completed 12 weeks of supervised aerobic exercise intervention. Perceptual rating of standardized somatic pressure stimulation (2 kg) on the right anterior mid-thigh and brain responses during functional magnetic resonance imaging (fMRI) were assessed at pre- and postexercise rehabilitation. Results There was a significant difference in the perceptual rating of innocuous somatic pressure stimulation between the chronic pain and control groups (P=0.02) but no difference following exercise rehabilitation. Whole brain voxel-wise analysis with correction for multiple comparisons revealed trends for differences in fMRI responses between the chronic pain and control groups in the superior temporal gyrus (chronic pain > control, corrected P=0.30), thalamus, and caudate (control > chronic, corrected P=0.23). Repeated measures of the regions of interest (5 mm radius) for blood oxygen level-dependent signal response revealed trend differences for superior temporal gyrus (P=0.06), thalamus (P=0.04), and caudate (P=0.21). Group-by-time interactions revealed trend differences in the caudate (P=0.10) and superior temporal gyrus (P=0.29). Conclusion Augmented perceptual and brain responses to innocuous somatic pressure stimulation were shown in the chronic pain group compared to the control group; however, 12-weeks of exercise rehabilitation did not significantly attenuate these responses. PMID:25210471

Putting a photon to biological work: lessons from novel photoactive yellow protein homologs

NASA Astrophysics Data System (ADS)

Hoff, Wouter; Hara, Miwa; Ren, Jie; Kumauchi, Masato; Xie, Aihua; Larsen, Delmar; Mix, Tyler; Haraguchi, Shojiro; Shingae, Takahito; Unno, Masashi

The photoactive yellow protein (PYP) is a photosensory protein from the bacterium Halorhodospira halophila that has been used extensively as a model system for functional protein dynamics and biological signaling. We have been studying PYP homologs from a diverse set of bacteria. The PYP from Salinibacter ruber (Srub PYP) revealed a novel ``spectral isotope effect'' when the protein is dissolved in D2O. We were able to assign this effect to H/D exchange of an active side COOH group that forms an ionic hydrogen bond to the deprotonated (negatively charged) light-absorbing chromophore in PYP. Srub PYP also allowed us to measure Raman Optical Activity (ROA) spectra under resonance and pre-resonance conditions. This work revealed that pre-resonance (ROA) spectra are informative for analyzing active site distortions in PYP. Finally, ultrafast pump-probe experiments on three different PYPs revealed that the primary I0 photoproduct observed in Hhal PYP is not populated in some other PYP homologs. This observation has implications for the mechanism of chromophore photoisomerization at the start of the functional photocycle of PYP. These results illustrate how studies of different members of a protein family can lead to novel insights into basic mechanisms underlying protein function

Efficacy of Manual Therapy Including Neurodynamic Techniques for the Treatment of Carpal Tunnel Syndrome: A Randomized Controlled Trial.

PubMed

Wolny, Tomasz; Saulicz, Edward; Linek, Paweł; Shacklock, Michael; Myśliwiec, Andrzej

2017-05-01

The purpose of this randomized trial was to compare the efficacy of manual therapy, including the use of neurodynamic techniques, with electrophysical modalities on patients with mild and moderate carpal tunnel syndrome (CTS). The study included 140 CTS patients who were randomly assigned to the manual therapy (MT) group, which included the use of neurodynamic techniques, functional massage, and carpal bone mobilizations techniques, or to the electrophysical modalities (EM) group, which included laser and ultrasound therapy. Nerve conduction, pain severity, symptom severity, and functional status measured by the Boston Carpal Tunnel Questionnaire were assessed before and after treatment. Therapy was conducted twice weekly and both groups received 20 therapy sessions. A baseline assessment revealed group differences in sensory conduction of the median nerve (P < .01) but not in motor conduction (P = .82). Four weeks after the last treatment procedure, nerve conduction was examined again. In the MT group, median nerve sensory conduction velocity increased by 34% and motor conduction velocity by 6% (in both cases, P < .01). There was no change in median nerve sensory and motor conduction velocities in the EM. Distal motor latency was decreased (P < .01) in both groups. A baseline assessment revealed no group differences in pain severity, symptom severity, or functional status. Immediately after therapy, analysis of variance revealed group differences in pain severity (P < .01), with a reduction in pain in both groups (MT: 290%, P < .01; EM: 47%, P < .01). There were group differences in symptom severity (P < .01) and function (P < .01) on the Boston Carpal Tunnel Questionnaire. Both groups had an improvement in functional status (MT: 47%, P < .01; EM: 9%, P < .01) and a reduction in subjective CTS symptoms (MT: 67%, P < .01; EM: 15%, P < .01). Both therapies had a positive effect on nerve conduction, pain reduction, functional status, and subjective symptoms in individuals with CTS. However, the results regarding pain reduction, subjective symptoms, and functional status were better in the MT group. Copyright © 2017. Published by Elsevier Inc.

Brain structure differences between Chinese and Caucasian cohorts: A comprehensive morphometry study.

PubMed

Tang, Yuchun; Zhao, Lu; Lou, Yunxia; Shi, Yonggang; Fang, Rui; Lin, Xiangtao; Liu, Shuwei; Toga, Arthur

2018-05-01

Numerous behavioral observations and brain function studies have demonstrated that neurological differences exist between East Asians and Westerners. However, the extent to which these factors relate to differences in brain structure is still not clear. As the basis of brain functions, the anatomical differences in brain structure play a primary and critical role in the origination of functional and behavior differences. To investigate the underlying differences in brain structure between the two cultural/ethnic groups, we conducted a comparative study on education-matched right-handed young male adults (age = 22-29 years) from two cohorts, Han Chinese (n = 45) and Caucasians (n = 45), using high-dimensional structural magnetic resonance imaging (MRI) data. Using two well-validated imaging analysis techniques, surface-based morphometry (SBM) and voxel-based morphometry (VBM), we performed a comprehensive vertex-wise morphometric analysis of the brain structures between Chinese and Caucasian cohorts. We identified consistent significant between-group differences in cortical thickness, volume, and surface area in the frontal, temporal, parietal, occipital, and insular lobes as well as the cingulate cortices. The SBM analyses revealed that compared with Caucasians, the Chinese population showed larger cortical structures in the temporal and cingulate regions, and smaller structural measures in the frontal and parietal cortices. The VBM data of the same sample was well-aligned with the SBM findings. Our findings systematically revealed comprehensive brain structural differences between young male Chinese and Caucasians, and provided new neuroanatomical insights to the behavioral and functional distinctions in the two cultural/ethnic populations. © 2018 Wiley Periodicals, Inc.

Functional associations at global brain level during perception of an auditory illusion by applying maximal information coefficient

NASA Astrophysics Data System (ADS)

Bhattacharya, Joydeep; Pereda, Ernesto; Ioannou, Christos

2018-02-01

Maximal information coefficient (MIC) is a recently introduced information-theoretic measure of functional association with a promising potential of application to high dimensional complex data sets. Here, we applied MIC to reveal the nature of the functional associations between different brain regions during the perception of binaural beat (BB); BB is an auditory illusion occurring when two sinusoidal tones of slightly different frequency are presented separately to each ear and an illusory beat at the different frequency is perceived. We recorded sixty-four channels EEG from two groups of participants, musicians and non-musicians, during the presentation of BB, and systematically varied the frequency difference from 1 Hz to 48 Hz. Participants were also presented non-binuaral beat (NBB) stimuli, in which same frequencies were presented to both ears. Across groups, as compared to NBB, (i) BB conditions produced the most robust changes in the MIC values at the whole brain level when the frequency differences were in the classical alpha range (8-12 Hz), and (ii) the number of electrode pairs showing nonlinear associations decreased gradually with increasing frequency difference. Between groups, significant effects were found for BBs in the broad gamma frequency range (34-48 Hz), but such effects were not observed between groups during NBB. Altogether, these results revealed the nature of functional associations at the whole brain level during the binaural beat perception and demonstrated the usefulness of MIC in characterizing interregional neural dependencies.

Individual Differences and Possible Effects from Outdoor Education: Long Time and Short Time Benefits

ERIC Educational Resources Information Center

Fiskum, Tove Anita; Jacobsen, Karl

2012-01-01

This study explores differences in the children's outcomes from outdoor education. The results revealed different outcomes within different subgroups: The children with an easy or a withdrawal temperament are good functioning both indoor and outdoor. Their outcomes from outdoor education are an increased vitality, which might be seen as a short…

Sparse genetic tracing reveals regionally specific functional organization of mammalian nociceptors.

PubMed

Olson, William; Abdus-Saboor, Ishmail; Cui, Lian; Burdge, Justin; Raabe, Tobias; Ma, Minghong; Luo, Wenqin

2017-10-12

The human distal limbs have a high spatial acuity for noxious stimuli but a low density of pain-sensing neurites. To elucidate mechanisms underlying regional differences in processing nociception, we sparsely traced non-peptidergic nociceptors across the body using a newly generated Mrgprd CreERT2 mouse line. We found that mouse plantar paw skin is also innervated by a low density of Mrgprd + nociceptors, while individual arbors in different locations are comparable in size. Surprisingly, the central arbors of plantar paw and trunk innervating nociceptors have distinct morphologies in the spinal cord. This regional difference is well correlated with a heightened signal transmission for plantar paw circuits, as revealed by both spinal cord slice recordings and behavior assays. Taken together, our results elucidate a novel somatotopic functional organization of the mammalian pain system and suggest that regional central arbor structure could facilitate the "enlarged representation" of plantar paw regions in the CNS.

The cerebellum and cognition: evidence from functional imaging studies.

PubMed

Stoodley, Catherine J

2012-06-01

Evidence for a role of the human cerebellum in cognitive functions comes from anatomical, clinical and neuroimaging data. Functional neuroimaging reveals cerebellar activation during a variety of cognitive tasks, including language, visual-spatial, executive, and working memory processes. It is important to note that overt movement is not a prerequisite for cerebellar activation: the cerebellum is engaged during conditions which either control for motor output or do not involve motor responses. Resting-state functional connectivity data reveal that, in addition to networks underlying motor control, the cerebellum is part of "cognitive" networks with prefrontal and parietal association cortices. Consistent with these findings, regional differences in activation patterns within the cerebellum are evident depending on the task demands, suggesting that the cerebellum can be broadly divided into functional regions based on the patterns of anatomical connectivity between different regions of the cerebellum and sensorimotor and association areas of the cerebral cortex. However, the distinct contribution of the cerebellum to cognitive tasks is not clear. Here, the functional neuroimaging evidence for cerebellar involvement in cognitive functions is reviewed and related to hypotheses as to why the cerebellum is active during such tasks. Identifying the precise role of the cerebellum in cognition-as well as the mechanism by which the cerebellum modulates performance during a wide range of tasks-remains a challenge for future investigations.

Functional gene profiling through metaRNAseq approach reveals diet-dependent variation in rumen microbiota of buffalo (Bubalus bubalis).

PubMed

Hinsu, Ankit T; Parmar, Nidhi R; Nathani, Neelam M; Pandit, Ramesh J; Patel, Anand B; Patel, Amrutlal K; Joshi, Chaitanya G

2017-04-01

Recent advances in next generation sequencing technology have enabled analysis of complex microbial community from genome to transcriptome level. In the present study, metatranscriptomic approach was applied to elucidate functionally active bacteria and their biological processes in rumen of buffalo (Bubalus bubalis) adapted to different dietary treatments. Buffaloes were adapted to a diet containing 50:50, 75:25 and 100:0 forage to concentrate ratio, each for 6 weeks, before ruminal content sample collection. Metatranscriptomes from rumen fiber adherent and fiber-free active bacteria were sequenced using Ion Torrent PGM platform followed by annotation using MG-RAST server and CAZYmes (Carbohydrate active enzymes) analysis toolkit. In all the samples Bacteroidetes was the most abundant phylum followed by Firmicutes. Functional analysis using KEGG Orthology database revealed Metabolism as the most abundant category at level 1 within which Carbohydrate metabolism was dominating. Diet treatments also exerted significant differences in proportion of enzymes involved in metabolic pathways for VFA production. Carbohydrate Active Enzyme(CAZy) analysis revealed the abundance of genes encoding glycoside hydrolases with the highest representation of GH13 CAZy family in all the samples. The findings provide an overview of the activities occurring in the rumen as well as active bacterial population and the changes occurring through different dietary treatments. Copyright © 2017 Elsevier Ltd. All rights reserved.

Oceanic protists with different forms of acquired phototrophy display contrasting biogeographies and abundance.

PubMed

Leles, S G; Mitra, A; Flynn, K J; Stoecker, D K; Hansen, P J; Calbet, A; McManus, G B; Sanders, R W; Caron, D A; Not, F; Hallegraeff, G M; Pitta, P; Raven, J A; Johnson, M D; Glibert, P M; Våge, S

2017-08-16

This first comprehensive analysis of the global biogeography of marine protistan plankton with acquired phototrophy shows these mixotrophic organisms to be ubiquitous and abundant; however, their biogeography differs markedly between different functional groups. These mixotrophs, lacking a constitutive capacity for photosynthesis (i.e. non-constitutive mixotrophs, NCMs), acquire their phototrophic potential through either integration of prey-plastids or through endosymbiotic associations with photosynthetic microbes. Analysis of field data reveals that 40-60% of plankton traditionally labelled as (non-phototrophic) microzooplankton are actually NCMs, employing acquired phototrophy in addition to phagotrophy. Specialist NCMs acquire chloroplasts or endosymbionts from specific prey, while generalist NCMs obtain chloroplasts from a variety of prey. These contrasting functional types of NCMs exhibit distinct seasonal and spatial global distribution patterns. Mixotrophs reliant on 'stolen' chloroplasts, controlled by prey diversity and abundance, dominate in high-biomass areas. Mixotrophs harbouring intact symbionts are present in all waters and dominate particularly in oligotrophic open ocean systems. The contrasting temporal and spatial patterns of distribution of different mixotroph functional types across the oceanic provinces, as revealed in this study, challenges traditional interpretations of marine food web structures. Mixotrophs with acquired phototrophy (NCMs) warrant greater recognition in marine research. © 2017 The Author(s).

Revealed and stated preference valuation and transfer: A within-sample comparison of water quality improvement values

NASA Astrophysics Data System (ADS)

Ferrini, Silvia; Schaafsma, Marije; Bateman, Ian

2014-06-01

Benefit transfer (BT) methods are becoming increasingly important for environmental policy, but the empirical findings regarding transfer validity are mixed. A novel valuation survey was designed to obtain both stated preference (SP) and revealed preference (RP) data concerning river water quality values from a large sample of households. Both dichotomous choice and payment card contingent valuation (CV) and travel cost (TC) data were collected. Resulting valuations were directly compared and used for BT analyses using both unit value and function transfer approaches. WTP estimates are found to pass the convergence validity test. BT results show that the CV data produce lower transfer errors, below 20% for both unit value and function transfer, than TC data especially when using function transfer. Further, comparison of WTP estimates suggests that in all cases, differences between methods are larger than differences between study areas. Results show that when multiple studies are available, using welfare estimates from the same area but based on a different method consistently results in larger errors than transfers across space keeping the method constant.

Differential Adjustment Among Rural Adolescents Exposed to Family Violence.

PubMed

Sianko, Natallia; Hedge, Jasmine M; McDonell, James R

2016-04-22

This study examines differences in psychological adjustment in a sample of rural adolescents who have been exposed to family violence. Self-report questionnaires were administered to 580 adolescents and their primary caregivers. The results revealed that over two thirds of the study participants (68.8%) had been exposed to violence in their families. As hypothesized, cluster analysis identified several profiles among adolescents, distinguished by their psychological and emotional functioning: well adjusted (46.2%), moderately adjusted (44.3%), and struggling (9.5%). Discriminant function analysis confirmed the groupings and revealed that family functioning was among the most influential factors explaining adjustment differences. Multivariate analyses of variance (MANOVAs) further showed that adolescents from each of the three adjustment profiles reported significantly different levels of family social support, parental involvement, and perceived neighborhood safety. Overall, the results confirm heterogeneity of adolescent adaptation in the aftermath of family violence and provide insights into family and neighborhood factors that account for variability in adolescents' reactions to violence. Implications for future research and practical interventions are discussed. © The Author(s) 2016.

Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics

PubMed Central

Eiler, Alexander; Zaremba-Niedzwiedzka, Katarzyna; Martínez-García, Manuel; McMahon, Katherine D; Stepanauskas, Ramunas; Andersson, Siv G E; Bertilsson, Stefan

2014-01-01

Little is known about the diversity and structuring of freshwater microbial communities beyond the patterns revealed by tracing their distribution in the landscape with common taxonomic markers such as the ribosomal RNA. To address this gap in knowledge, metagenomes from temperate lakes were compared to selected marine metagenomes. Taxonomic analyses of rRNA genes in these freshwater metagenomes confirm the previously reported dominance of a limited subset of uncultured lineages of freshwater bacteria, whereas Archaea were rare. Diversification into marine and freshwater microbial lineages was also reflected in phylogenies of functional genes, and there were also significant differences in functional beta-diversity. The pathways and functions that accounted for these differences are involved in osmoregulation, active transport, carbohydrate and amino acid metabolism. Moreover, predicted genes orthologous to active transporters and recalcitrant organic matter degradation were more common in microbial genomes from oligotrophic versus eutrophic lakes. This comparative metagenomic analysis allowed us to formulate a general hypothesis that oceanic- compared with freshwater-dwelling microorganisms, invest more in metabolism of amino acids and that strategies of carbohydrate metabolism differ significantly between marine and freshwater microbial communities. PMID:24118837

[The post-discectomy syndrome: clinical and electroneuromyographic characteristics and methods of treatment].

PubMed

Musaev, A V; Guseĭnova, S G; Musaeva, I R

2008-01-01

The data of the Azerbaijan Neurosurgical Center, including 2618 case-reports of patients operated on for low back discal hernia between 1997 and 2002, have been analyzed. The retrospective analysis of the data reveals that 26,4% of patients need further restorative treatment due to the presence of various neurological disturbances: pain syndromes of different intensity, motor deficits (pareses), sensory disorders and functional disorders of pelvic organs. The retrospective analysis of the data reveals that 26,4% of patients need further restorative treatment due to the presence of various neurological disturbances: pain syndromes of different intensity, motor deficits (pareses), sensory disorders and functional disorders of pelvic organs. Along with these data, the results of our own clinical and neurophysiological study of 110 patients have been summarized as well. Along with these data, the results of our own clinical and neurophysiological study of 110 patients have been summarized as well. A high effectiveness of electrostimulation and naphthalan therapy alone and in combination with massage and medical gymnastics has been revealed. A high effectiveness of electrostimulation and naphthalan therapy alone and in combination with massage and medical gymnastics has been revealed. Electroneuromyographic data revealing the positive dynamics as a result of the treatment of patients with the post-discectomy syndrome are presented. Electroneuromyographic data revealing the positive dynamics as a result of the treatment of patients with the post-discectomy syndrome are presented.

Dissociated language functions: a matter of atypical language lateralization or cerebral plasticity?

PubMed

Acioly, Marcus Andre; Gharabaghi, Alireza; Zimmermann, Christoph; Erb, Michael; Heckl, Stefan; Tatagiba, Marcos

2014-01-01

The left hemisphere is generally considered to harbor language functions. Atypical cortical language lateralization is mainly demonstrated in left-handed and ambidextrous individuals, whereas dissociated language functions have been reported in association with brain injuries as a part of the reorganization process. We present a thoughtful discussion on the underlying mechanisms of dissociated language functions through an illustrative case of dissociated expressive language. A 31-year-old left-handed woman presented with a recurrent left frontal glioma. Preoperative language functional magnetic resonance imaging (fMRI) panel revealed right-sided dominance for two different language tasks (verbal fluency and visual naming), and the word chain task demonstrated maximal activation in the left hemisphere at the posterior margin of the tumor. The patient was operated on awake to assess language functions intraoperatively. Preoperative fMRI findings were confirmed revealing a task-specific dissociation of expressive language functions. Surgical resection was taken to the functional boundaries. Postoperatively, no language dysfunction occurred. Dissociated language functions are prone to occur in long-standing lesions. Different patterns of dissociation may be encountered due to interindividual particularities and cerebral plasticity. The presented patient is unique by demonstrating new insight into expressive language dissociation, emphasizing the role of a preoperative language fMRI panel and the capability of intraoperative language mapping for identifying special language networks. Georg Thieme Verlag KG Stuttgart · New York.

Sex Differences in the Relationship of Anger and Depression: An Empirical Study.

ERIC Educational Resources Information Center

Newman, Jody L.; Gray, Elizabeth A.; Fuqua, Dale R.

1999-01-01

A comparison of mean scores on the Beck Depression Inventory and State-Trait Anger Expression Inventory scales revealed that women scored significantly higher than men on depression, whereas there were no significant differences on any of the six anger scales. These findings support further research on functional affective differences between men…

Whole Brain Functional Connectivity Pattern Homogeneity Mapping.

PubMed

Wang, Lijie; Xu, Jinping; Wang, Chao; Wang, Jiaojian

2018-01-01

Mounting studies have demonstrated that brain functions are determined by its external functional connectivity patterns. However, how to characterize the voxel-wise similarity of whole brain functional connectivity pattern is still largely unknown. In this study, we introduced a new method called functional connectivity homogeneity (FcHo) to delineate the voxel-wise similarity of whole brain functional connectivity patterns. FcHo was defined by measuring the whole brain functional connectivity patterns similarity of a given voxel with its nearest 26 neighbors using Kendall's coefficient concordance (KCC). The robustness of this method was tested in four independent datasets selected from a large repository of MRI. Furthermore, FcHo mapping results were further validated using the nearest 18 and six neighbors and intra-subject reproducibility with each subject scanned two times. We also compared FcHo distribution patterns with local regional homogeneity (ReHo) to identify the similarity and differences of the two methods. Finally, FcHo method was used to identify the differences of whole brain functional connectivity patterns between professional Chinese chess players and novices to test its application. FcHo mapping consistently revealed that the high FcHo was mainly distributed in association cortex including parietal lobe, frontal lobe, occipital lobe and default mode network (DMN) related areas, whereas the low FcHo was mainly found in unimodal cortex including primary visual cortex, sensorimotor cortex, paracentral lobule and supplementary motor area. These results were further supported by analyses of the nearest 18 and six neighbors and intra-subject similarity. Moreover, FcHo showed both similar and different whole brain distribution patterns compared to ReHo. Finally, we demonstrated that FcHo can effectively identify the whole brain functional connectivity pattern differences between professional Chinese chess players and novices. Our findings indicated that FcHo is a reliable method to delineate the whole brain functional connectivity pattern similarity and may provide a new way to study the functional organization and to reveal neuropathological basis for brain disorders.

Amygdala subnuclei connectivity in response to violence reveals unique influences of individual differences in psychopathic traits in a non-forensic sample

PubMed Central

Yoder, Keith J.; Porges, Eric C.; Decety, Jean

2016-01-01

Atypical amygdala function and connectivity have reliably been associated with psychopathy. However, the amygdala is not a unitary structure. To examine how psychopathic traits in a non-forensic sample are linked to amygdala response to violence, the current study used probabilistic tractography to classify amygdala subnuclei based on anatomical projections to and from amygdala subnuclei in a group of 43 male participants. The segmentation identified the basolateral complex (BLA; lateral, basal, and accessory basal subnuclei) and the central subnucleus (CE), which were used as seeds in a functional connectivity analysis to identify differences in neuronal coupling specific to observed violence. While a full amygdala seed showed significant connectivity only to right middle occipital gyrus, subnuclei seeds revealed unique connectivity patterns. BLA showed enhanced coupling with anterior cingulate and prefrontal regions, while CE showed increased connectivity with the brainstem, but reduced connectivity with superior parietal and precentral gyrus. Further, psychopathic personality factors were related to specific patterns of connectivity. Fearless Dominance scores on the psychopathic personality inventory predicted increased coupling between the BLA seed and sensory integration cortices, and increased connectivity between the CE seed and posterior insula. Conversely, Self-Centered Impulsivity scores were negatively correlated with coupling between BLA and ventrolateral prefrontal cortex, and Coldheartedness scores predicted increased functional connectivity between BLA and dorsal anterior cingulate cortex. Taken together, these findings demonstrate how subnuclei segmentations reveal important functional connectivity differences that are otherwise inaccessible. Such an approach yields a better understanding of amygdala dysfunction in psychopathy. PMID:25557777

Amygdala subnuclei connectivity in response to violence reveals unique influences of individual differences in psychopathic traits in a nonforensic sample.

PubMed

Yoder, Keith J; Porges, Eric C; Decety, Jean

2015-04-01

Atypical amygdala function and connectivity have reliably been associated with psychopathy. However, the amygdala is not a unitary structure. To examine how psychopathic traits in a nonforensic sample are linked to amygdala response to violence, this study used probabilistic tractography to classify amygdala subnuclei based on anatomical projections to and from amygdala subnuclei in a group of 43 male participants. The segmentation identified the basolateral complex (BLA; lateral, basal, and accessory basal subnuclei) and the central subnucleus (CE), which were used as seeds in a functional connectivity analysis to identify differences in neuronal coupling specific to observed violence. While a full amygdala seed showed significant connectivity only to right middle occipital gyrus, subnuclei seeds revealed unique connectivity patterns. BLA showed enhanced coupling with anterior cingulate and prefrontal regions, while CE showed increased connectivity with the brainstem, but reduced connectivity with superior parietal and precentral gyrus. Further, psychopathic personality factors were related to specific patterns of connectivity. Fearless Dominance scores on the psychopathic personality inventory predicted increased coupling between the BLA seed and sensory integration cortices, and increased connectivity between the CE seed and posterior insula. Conversely, Self-Centered Impulsivity scores were negatively correlated with coupling between BLA and ventrolateral prefrontal cortex, and Coldheartedness scores predicted increased functional connectivity between BLA and dorsal anterior cingulate cortex. Taken together, these findings demonstrate how subnuclei segmentations reveal important functional connectivity differences that are otherwise inaccessible. Such an approach yields a better understanding of amygdala dysfunction in psychopathy. © 2014 Wiley Periodicals, Inc.

Comparative Genomics Unravels the Functional Roles of Co-occurring Acidophilic Bacteria in Bioleaching Heaps

PubMed Central

Zhang, Xian; Liu, Xueduan; Liang, Yili; Xiao, Yunhua; Ma, Liyuan; Guo, Xue; Miao, Bo; Liu, Hongwei; Peng, Deliang; Huang, Wenkun; Yin, Huaqun

2017-01-01

The spatial-temporal distribution of populations in various econiches is thought to be potentially related to individual differences in the utilization of nutrients or other resources, but their functional roles in the microbial communities remain elusive. We compared differentiation in gene repertoire and metabolic profiles, with a focus on the potential functional traits of three commonly recognized members (Acidithiobacillus caldus, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans) in bioleaching heaps. Comparative genomics revealed that intra-species divergence might be driven by horizontal gene transfer. These co-occurring bacteria shared a few homologous genes, which significantly suggested the genomic differences between these organisms. Notably, relatively more genes assigned to the Clusters of Orthologous Groups category [G] (carbohydrate transport and metabolism) were identified in Sulfobacillus thermosulfidooxidans compared to the two other species, which probably indicated their mixotrophic capabilities that assimilate both organic and inorganic forms of carbon. Further inspection revealed distinctive metabolic capabilities involving carbon assimilation, nitrogen uptake, and iron-sulfur cycling, providing robust evidence for functional differences with respect to nutrient utilization. Therefore, we proposed that the mutual compensation of functionalities among these co-occurring organisms might provide a selective advantage for efficiently utilizing the limited resources in their habitats. Furthermore, it might be favorable to chemoautotrophs' lifestyles to form mutualistic interactions with these heterotrophic and/or mixotrophic acidophiles, whereby the latter could degrade organic compounds to effectively detoxify the environments. Collectively, the findings shed light on the genetic traits and potential metabolic activities of these organisms, and enable us to make some inferences about genomic and functional differences that might allow them to co-exist. PMID:28529505

Testing complex animal cognition: Concept learning, proactive interference, and list memory.

PubMed

Wright, Anthony A

2018-01-01

This article describes an approach for assessing and comparing complex cognition in rhesus monkeys and pigeons by training them in a sequence of synergistic tasks, each yielding a whole function for enhanced comparisons. These species were trained in similar same/different tasks with expanding training sets (8, 16, 32, 64, 128 … 1024 pictures) followed by novel-stimulus transfer eventually resulting in full abstract-concept learning. Concept-learning functions revealed better rhesus transfer throughout and full concept learning at the 128 set, versus pigeons at the 256 set. They were then tested in delayed same/different tasks for proactive interference by inserting occasional tests within trial-unique sessions where the test stimulus matched a previous sample stimulus (1, 2, 4, 8, 16 trials prior). Proactive-interference functions revealed time-based interference for pigeons (1, 10 s delays), but event-based interference for rhesus (no effect of 1, 10, 20 s delays). They were then tested in list-memory tasks by expanding the sample to four samples in trial-unique sessions (minimizing proactive interference). The four-item, list-memory functions revealed strong recency memory at short delays, gradually changing to strong primacy memory at long delays over 30 s for rhesus, and 10 s for pigeons. Other species comparisons and future directions are discussed. © 2018 Society for the Experimental Analysis of Behavior.

Tapping natural variation at functional level reveals allele specific molecular characteristics of potato invertase Pain-1.

PubMed

Draffehn, Astrid M; Durek, Pawel; Nunes-Nesi, Adriano; Stich, Benjamin; Fernie, Alisdair R; Gebhardt, Christiane

2012-12-01

Biochemical, molecular and genetic studies emphasize the role of the potato vacuolar invertase Pain-1 in the accumulation of reducing sugars in potato tubers upon cold storage, and thereby its influence on the quality of potato chips and French fries. Previous studies showed that natural Pain-1 cDNA alleles were associated with better chip quality and higher tuber starch content. In this study, we focused on the functional characterization of these alleles. A genotype-dependent transient increase of total Pain-1 transcript levels in cold-stored tubers of six different genotypes as well as allele-specific expression patterns were detected. 3D modelling revealed putative structural differences between allelic Pain-1 proteins at the molecule's surface and at the substrate binding site. Furthermore, the yeast SUC2 mutant was complemented with Pain-1 cDNA alleles and enzymatic parameters of the heterologous expressed proteins were measured at 30 and 4 °C. Significant differences between the alleles were detected. The observed functional differences between Pain-1 alleles did not permit final conclusions on the mechanism of their association with tuber quality traits. Our results show that natural allelic variation at the functional level is present in potato, and that the heterozygous genetic background influences the manifestation of this variation. © 2012 Blackwell Publishing Ltd.

Characterization of Different Types of Excitability in Large Somatosensory Neurons and Its Plastic Changes in Pathological Pain States

PubMed Central

Xie, Rou-Gang; Chu, Wen-Guang; Hu, San-Jue; Luo, Ceng

2018-01-01

Sensory neuron types have been distinguished by distinct morphological and transcriptional characteristics. Excitability is the most fundamental functional feature of neurons. Mathematical models described by Hodgkin have revealed three types of neuronal excitability based on the relationship between firing frequency and applied current intensity. However, whether natural sensory neurons display different functional characteristics in terms of excitability and whether this excitability type undergoes plastic changes under pathological pain states have remained elusive. Here, by utilizing whole-cell patch clamp recordings, behavioral and pharmacological assays, we demonstrated that large dorsal root ganglion (DRG) neurons can be classified into three classes and four subclasses based on their excitability patterns, which is similar to mathematical models raised by Hodgkin. Analysis of hyperpolarization-activated cation current (Ih) revealed different magnitude of Ih in different excitability types of large DRG neurons, with higher Ih in Class 2-1 than that in Class 1, 2-2 and 3. This indicates a crucial role of Ih in the determination of excitability type of large DRG neurons. More importantly, this pattern of excitability displays plastic changes and transition under pathological pain states caused by peripheral nerve injury. This study sheds new light on the functional characteristics of large DRG neurons and extends functional classification of large DRG neurons by integration of transcriptomic and morphological characteristics. PMID:29303989

An exemplar-based approach to individualized parcellation reveals the need for sex specific functional networks.

PubMed

Salehi, Mehraveh; Karbasi, Amin; Shen, Xilin; Scheinost, Dustin; Constable, R Todd

2018-04-15

Recent work with functional connectivity data has led to significant progress in understanding the functional organization of the brain. While the majority of the literature has focused on group-level parcellation approaches, there is ample evidence that the brain varies in both structure and function across individuals. In this work, we introduce a parcellation technique that incorporates delineation of functional networks both at the individual- and group-level. The proposed technique deploys the notion of "submodularity" to jointly parcellate the cerebral cortex while establishing an inclusive correspondence between the individualized functional networks. Using this parcellation technique, we successfully established a cross-validated predictive model that predicts individuals' sex, solely based on the parcellation schemes (i.e. the node-to-network assignment vectors). The sex prediction finding illustrates that individualized parcellation of functional networks can reveal subgroups in a population and suggests that the use of a global network parcellation may overlook fundamental differences in network organization. This is a particularly important point to consider in studies comparing patients versus controls or even patient subgroups. Network organization may differ between individuals and global configurations should not be assumed. This approach to the individualized study of functional organization in the brain has many implications for both neuroscience and clinical applications. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Extraversion modulates functional connectivity hubs of resting-state brain networks.

PubMed

Pang, Yajing; Cui, Qian; Duan, Xujun; Chen, Heng; Zeng, Ling; Zhang, Zhiqiang; Lu, Guangming; Chen, Huafu

2017-09-01

Personality dimension extraversion describes individual differences in social behaviour and socio-emotional functioning. The intrinsic functional connectivity patterns of the brain are reportedly associated with extraversion. However, whether or not extraversion is associated with functional hubs warrants clarification. Functional hubs are involved in the rapid integration of neural processing, and their dysfunction contributes to the development of neuropsychiatric disorders. In this study, we employed the functional connectivity density (FCD) method for the first time to distinguish the energy-efficient hubs associated with extraversion. The resting-state functional magnetic resonance imaging data of 71 healthy subjects were used in the analysis. Short-range FCD was positively correlated with extraversion in the left cuneus, revealing a link between the local functional activity of this region and extraversion in risk-taking. Long-range FCD was negatively correlated with extraversion in the right superior frontal gyrus and the inferior frontal gyrus. Seed-based resting-state functional connectivity (RSFC) analyses revealed that a decreased long-range FCD in individuals with high extraversion scores showed a low long-range functional connectivity pattern between the medial and dorsolateral prefrontal cortex, middle temporal gyrus, and anterior cingulate cortex. This result suggests that decreased RSFC patterns are responsible for self-esteem, self-evaluation, and inhibitory behaviour system that account for the modulation and shaping of extraversion. Overall, our results emphasize specific brain hubs, and reveal long-range functional connections in relation to extraversion, thereby providing a neurobiological basis of extraversion. © 2015 The British Psychological Society.

A density difference based analysis of orbital-dependent exchange-correlation functionals

NASA Astrophysics Data System (ADS)

Grabowski, Ireneusz; Teale, Andrew M.; Fabiano, Eduardo; Śmiga, Szymon; Buksztel, Adam; Della Sala, Fabio

2014-03-01

We present a density difference based analysis for a range of orbital-dependent Kohn-Sham functionals. Results for atoms, some members of the neon isoelectronic series and small molecules are reported and compared with ab initio wave function calculations. Particular attention is paid to the quality of approximations to the exchange-only optimised effective potential (OEP) approach: we consider both the localised Hartree-Fock as well as the Krieger-Li-Iafrate methods. Analysis of density differences at the exchange-only level reveals the impact of the approximations on the resulting electronic densities. These differences are further quantified in terms of the ground state energies, frontier orbital energy differences and highest occupied orbital energies obtained. At the correlated level, an OEP approach based on a perturbative second-order correlation energy expression is shown to deliver results comparable with those from traditional wave function approaches, making it suitable for use as a benchmark against which to compare standard density functional approximations.

Empirically Defined Patterns of Executive Function Deficits in Schizophrenia and Their Relation to Everyday Functioning: A Person-Centered Approach

PubMed Central

Iampietro, Mary; Giovannetti, Tania; Drabick, Deborah A. G.; Kessler, Rachel K.

2013-01-01

Executive function (EF) deficits in schizophrenia (SZ) are well documented, although much less is known about patterns of EF deficits and their association to differential impairments in everyday functioning. The present study empirically defined SZ groups based on measures of various EF abilities and then compared these EF groups on everyday action errors. Participants (n=45) completed various subtests from the Delis–Kaplan Executive Function System (D-KEFS) and the Naturalistic Action Test (NAT), a performance-based measure of everyday action that yields scores reflecting total errors and a range of different error types (e.g., omission, perseveration). Results of a latent class analysis revealed three distinct EF groups, characterized by (a) multiple EF deficits, (b) relatively spared EF, and (c) perseverative responding. Follow-up analyses revealed that the classes differed significantly on NAT total errors, total commission errors, and total perseveration errors; the two classes with EF impairment performed comparably on the NAT but performed worse than the class with relatively spared EF. In sum, people with SZ demonstrate variable patterns of EF deficits, and distinct aspects of these EF deficit patterns (i.e., poor mental control abilities) may be associated with everyday functioning capabilities. PMID:23035705

Resting-State Functional Connectivity Predicts Cognitive Impairment Related to Alzheimer's Disease.

PubMed

Lin, Qi; Rosenberg, Monica D; Yoo, Kwangsun; Hsu, Tiffany W; O'Connell, Thomas P; Chun, Marvin M

2018-01-01

Resting-state functional connectivity (rs-FC) is a promising neuromarker for cognitive decline in aging population, based on its ability to reveal functional differences associated with cognitive impairment across individuals, and because rs-fMRI may be less taxing for participants than task-based fMRI or neuropsychological tests. Here, we employ an approach that uses rs-FC to predict the Alzheimer's Disease Assessment Scale (11 items; ADAS11) scores, which measure overall cognitive functioning, in novel individuals. We applied this technique, connectome-based predictive modeling, to a heterogeneous sample of 59 subjects from the Alzheimer's Disease Neuroimaging Initiative, including normal aging, mild cognitive impairment, and AD subjects. First, we built linear regression models to predict ADAS11 scores from rs-FC measured with Pearson's r correlation. The positive network model tested with leave-one-out cross validation (LOOCV) significantly predicted individual differences in cognitive function from rs-FC. In a second analysis, we considered other functional connectivity features, accordance and discordance, which disentangle the correlation and anticorrelation components of activity timecourses between brain areas. Using partial least square regression and LOOCV, we again built models to successfully predict ADAS11 scores in novel individuals. Our study provides promising evidence that rs-FC can reveal cognitive impairment in an aging population, although more development is needed for clinical application.

Functional Roles of Slow Enzyme Conformational Changes in Network Dynamics

PubMed Central

Wu, Zhanghan; Xing, Jianhua

2012-01-01

Extensive studies from different fields reveal that many macromolecules, especially enzymes, show slow transitions among different conformations. This phenomenon is named such things as dynamic disorder, heterogeneity, hysteretic or mnemonic enzymes across these different fields, and has been directly demonstrated by single molecule enzymology and NMR studies recently. We analyzed enzyme slow conformational changes in the context of regulatory networks. A single enzymatic reaction with slow conformational changes can filter upstream network noises, and can either resonantly respond to the system stimulus at certain frequencies or respond adaptively for sustained input signals of the network fluctuations. It thus can serve as a basic functional motif with properties that are normally for larger intermolecular networks in the field of systems biology. We further analyzed examples including enzymes functioning against pH fluctuations, metabolic state change of Artemia embryos, and kinetic insulation of fluctuations in metabolic networks. The study also suggests that hysteretic enzymes may be building blocks of synthetic networks with various properties such as narrow-banded filtering. The work fills the missing gap between studies on enzyme biophysics and network level dynamics, and reveals that the coupling between the two is functionally important; it also suggests that the conformational dynamics of some enzymes may be evolutionally selected. PMID:23009855

Greater widespread functional connectivity of the caudate in older adults who practice kripalu yoga and vipassana meditation than in controls

PubMed Central

Gard, Tim; Taquet, Maxime; Dixit, Rohan; Hölzel, Britta K.; Dickerson, Bradford C.; Lazar, Sara W.

2015-01-01

There has been a growing interest in understanding how contemplative practices affect brain functional organization. However, most studies have restricted their exploration to predefined networks. Furthermore, scientific comparisons of different contemplative traditions are largely lacking. Here we explored differences in whole brain resting state functional connectivity between experienced yoga practitioners, experienced meditators, and matched controls. Analyses were repeated in an independent sample of experienced meditators and matched controls. Analyses utilizing Network-Based Statistics (Zalesky et al., 2010) revealed difference components for yoga practitioners > controls and meditators > controls in which the right caudate was a central node. Follow up analyses revealed that yoga practitioners and meditators had significantly greater degree centrality in the caudate than controls. This greater degree centrality was not driven by single connections but by greater connectivity between the caudate and numerous brain regions. Findings of greater caudate connectivity in meditators than in controls was replicated in an independent dataset. These findings suggest that yoga and meditation practitioners have stronger functional connectivity within basal ganglia cortico-thalamic feedback loops than non-practitioners. Although we could not provide evidence for its mechanistic role, this greater connectivity might be related to the often reported effects of meditation and yoga on behavioral flexibility, mental health, and well-being. PMID:25852521

Microvalve controlled multi-functional microfluidic chip for divisional cell co-culture.

PubMed

Li, Rui; Zhang, Xingjian; Lv, Xuefei; Geng, Lina; Li, Yongrui; Qin, Kuiwei; Deng, Yulin

2017-12-15

Pneumatic micro-valve controlled microfluidic chip provides precise fluidic control for cell manipulation. In this paper, a multi-functional microfluidic chip was designed for three separate experiments: 1. Different cell lines were dispensed and cultured; 2. Three transfected SH-SY5Y cells were introduced and treated with methyl-phenyl-pyridinium (MPP + ) as drug delivery mode; 3. Specific protection and interaction were observed among cell co-culture after nerve damage. The outcomes revealed the potential and practicability of our entire multi-functional pneumatic chip system on different cell biology applications. Copyright © 2017. Published by Elsevier Inc.

Tagging methyl-CpG-binding domain proteins reveals different spatiotemporal expression and supports distinct functions.

PubMed

Wood, Kathleen H; Johnson, Brian S; Welsh, Sarah A; Lee, Jun Y; Cui, Yue; Krizman, Elizabeth; Brodkin, Edward S; Blendy, Julie A; Robinson, Michael B; Bartolomei, Marisa S; Zhou, Zhaolan

2016-04-01

DNA methylation is recognized by methyl-CpG-binding domain (MBD) proteins. Multiple MBDs are linked to neurodevelopmental disorders in humans and mice. However, the functions of MBD2 are poorly understood. We characterized Mbd2 knockout mice and determined spatiotemporal expression of MBDs and MBD2-NuRD (nucleosome remodeling deacetylase) interactions. We analyzed behavioral phenotypes, generated biotin-tagged MBD1 and MBD2 knockin mice, and performed biochemical studies of MBD2-NuRD. Most behavioral measures are minimally affected in Mbd2 knockout mice. In contrast to other MBDs, MBD2 shows distinct expression patterns. Unlike most MBDs, MBD2 is ubiquitously expressed in all tissues examined and appears dispensable for brain functions measured in this study. We provide novel genetic tools and reveal new directions to investigate MBD2 functions in vivo.

A study of accurate exchange-correlation functionals through adiabatic connection

NASA Astrophysics Data System (ADS)

Singh, Rabeet; Harbola, Manoj K.

2017-10-01

A systematic way of improving exchange-correlation energy functionals of density functional theory has been to make them satisfy more and more exact relations. Starting from the initial generalized gradient approximation (GGA) functionals, this has culminated into the recently proposed SCAN (strongly constrained and appropriately normed) functional that satisfies several known constraints and is appropriately normed. The ultimate test for the functionals developed is the accuracy of energy calculated by employing them. In this paper, we test these exchange-correlation functionals—the GGA hybrid functionals B3LYP and PBE0 and the meta-GGA functional SCAN—from a different perspective. We study how accurately these functionals reproduce the exchange-correlation energy when electron-electron interaction is scaled as αVee with α varying between 0 and 1. Our study reveals interesting comparison between these functionals and the associated difference Tc between the interacting and the non-interacting kinetic energy for the same density.

Application of a Novel Functional Gene Microarray to Probe the Functional Ecology of Ammonia Oxidation in Nitrifying Activated Sludge

PubMed Central

Short, Michael D.; Abell, Guy C. J.; Bodrossy, Levente; van den Akker, Ben

2013-01-01

We report on the first study trialling a newly-developed, functional gene microarray (FGA) for characterising bacterial and archaeal ammonia oxidisers in activated sludge. Mixed liquor (ML) and media biofilm samples from a full-scale integrated fixed-film activated sludge (IFAS) plant were analysed with the FGA to profile the diversity and relative abundance of ammonia-oxidising archaea and bacteria (AOA and AOB respectively). FGA analyses of AOA and AOB communities revealed ubiquitous distribution of AOA across all samples – an important finding for these newly-discovered and poorly characterised organisms. Results also revealed striking differences in the functional ecology of attached versus suspended communities within the IFAS reactor. Quantitative assessment of AOB and AOA functional gene abundance revealed a dominance of AOB in the ML and approximately equal distribution of AOA and AOB in the media-attached biofilm. Subsequent correlations of functional gene abundance data with key water quality parameters suggested an important functional role for media-attached AOB in particular for IFAS reactor nitrification performance and indicate possible functional redundancy in some IFAS ammonia oxidiser communities. Results from this investigation demonstrate the capacity of the FGA to resolve subtle ecological shifts in key microbial communities in nitrifying activated sludge and indicate its value as a tool for better understanding the linkages between the ecology and performance of these engineered systems. PMID:24155925

Consumer diversity across kingdoms supports multiple functions in a coastal ecosystem

PubMed Central

Hensel, Marc J. S.; Silliman, Brian R.

2013-01-01

The global biodiversity crisis impairs the valuable benefits ecosystems provide humans. These nature-generated benefits are defined by a multitude of different ecosystem functions that operate simultaneously. Although several studies have simulated species loss in communities and tracked the response of single functions such as productivity or nutrient cycling, these studies have involved relatively similar taxa, and seldom are strikingly different functions examined. With the exception of highly managed ecosystems such as agricultural fields, rarely are we interested in only one function being performed well. Instead, we rely on ecosystems to deliver several different functions at the same time. Here, we experimentally investigated the extinction impacts of dominant consumers in a salt marsh. These consumers are remarkably phylogenetically diverse, spanning two kingdoms (i.e., Animalia and Fungi). Our field studies reveal that a diverse consumer assemblage significantly enhances simultaneous functioning of disparate ecosystem processes (i.e., productivity, decomposition, and infiltration). Extreme functional and phylogenetic differences among consumers underlie this relationship. Each marsh consumer affected at least one different ecosystem function, and each individual function was affected by no more than two consumers. The implications of these findings are profound: If we want ecosystems to perform many different functions well, it is not just number of species that matter. Rather, the presence of species representing markedly different ecologies and biology is also essential to maximizing multiple functions. Moreover, this work emphasizes the need to incorporate both microcomponents and macrocomponents of food webs to accurately predict biodiversity declines on integrated-ecosystem functioning. PMID:24297926

Metabolomic and functional genomic analyses reveal varietal differences in bioactive compounds of cooked rice

USDA-ARS?s Scientific Manuscript database

Emerging evidence supports that cooked brown rice (Oryza sativa L.) contains metabolites with biomedical activities, yet little is known about the genetic diversity that is responsible for metabolite variation and differences in health beneficial traits. Metabolites from cooked brown rice of ten div...

Vibration responses of h-BN sheet to charge doping and external strain

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

Yang, Wei; Yang, Yu; Zheng, Fawei

2013-12-07

Based on density functional theory and density functional perturbation theory calculations, we systematically investigate the vibration responses of h-BN sheet to charge doping and external strains. It is found that under hole doping, the phonon frequencies of the ZO and TO branches at different wave vector q shift linearly with different slopes. Under electron doping, although the phonon frequencies shift irregularly, the shifting values are different at different phonon wave vectors. Interestingly, we find that external strain can restrain the irregular vibration responses of h-BN sheet to electron doping. The critical factor is revealed to be the relative position ofmore » the nearly free electron and boron p{sub z} states of h-BN sheet. Under external strains, the vibration responses of h-BN sheet are also found to be highly dependent on the phonon branches. Different vibration modes at different q points are revealed to be responsible for the vibration responses of h-BN sheet to charge doping and external strain. Our results point out a new way to detect the doping or strain status of h-BN sheet by measuring the vibration frequencies at different wave vector.« less

Evolution of the stellar mass function in multiple-population globular clusters

NASA Astrophysics Data System (ADS)

Vesperini, Enrico; Hong, Jongsuk; Webb, Jeremy J.; D'Antona, Franca; D'Ercole, Annibale

2018-05-01

We present the results of a survey of N-body simulations aimed at studying the effects of the long-term dynamical evolution on the stellar mass function (MF) of multiple stellar populations in globular clusters. Our simulations show that if first-(1G) and second-generation (2G) stars have the same initial MF (IMF), the global MFs of the two populations are affected similarly by dynamical evolution and no significant differences between the 1G and 2G MFs arise during the cluster's evolution. If the two populations have different IMFs, dynamical effects do not completely erase memory of the initial differences. Should observations find differences between the global 1G and 2G MFs, these would reveal the fingerprints of differences in their IMFs. Irrespective of whether the 1G and 2G populations have the same global IMF or not, dynamical effects can produce differences between the local (measured at various distances from the cluster centre) 1G and 2G MFs; these differences are a manifestation of the process of mass segregation in populations with different initial structural properties. In dynamically old and spatially mixed clusters, however, differences between the local 1G and 2G MFs can reveal differences between the 1G and 2G global MFs. In general, for clusters with any dynamical age, large differences between the local 1G and 2G MFs are more likely to be associated with differences in the global MF. Our study also reveals a dependence of the spatial mixing rate on the stellar mass, another dynamical consequence of the multiscale nature of multiple-population clusters.

Dimensional change card sort performance associated with age-related differences in functional connectivity of lateral prefrontal cortex.

PubMed

Ezekiel, Fredrick; Bosma, Rachael; Morton, J Bruce

2013-07-01

The Dimensional Change Card Sort (DCCS) is a standard procedure for assessing executive functioning early in development. In the task, participants switch from sorting cards one way (e.g., by color) to sorting them a different way (e.g., by shape). Traditional accounts associate age-related changes in DCCS performance with circumscribed changes in lateral prefrontal cortex (lPFC) functioning, but evidence of age-related differences in the modulation of lPFC activity by switching is mixed. The current study therefore tested for possible age-related differences in functional connectivity of lPFC with regions that comprise a larger cognitive control network. Functional magnetic resonance imaging (fMRI) data collected from children and adults performing the DCCS were analyzed by means of independent components analysis (ICA). The analysis revealed several important age-related differences in functional connectivity of lPFC. In particular, lPFC was more strongly connected with the anterior cingulate, inferior parietal cortex, and the ventral tegmental area in adults than in children. Theoretical implications are discussed. Copyright © 2012 Elsevier Ltd. All rights reserved.

Differential Effects of the Catechol-O-Methyltransferase Val158Met Genotype on the Cognitive Function of Schizophrenia Patients and Healthy Japanese Individuals

PubMed Central

Tsuchimine, Shoko; Yasui-Furukori, Norio; Kaneda, Ayako; Kaneko, Sunao

2013-01-01

Background The functional polymorphism Val158Met in the catechol-O-methyltransferase (COMT) gene has been associated with differences in prefrontal cognitive functions in patients with schizophrenia and healthy individuals. Several studies have indicated that the Met allele is associated with better performance on measures of cognitive function. We investigated whether the COMT Val158Met genotype was associated with cognitive function in 149 healthy controls and 118 patients with schizophrenia. Methods Cognitive function, including verbal memory, working memory, motor speed, attention, executive function and verbal fluency, was assessed by the Brief Assessment of Cognition in Schizophrenia (BACS-J). We employed a one-way analysis of variance (ANOVA) and a multiple regression analysis to determine the associations between the COMT Val158Met genotype and the BACS-J measurements. Results The one-way ANOVA revealed a significant difference in the scores on the Tower of London, a measure of executive function, between the different Val158Met genotypes in the healthy controls (p = 0.023), and a post-hoc analysis showed significant differences between the scores on the Tower of London in the val/val genotype group (18.6 ± 2.4) compared to the other two groups (17.6 ± 2.7 for val/met and 17.1 ± 3.2 for met/met; p = 0.027 and p = 0.024, respectively). Multiple regression analyses revealed that executive function was significantly correlated with the Val158Met genotype (p = 0.003). However, no evidence was found for an effect of the COMT on any cognitive domains of the BACS-J in the patients with schizophrenia. Conclusion These data support the hypothesis that the COMT Val158Met genotype maintains an optimal level of dopamine activity. Further studies should be performed that include a larger sample size and include patients on and off medication, as these patients would help to confirm our findings. PMID:24282499

Evolutionary Functions of Social Play: Life Histories, Sex Differences, and Emotion Regulation

ERIC Educational Resources Information Center

LaFreniere, Peter

2011-01-01

Many research findings about animal play apply to children's play, revealing structural and functional similarities with mammals in general and primates in particular. After an introduction to life-history theory, and before turning to humans, the author reviews research about the two mammals in which play has been studied the most extensively:…

Using Differential Item Functioning Procedures to Explore Sources of Item Difficulty and Group Performance Characteristics.

ERIC Educational Resources Information Center

Scheuneman, Janice Dowd; Gerritz, Kalle

1990-01-01

Differential item functioning (DIF) methodology for revealing sources of item difficulty and performance characteristics of different groups was explored. A total of 150 Scholastic Aptitude Test items and 132 Graduate Record Examination general test items were analyzed. DIF was evaluated for males and females and Blacks and Whites. (SLD)

Emotional Regulation and Executive Function Deficits in Unmedicated Chinese Children with Oppositional Defiant Disorder.

PubMed

Jiang, Wenqing; Li, Yan; Du, Yasong; Fan, Juan

2016-05-01

This study aims to explore the feature of emotional regulation and executive functions in oppositional defiant disorder (ODD) children. The emotional regulation and executive functions of adolescents with ODD, as well as the relationship between the two factors were analyzed using tools including Adolescent Daily Emotional Regulation Questionnaire (ADERQ), Wisconsin Card Sorting Test (WCST) and Cambridge Neuropsychological Test Automated Battery (CANTAB), in comparison with attention deficit hyperactivity disorder (ADHD) children without behavioral problem and healthy children; the ADERQ assessed emotional regulation ability and others were used to assess executive function. Compared to normal children, the ODD group displayed significant differences in the scores of cognitive reappraisal, rumination, expressive suppression, and revealing of negative emotions, as well as in the score of cognitive reappraisal of positive emotions. WCST perseverative errors were well correlated with rumination of negative emotions (r=0.47). Logistic regression revealed that the minimum number of moves in the Stocking of Cambridge (SOC) test (one test in CANTAB) and negative emotion revealing, were strongly associated with ODD diagnosis. Children with ODD showed emotion dysregulation, with negative emotion dysregulation as the main feature. Emotion dysregulation and the lack of ability to plan lead to executive function deficits. The executive function deficits may guide us to understand the deep mechanism under ODD.

A genetic screen for vascular mutants in zebrafish reveals dynamic roles for Vegf/Plcg1 signaling during artery development.

PubMed

Covassin, L D; Siekmann, A F; Kacergis, M C; Laver, E; Moore, J C; Villefranc, J A; Weinstein, B M; Lawson, N D

2009-05-15

In this work we describe a forward genetic approach to identify mutations that affect blood vessel development in the zebrafish. By applying a haploid screening strategy in a transgenic background that allows direct visualization of blood vessels, it was possible to identify several classes of mutant vascular phenotypes. Subsequent characterization of mutant lines revealed that defects in Vascular endothelial growth factor (Vegf) signaling specifically affected artery development. Comparison of phenotypes associated with different mutations within a functional zebrafish Vegf receptor-2 ortholog (referred to as kdr-like, kdrl) revealed surprisingly varied effects on vascular development. In parallel, we identified an allelic series of mutations in phospholipase c gamma 1 (plcg1). Together with in vivo structure-function analysis, our results suggest a requirement for Plcg1 catalytic activity downstream of receptor tyrosine kinases. We further find that embryos lacking both maternal and zygotic plcg1 display more severe defects in artery differentiation but are otherwise similar to zygotic mutants. Finally, we demonstrate through mosaic analysis that plcg1 functions autonomously in endothelial cells. Together our genetic analyses suggest that Vegf/Plcg1 signaling acts at multiple time points and in different signaling contexts to mediate distinct aspects of artery development.

A genetic screen for vascular mutants in zebrafish reveals dynamic roles for Vegf/Plcg1 signaling during artery development

PubMed Central

Covassin, L. D.; Siekmann, A. F.; Kacergis, M. C.; Laver, E.; Moore, J. C.; Villefranc, J. A.; Weinstein, B. M.; Lawson, N. D.

2009-01-01

In this work we describe a forward genetic approach to identify mutations that affect blood vessel development in the zebrafish. By applying a haploid screening strategy in a transgenic background that allows direct visualization of blood vessels, it was possible to identify several classes of mutant vascular phenotypes. Subsequent characterization of mutant lines revealed that defects in Vascular endothelial growth factor (Vegf) signaling specifically affected artery development. Comparison of phenotypes associated with different mutations within a functional zebrafish Vegf receptor-2 ortholog (referred to as kdr-like, kdrl) revealed surprisingly varied effects on vascular development. In parallel, we identified an allelic series of mutations in phospholipase c gamma 1 (plcg1). Together with in vivo structure-function analysis, our results suggest a requirement for Plcg1 catalytic activity downstream of receptor tyrosine kinases. We further find that embryos lacking both maternal and zygotic plcg1 display more severe defects in artery differentiation but are otherwise similar to zygotic mutants. Finally, we demonstrate through mosaic analysis that plcg1 functions autonomously in endothelial cells. Together our genetic analyses suggest that Vegf/Plcg1 signaling acts at multiple time points and in different signaling contexts to mediate distinct aspects of artery development. PMID:19269286

A simple method for assessment of muscle force, velocity, and power producing capacities from functional movement tasks.

PubMed

Zivkovic, Milena Z; Djuric, Sasa; Cuk, Ivan; Suzovic, Dejan; Jaric, Slobodan

2017-07-01

A range of force (F) and velocity (V) data obtained from functional movement tasks (e.g., running, jumping, throwing, lifting, cycling) performed under variety of external loads have typically revealed strong and approximately linear F-V relationships. The regression model parameters reveal the maximum F (F-intercept), V (V-intercept), and power (P) producing capacities of the tested muscles. The aim of the present study was to evaluate the level of agreement between the routinely used "multiple-load model" and a simple "two-load model" based on direct assessment of the F-V relationship from only 2 external loads applied. Twelve participants were tested on the maximum performance vertical jumps, cycling, bench press throws, and bench pull performed against a variety of different loads. All 4 tested tasks revealed both exceptionally strong relationships between the parameters of the 2 models (median R = 0.98) and a lack of meaningful differences between their magnitudes (fixed bias below 3.4%). Therefore, addition of another load to the standard tests of various functional tasks typically conducted under a single set of mechanical conditions could allow for the assessment of the muscle mechanical properties such as the muscle F, V, and P producing capacities.

Acetylproteomic Analysis Reveals Functional Implications of Lysine Acetylation in Human Spermatozoa (sperm)*

PubMed Central

Yu, Heguo; Diao, Hua; Wang, Chunmei; Lin, Yan; Yu, Fudong; Lu, Hui; Xu, Wei; Li, Zheng; Shi, Huijuan; Zhao, Shimin; Zhou, Yuchuan; Zhang, Yonglian

2015-01-01

Male infertility is a medical condition that has been on the rise globally. Lysine acetylation of human sperm, an essential posttranslational modification involved in the etiology of sperm abnormality, is not fully understood. Therefore, we first generated a qualified pan-anti-acetyllysine monoclonal antibody to characterize the global lysine acetylation of uncapacitated normal human sperm with a proteomics approach. With high enrichment ratios that were up to 31%, 973 lysine-acetylated sites that matched to 456 human sperm proteins, including 671 novel lysine acetylation sites and 205 novel lysine-acetylated proteins, were identified. These proteins exhibited conserved motifs XXXKYXXX, XXXKFXXX, and XXXKHXXX, were annotated to function in multiple metabolic processes, and were localized predominantly in the mitochondrion and cytoplasmic fractions. Between the uncapacitated and capacitated sperm, different acetylation profiles in regard to functional proteins involved in sperm capacitation, sperm-egg recognition, sperm-egg plasma fusion, and fertilization were observed, indicating that acetylation of functional proteins may be required during sperm capacitation. Bioinformatics analysis revealed association of acetylated proteins with diseases and drugs. Novel acetylation of voltage-dependent anion channel proteins was also found. With clinical sperm samples, we observed differed lysine acetyltransferases and lysine deacetylases expression between normal sperm and abnormal sperm of asthenospermia or necrospermia. Furthermore, with sperm samples impaired by epigallocatechin gallate to mimic asthenospermia, we observed that inhibition of sperm motility was partly through the blockade of voltage-dependent anion channel 2 Lys-74 acetylation combined with reduced ATP levels and mitochondrial membrane potential. Taken together, we obtained a qualified pan-anti-acetyllysine monoclonal antibody, analyzed the acetylproteome of uncapacitated human sperm, and revealed associations between functional protein acetylation and sperm functions. PMID:25680958

Rebelling for a Reason: Protein Structural “Outliers”

PubMed Central

Arumugam, Gandhimathi; Nair, Anu G.; Hariharaputran, Sridhar; Ramanathan, Sowdhamini

2013-01-01

Analysis of structural variation in domain superfamilies can reveal constraints in protein evolution which aids protein structure prediction and classification. Structure-based sequence alignment of distantly related proteins, organized in PASS2 database, provides clues about structurally conserved regions among different functional families. Some superfamily members show large structural differences which are functionally relevant. This paper analyses the impact of structural divergence on function for multi-member superfamilies, selected from the PASS2 superfamily alignment database. Functional annotations within superfamilies, with structural outliers or ‘rebels’, are discussed in the context of structural variations. Overall, these data reinforce the idea that functional similarities cannot be extrapolated from mere structural conservation. The implication for fold-function prediction is that the functional annotations can only be inherited with very careful consideration, especially at low sequence identities. PMID:24073209

Functional performance testing in participants with functional ankle instability and in a healthy control group.

PubMed

Buchanan, Amanda S; Docherty, Carrie L; Schrader, John

2008-01-01

Functional ankle instability (FAI) affects a large part of the population. Inconsistent findings have been reported regarding the existence of functional performance deficits in individuals with FAI. To examine functional performance in participants with FAI compared with participants in a control group during 2 hopping tests. Case-control study. Athletic training research laboratory. There were 40 college-aged individuals who participated in our study: 20 with FAI and 20 without FAI. We defined FAI as history of an ankle sprain and residual episodes of "giving way." Participants completed 2 functional performance tests (FPTs): the single-limb hopping and the single-limb hurdle tests. Time to complete each test was recorded. Following each FPT, participants were asked if their ankles felt unstable during the test. We found no difference between participants in the FAI and control groups for the hopping or hurdle tests (P > .05). When asked if their ankles felt unstable during the FPTs, approximately half of the participants in the FAI group and none of the participants in the control group reported a feeling of instability. Subsequently, a secondary analysis of variance was calculated with participants grouped into 3 categories: control participants, FAI participants reporting instability symptoms during FPT (FAI-S), and FAI participants not reporting instability symptoms during FPT (FAI-NS). Results revealed a difference among the 3 groups for the single-limb hopping test (P < .01). Post hoc analysis revealed a difference between the FAI-S participants and both the control and the FAI-NS participants. No difference was identified for the single-limb hurdle test (P = .41). The FAI-S participants had performance deficits during the single-limb hopping test. Therefore, clinicians could use this simple hopping test as an additional method to determine the presence of FAI.

Effects of aripiprazole and haloperidol on neural activation during a simple motor task in healthy individuals: A functional MRI study.

PubMed

Goozee, Rhianna; O'Daly, Owen; Handley, Rowena; Reis Marques, Tiago; Taylor, Heather; McQueen, Grant; Hubbard, Kathryn; Pariante, Carmine; Mondelli, Valeria; Reinders, Antje A T S; Dazzan, Paola

2017-04-01

The dopaminergic system plays a key role in motor function and motor abnormalities have been shown to be a specific feature of psychosis. Due to their dopaminergic action, antipsychotic drugs may be expected to modulate motor function, but the precise effects of these drugs on motor function remain unclear. We carried out a within-subject, double-blind, randomized study of the effects of aripiprazole, haloperidol and placebo on motor function in 20 healthy men. For each condition, motor performance on an auditory-paced task was investigated. We entered maps of neural activation into a random effects general linear regression model to investigate motor function main effects. Whole-brain imaging revealed a significant treatment effect in a distributed network encompassing posterior orbitofrontal/anterior insula cortices, and the inferior temporal and postcentral gyri. Post-hoc comparison of treatments showed neural activation after aripiprazole did not differ significantly from placebo in either voxel-wise or region of interest analyses, with the results above driven primarily by haloperidol. We also observed a simple main effect of haloperidol compared with placebo, with increased task-related recruitment of posterior cingulate and precentral gyri. Furthermore, region of interest analyses revealed greater activation following haloperidol compared with placebo in the precentral and post-central gyri, and the putamen. These diverse modifications in cortical motor activation may relate to the different pharmacological profiles of haloperidol and aripiprazole, although the specific mechanisms underlying these differences remain unclear. Evaluating healthy individuals can allow investigation of the effects of different antipsychotics on cortical activation, independently of either disease-related pathology or previous treatment. Hum Brain Mapp 38:1833-1845, 2017. © 2017 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Transcriptomic basis for drought-resistance in Brassica napus L.

NASA Astrophysics Data System (ADS)

Wang, Pei; Yang, Cuiling; Chen, Hao; Song, Chunpeng; Zhang, Xiao; Wang, Daojie

2017-01-01

Based on transcriptomic data from four experimental settings with drought-resistant and drought-sensitive cultivars under drought and well-watered conditions, statistical analysis revealed three categories encompassing 169 highly differentially expressed genes (DEGs) in response to drought in Brassica napus L., including 37 drought-resistant cultivar-related genes, 35 drought-sensitive cultivar-related genes and 97 cultivar non-specific ones. We provide evidence that the identified DEGs were fairly uniformly distributed on different chromosomes and their expression patterns are variety specific. Except commonly enriched in response to various stimuli or stresses, different categories of DEGs show specific enrichment in certain biological processes or pathways, which indicated the possibility of functional differences among the three categories. Network analysis revealed relationships among the 169 DEGs, annotated biological processes and pathways. The 169 DEGs can be classified into different functional categories via preferred pathways or biological processes. Some pathways might simultaneously involve a large number of shared DEGs, and these pathways are likely to cross-talk and have overlapping biological functions. Several members of the identified DEGs fit to drought stress signal transduction pathway in Arabidopsis thaliana. Finally, quantitative real-time PCR validations confirmed the reproducibility of the RNA-seq data. These investigations are profitable for the improvement of crop varieties through transgenic engineering.

A multivariate analysis of age-related differences in functional networks supporting conflict resolution.

PubMed

Salami, Alireza; Rieckmann, Anna; Fischer, Håkan; Bäckman, Lars

2014-02-01

Functional neuroimaging studies demonstrate age-related differences in recruitment of a large-scale attentional network during interference resolution, especially within dorsolateral prefrontal cortex (DLPFC) and anterior cingulate cortex (ACC). These alterations in functional responses have been frequently observed despite equivalent task performance, suggesting age-related reallocation of neural resources, although direct evidence for a facilitating effect in aging is sparse. We used the multi-source interference task and multivariate partial-least-squares to investigate age-related differences in the neuronal signature of conflict resolution, and their behavioral implications in younger and older adults. There were interference-related increases in activity, involving fronto-parietal and basal ganglia networks that generalized across age. In addition an age-by-task interaction was observed within a distributed network, including DLPFC and ACC, with greater activity during interference in the old. Next, we combined brain-behavior and functional connectivity analyses to investigate whether compensatory brain changes were present in older adults, using DLPFC and ACC as regions of interest (i.e. seed regions). This analysis revealed two networks differentially related to performance across age groups. A structural analysis revealed age-related gray-matter losses in regions facilitating performance in the young, suggesting that functional reorganization may partly reflect structural alterations in aging. Collectively, these findings suggest that age-related structural changes contribute to reductions in the efficient recruitment of a youth-like interference network, which cascades into instantiation of a different network facilitating conflict resolution in elderly people. © 2013. Published by Elsevier Inc. All rights reserved.

Triple representation of language, working memory, social and emotion processing in the cerebellum: convergent evidence from task and seed-based resting-state fMRI analyses in a single large cohort.

PubMed

Guell, Xavier; Gabrieli, John D E; Schmahmann, Jeremy D

2018-05-15

Delineation of functional topography is critical to the evolving understanding of the cerebellum's role in a wide range of nervous system functions. We used data from the Human Connectome Project (n = 787) to analyze cerebellar fMRI task activation (motor, working memory, language, social and emotion processing) and resting-state functional connectivity calculated from cerebral cortical seeds corresponding to the peak Cohen's d of each task contrast. The combination of exceptional statistical power, activation from both motor and multiple non-motor tasks in the same participants, and convergent resting-state networks in the same participants revealed novel aspects of the functional topography of the human cerebellum. Consistent with prior studies there were two distinct representations of motor activation. Newly revealed were three distinct representations each for working memory, language, social, and emotional task processing that were largely separate for these four cognitive and affective domains. In most cases, the task-based activations and the corresponding resting-network correlations were congruent in identifying the two motor representations and the three non-motor representations that were unique to working memory, language, social cognition, and emotion. The definitive localization and characterization of distinct triple representations for cognition and emotion task processing in the cerebellum opens up new basic science questions as to why there are triple representations (what different functions are enabled by the different representations?) and new clinical questions (what are the differing consequences of lesions to the different representations?). Copyright © 2018 Elsevier Inc. All rights reserved.

Functional network connectivity analysis based on partial correlation in Alzheimer's disease

NASA Astrophysics Data System (ADS)

Zhang, Nan; Guan, Xiaoting; Zhang, Yumei; Li, Jingjing; Chen, Hongyan; Chen, Kewei; Fleisher, Adam; Yao, Li; Wu, Xia

2009-02-01

Functional network connectivity (FNC) measures the temporal dependency among the time courses of functional networks. However, the marginal correlation between two networks used in the classic FNC analysis approach doesn't separate the FNC from the direct/indirect effects of other networks. In this study, we proposed an alternative approach based on partial correlation to evaluate the FNC, since partial correlation based FNC can reveal the direct interaction between a pair of networks, removing dependencies or influences from others. Previous studies have demonstrated less task-specific activation and less rest-state activity in Alzheimer's disease (AD). We applied present approach to contrast FNC differences of resting state network (RSN) between AD and normal controls (NC). The fMRI data under resting condition were collected from 15 AD and 16 NC. FNC was calculated for each pair of six RSNs identified using Group ICA, thus resulting in 15 (2 out of 6) pairs for each subject. Partial correlation based FNC analysis indicated 6 pairs significant differences between groups, while marginal correlation only revealed 2 pairs (involved in the partial correlation results). Additionally, patients showed lower correlation than controls among most of the FNC differences. Our results provide new evidences for the disconnection hypothesis in AD.

Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality.

PubMed

Jiang, Yue; Xiong, Xuejian; Danska, Jayne; Parkinson, John

2016-01-12

Metatranscriptomics is emerging as a powerful technology for the functional characterization of complex microbial communities (microbiomes). Use of unbiased RNA-sequencing can reveal both the taxonomic composition and active biochemical functions of a complex microbial community. However, the lack of established reference genomes, computational tools and pipelines make analysis and interpretation of these datasets challenging. Systematic studies that compare data across microbiomes are needed to demonstrate the ability of such pipelines to deliver biologically meaningful insights on microbiome function. Here, we apply a standardized analytical pipeline to perform a comparative analysis of metatranscriptomic data from diverse microbial communities derived from mouse large intestine, cow rumen, kimchi culture, deep-sea thermal vent and permafrost. Sequence similarity searches allowed annotation of 19 to 76% of putative messenger RNA (mRNA) reads, with the highest frequency in the kimchi dataset due to its relatively low complexity and availability of closely related reference genomes. Metatranscriptomic datasets exhibited distinct taxonomic and functional signatures. From a metabolic perspective, we identified a common core of enzymes involved in amino acid, energy and nucleotide metabolism and also identified microbiome-specific pathways such as phosphonate metabolism (deep sea) and glycan degradation pathways (cow rumen). Integrating taxonomic and functional annotations within a novel visualization framework revealed the contribution of different taxa to metabolic pathways, allowing the identification of taxa that contribute unique functions. The application of a single, standard pipeline confirms that the rich taxonomic and functional diversity observed across microbiomes is not simply an artefact of different analysis pipelines but instead reflects distinct environmental influences. At the same time, our findings show how microbiome complexity and availability of reference genomes can impact comprehensive annotation of metatranscriptomes. Consequently, beyond the application of standardized pipelines, additional caution must be taken when interpreting their output and performing downstream, microbiome-specific, analyses. The pipeline used in these analyses along with a tutorial has been made freely available for download from our project website: http://www.compsysbio.org/microbiome .

Comparison of S. cerevisiae F-BAR domain structures reveals a conserved inositol phosphate binding site

PubMed Central

Moravcevic, Katarina; Alvarado, Diego; Schmitz, Karl R.; Kenniston, Jon A.; Mendrola, Jeannine M.; Ferguson, Kathryn M.; Lemmon, Mark A.

2015-01-01

SUMMARY F-BAR domains control membrane interactions in endocytosis, cytokinesis, and cell signaling. Although generally thought to bind curved membranes containing negatively charged phospholipids, numerous functional studies argue that differences in lipid-binding selectivities of F-BAR domains are functionally important. Here, we compare membrane-binding properties of the S. cerevisiae F-BAR domains in vitro and in vivo. Whereas some F-BAR domains (such as Bzz1p and Hof1p F-BARs) bind equally well to all phospholipids, the F-BAR domain from the RhoGAP Rgd1p preferentially binds phosphoinositides. We determined X-ray crystal structures of F-BAR domains from Hof1p and Rgd1p, the latter bound to an inositol phosphate. The structures explain phospholipid-binding selectivity differences, and reveal an F-BAR phosphoinositide binding site that is fully conserved in a mammalian RhoGAP called Gmip, and is partly retained in certain other F-BAR domains. Our findings reveal previously unappreciated determinants of F-BAR domain lipid-binding specificity, and provide a basis for its prediction from sequence. PMID:25620000

Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit

PubMed Central

Baerenfaller, Katja; Massonnet, Catherine; Walsh, Sean; Baginsky, Sacha; Bühlmann, Peter; Hennig, Lars; Hirsch-Hoffmann, Matthias; Howell, Katharine A; Kahlau, Sabine; Radziejwoski, Amandine; Russenberger, Doris; Rutishauser, Dorothea; Small, Ian; Stekhoven, Daniel; Sulpice, Ronan; Svozil, Julia; Wuyts, Nathalie; Stitt, Mark; Hilson, Pierre; Granier, Christine; Gruissem, Wilhelm

2012-01-01

Leaves have a central role in plant energy capture and carbon conversion and therefore must continuously adapt their development to prevailing environmental conditions. To reveal the dynamic systems behaviour of leaf development, we profiled Arabidopsis leaf number six in depth at four different growth stages, at both the end-of-day and end-of-night, in plants growing in two controlled experimental conditions: short-day conditions with optimal soil water content and constant reduced soil water conditions. We found that the lower soil water potential led to reduced, but prolonged, growth and an adaptation at the molecular level without a drought stress response. Clustering of the protein and transcript data using a decision tree revealed different patterns in abundance changes across the growth stages and between end-of-day and end-of-night that are linked to specific biological functions. Correlations between protein and transcript levels depend on the time-of-day and also on protein localisation and function. Surprisingly, only very few of >1700 quantified proteins showed diurnal abundance fluctuations, despite strong fluctuations at the transcript level. PMID:22929616

MAP kinase pathways in the yeast Saccharomyces cerevisiae

NASA Technical Reports Server (NTRS)

Gustin, M. C.; Albertyn, J.; Alexander, M.; Davenport, K.; McIntire, L. V. (Principal Investigator)

1998-01-01

A cascade of three protein kinases known as a mitogen-activated protein kinase (MAPK) cascade is commonly found as part of the signaling pathways in eukaryotic cells. Almost two decades of genetic and biochemical experimentation plus the recently completed DNA sequence of the Saccharomyces cerevisiae genome have revealed just five functionally distinct MAPK cascades in this yeast. Sexual conjugation, cell growth, and adaptation to stress, for example, all require MAPK-mediated cellular responses. A primary function of these cascades appears to be the regulation of gene expression in response to extracellular signals or as part of specific developmental processes. In addition, the MAPK cascades often appear to regulate the cell cycle and vice versa. Despite the success of the gene hunter era in revealing these pathways, there are still many significant gaps in our knowledge of the molecular mechanisms for activation of these cascades and how the cascades regulate cell function. For example, comparison of different yeast signaling pathways reveals a surprising variety of different types of upstream signaling proteins that function to activate a MAPK cascade, yet how the upstream proteins actually activate the cascade remains unclear. We also know that the yeast MAPK pathways regulate each other and interact with other signaling pathways to produce a coordinated pattern of gene expression, but the molecular mechanisms of this cross talk are poorly understood. This review is therefore an attempt to present the current knowledge of MAPK pathways in yeast and some directions for future research in this area.

Fusion and Fission of Cognitive Functions in the Human Parietal Cortex

PubMed Central

Humphreys, Gina F.; Lambon Ralph, Matthew A.

2015-01-01

How is higher cognitive function organized in the human parietal cortex? A century of neuropsychology and 30 years of functional neuroimaging has implicated the parietal lobe in many different verbal and nonverbal cognitive domains. There is little clarity, however, on how these functions are organized, that is, where do these functions coalesce (implying a shared, underpinning neurocomputation) and where do they divide (indicating different underlying neural functions). Until now, there has been no multi-domain synthesis in order to reveal where there is fusion or fission of functions in the parietal cortex. This aim was achieved through a large-scale activation likelihood estimation (ALE) analysis of 386 studies (3952 activation peaks) covering 8 cognitive domains. A tripartite, domain-general neuroanatomical division and 5 principles of cognitive organization were established, and these are discussed with respect to a unified theory of parietal functional organization. PMID:25205661

Relationship between function of masticatory muscle in mouse and properties of muscle fibers.

PubMed

Abe, Shinichi; Hiroki, Emi; Iwanuma, Osamu; Sakiyama, Koji; Shirakura, Yoshitaka; Hirose, Daiki; Shimoo, Yoshiaki; Suzuki, Masashi; Ikari, Yasutoyo; Kikuchi, Ryusuke; Ide, Yoshinobu; Yoshinari, Masao

2008-05-01

Mammals exhibit marked morphological differences in the muscles surrounding the jaw bone due to differences in eating habits. Furthermore, the myofiber properties of the muscles differ with function. Since the muscles in the oral region have various functions such as eating, swallowing, and speech, it is believed that the functional role of each muscle differs. Therefore, to clarify the functional role of each masticatory muscle, the myofiber properties of the adult mouse masticatory muscles were investigated at the transcriptional level. Expression of MyHC-2b with a fast contraction rate and strong force was frequently noted in the temporal and masseter muscles. This suggests that the temporal and masseter muscles are closely involved in rapid antero-posterior masticatory movement, which is characteristic in mice. Furthermore, expression of MyHC-1 with a low contraction rate and weak continuous force was frequently detected in the lateral pterygoid muscle. This suggests that, in contrast to other masticatory muscles, mouse lateral pterygoid muscle is not involved in fast masticatory movement, but is involved in functions requiring continuous force such as retention of jaw position. This study revealed that muscles with different roles function comprehensively during complicated masticatory movement.

Differences in Brain Adaptive Functional Reorganization in Right and Left Total Brachial Plexus Injury Patients.

PubMed

Feng, Jun-Tao; Liu, Han-Qiu; Xu, Jian-Guang; Gu, Yu-Dong; Shen, Yun-Dong

2015-09-01

Total brachial plexus avulsion injury (BPAI) results in the total functional loss of the affected limb and induces extensive brain functional reorganization. However, because the dominant hand is responsible for more cognitive-related tasks, injuries on this side induce more adaptive changes in brain function. In this article, we explored the differences in brain functional reorganization after injuries in unilateral BPAI patients. We applied resting-state functional magnetic resonance imaging scanning to 10 left and 10 right BPAI patients and 20 healthy control subjects. The amplitude of low-frequency fluctuation (ALFF), which is a resting-state index, was calculated for all patients as an indication of the functional activity level of the brain. Two-sample t-tests were performed between left BPAI patients and controls, right BPAI patients and controls, and between left and right BPAI patients. Two-sample t-tests of the ALFF values revealed that right BPAIs induced larger scale brain reorganization than did left BPAIs. Both left and right BPAIs elicited a decreased ALFF value in the right precuneus (P < 0.05, Alphasim corrected). In addition, right BPAI patients exhibited increased ALFF values in a greater number of brain regions than left BPAI patients, including the inferior temporal gyrus, lingual gyrus, calcarine sulcus, and fusiform gyrus. Our results revealed that right BPAIs induced greater extents of brain functional reorganization than left BPAIs, which reflected the relatively more extensive adaptive process that followed injuries of the dominant hand. Copyright © 2015 Elsevier Inc. All rights reserved.

Relationships between regional cerebellar volume and sensorimotor and cognitive function in young and older adults

PubMed Central

Bernard, Jessica A.; Seidler, Rachael D.

2013-01-01

The cerebellum has been implicated in both sensorimotor and cognitive function, but is known to undergo volumetric declines with advanced age. Individual differences in regional cerebellar volume may therefore provide insight into performance variability across the lifespan, as has been shown with other brain structures and behaviors. Here, we investigated whether there are regional age differences in cerebellar volume in young and older adults, and whether these volumes explain, in part, individual differences in sensorimotor and cognitive task performance. We found that older adults had smaller cerebellar volume than young adults; specifically, lobules in the anterior cerebellum were more impacted by age. Multiple regression analyses for both age groups revealed associations between sensorimotor task performance in several domains (balance, choice reaction time, and timing) and regional cerebellar volume. There were also relationships with working memory, but none with measures of general cognitive or executive function. Follow-up analyses revealed several differential relationships with age between regional volume and sensorimotor performance. These relationships were predominantly selective to cerebellar regions that have been implicated in cognitive functions. Therefore, it may be the cognitive aspects of sensorimotor task performance that are best explained by individual differences in regional cerebellar volumes. In sum, our results demonstrate the importance of regional cerebellar volume with respect to both sensorimotor and cognitive performance, and we provide additional insight into the role of the cerebellum in age-related performance declines. PMID:23625382

The Rubber Hand Illusion Reveals Proprioceptive and Sensorimotor Differences in Autism Spectrum Disorders

ERIC Educational Resources Information Center

Paton, Bryan; Hohwy, Jakob; Enticott, Peter G.

2012-01-01

Autism spectrum disorder (ASD) is characterised by differences in unimodal and multimodal sensory and proprioceptive processing, with complex biases towards local over global processing. Many of these elements are implicated in versions of the rubber hand illusion (RHI), which were therefore studied in high-functioning individuals with ASD and a…

Comparative Job Attributes of Airmen and Civil Service Personnel Having Similar Job Types.

ERIC Educational Resources Information Center

Garza, Andrew T.; Carpenter, James B.

Military and civil service personnel having similar job types and from comparable accounting and finance career ladders were compared on several attributes. The data reveal certain distinct differences between the two populations with the magnitude of the differences being highly variable as functions of specific job types considered. Generally,…

Functional imaging of brain responses to different outcomes of hypothesis testing: revealed in a category induction task.

PubMed

Li, Fuhong; Cao, Bihua; Luo, Yuejia; Lei, Yi; Li, Hong

2013-02-01

Functional magnetic resonance imaging (fMRI) was used to examine differences in brain activation that occur when a person receives the different outcomes of hypothesis testing (HT). Participants were provided with a series of images of batteries and were asked to learn a rule governing what kinds of batteries were charged. Within each trial, the first two charged batteries were sequentially displayed, and participants would generate a preliminary hypothesis based on the perceptual comparison. Next, a third battery that served to strengthen, reject, or was irrelevant to the preliminary hypothesis was displayed. The fMRI results revealed that (1) no significant differences in brain activation were found between the 2 hypothesis-maintain conditions (i.e., strengthen and irrelevant conditions); and (2) compared with the hypothesis-maintain conditions, the hypothesis-reject condition activated the left medial frontal cortex, bilateral putamen, left parietal cortex, and right cerebellum. These findings are discussed in terms of the neural correlates of the subcomponents of HT and working memory manipulation. Copyright © 2012 Elsevier Inc. All rights reserved.

Transcriptional and functional defects of dendritic cells derived from the MUTZ-3 leukaemia line

PubMed Central

Rasaiyaah, Jane; Noursadeghi, Mahdad; Kellam, Paul; Chain, Benjamin

2009-01-01

Dendritic cells (DC) generated from MUTZ-3, an immortalized acute myeloid leukaemia-derived cell line, have potential application as a model for the study of human DC, and as a tool with which to stimulate immunotherapeutic responses to cancer. However, the relationship of MUTZ-3 DC to their non-transformed counterparts remains incompletely understood. Immunoselected CD14+ MUTZ-3 cells were used to generate a homogeneous population of DC (M3DC). These cells had a cell surface phentoype and morphology characteristic of conventional monocyte-derived DC (MDDC). Whole genome transcriptome comparison of M3DC and MDDC however, revealed extensive differences between these two cell types. Functional ontology-based data analysis revealed three enriched clusters of genes downregulated in M3DC, with functions in pathogen recognition, DC maturation and cytokine/chemokine signalling. Downregulation of protein expression was confirmed for several of these genes. The molecular differences were accompanied by a profoundly impaired phenotypic and functional response of M3DC to microbial stimulation. The immortalized phenotype of MUTZ-3 therefore reflects not only deregulated proliferative capacity, but substantial perturbation of normal antigen-presenting cell function. These results have important implications for studies using MUTZ-3 as a model of MDDC or for cancer immunotherapy. PMID:19538250

Community assembly of the ferns of Florida.

PubMed

Sessa, Emily B; Chambers, Sally M; Li, Daijiang; Trotta, Lauren; Endara, Lorena; Burleigh, J Gordon; Baiser, Benjamin

2018-03-01

Many ecological and evolutionary processes shape the assembly of organisms into local communities from a regional pool of species. We analyzed phylogenetic and functional diversity to understand community assembly of the ferns of Florida at two spatial scales. We built a phylogeny for 125 of the 141 species of ferns in Florida using five chloroplast markers. We calculated mean pairwise dissimilarity (MPD) and mean nearest taxon distance (MNTD) from phylogenetic distances and functional trait data for both spatial scales and compared the results to null models to assess significance. Our results for over vs. underdispersion in functional and phylogenetic diversity differed depending on spatial scale and metric considered. At the county scale, MPD revealed evidence for phylogenetic overdispersion, while MNTD revealed phylogenetic and functional underdispersion, and at the conservation area scale, MPD revealed phylogenetic and functional underdispersion while MNTD revealed evidence only of functional underdispersion. Our results are consistent with environmental filtering playing a larger role at the smaller, conservation area scale. The smaller spatial units are likely composed of fewer local habitat types that are selecting for closely related species, with the larger-scale units more likely to be composed of multiple habitat types that bring together a larger pool of species from across the phylogeny. Several aspects of fern biology, including their unique physiology and water relations and the importance of the independent gametophyte stage of the life cycle, make ferns highly sensitive to local, microhabitat conditions. © 2018 The Authors. American Journal of Botany is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America.

Resting-State Network Topology Differentiates Task Signals across the Adult Life Span.

PubMed

Chan, Micaela Y; Alhazmi, Fahd H; Park, Denise C; Savalia, Neil K; Wig, Gagan S

2017-03-08

Brain network connectivity differs across individuals. For example, older adults exhibit less segregated resting-state subnetworks relative to younger adults (Chan et al., 2014). It has been hypothesized that individual differences in network connectivity impact the recruitment of brain areas during task execution. While recent studies have described the spatial overlap between resting-state functional correlation (RSFC) subnetworks and task-evoked activity, it is unclear whether individual variations in the connectivity pattern of a brain area (topology) relates to its activity during task execution. We report data from 238 cognitively normal participants (humans), sampled across the adult life span (20-89 years), to reveal that RSFC-based network organization systematically relates to the recruitment of brain areas across two functionally distinct tasks (visual and semantic). The functional activity of brain areas (network nodes) were characterized according to their patterns of RSFC: nodes with relatively greater connections to nodes in their own functional system ("non-connector" nodes) exhibited greater activity than nodes with relatively greater connections to nodes in other systems ("connector" nodes). This "activation selectivity" was specific to those brain systems that were central to each of the tasks. Increasing age was accompanied by less differentiated network topology and a corresponding reduction in activation selectivity (or differentiation) across relevant network nodes. The results provide evidence that connectional topology of brain areas quantified at rest relates to the functional activity of those areas during task. Based on these findings, we propose a novel network-based theory for previous reports of the "dedifferentiation" in brain activity observed in aging. SIGNIFICANCE STATEMENT Similar to other real-world networks, the organization of brain networks impacts their function. As brain network connectivity patterns differ across individuals, we hypothesized that individual differences in network connectivity would relate to differences in brain activity. Using functional MRI in a group of individuals sampled across the adult life span (20-89 years), we measured correlations at rest and related the functional connectivity patterns to measurements of functional activity during two independent tasks. Brain activity varied in relation to connectivity patterns revealed by large-scale network analysis. This relationship tracked the differences in connectivity patterns accompanied by older age, providing important evidence for a link between the topology of areal connectivity measured at rest and the functional recruitment of these areas during task performance. Copyright © 2017 Chan et al.

[Architecture of receptor-operated ionic channels of biological membranes].

PubMed

Bregestovski, P D

2011-01-01

Ion channels of biological membranes are the key proteins, which provide bioelectric functioning of living systems. These proteins are homo- or heterooligomers assembled from several identical or different subunits. Understanding the architectural organization and functioning of ion channels has been significantly extended due to resolving the crystal structure of several types of voltage-gated and receptor-operated channels. This review summarizes the information obtained from crystal structures of potassium, nicotinic acetylcholine receptor, P2X, and other ligand-gated ion channels. Despite the differences in the function, topology, ionic selectivity, and the subunit stoichiometry, a high similarity in the principles of organization of these macromolecular complexes has been revealed.

Expressive communication of children with autism: the use of challenging behaviour.

PubMed

Chiang, Hsu-Min

2008-11-01

There is a lack of empirical research investigating challenging behaviour in children with autism with severe speech impairments in naturalistic settings. The aim of the present study was to investigate challenging behaviour among Australian and Taiwanese children with autism who are non-verbal or have limited speech (i.e. less than five functional words) in school settings and to address the following questions: (1) What are the communicative characteristics (e.g. communicative functions, partners, activities and partner's responses) of challenging behaviour? (2) Do sample characteristics (e.g. age, severity of autism, adaptive behaviour level, the use of graphic symbols, the use of non-symbolic acts, the use of speech) associate with the amount of challenging behaviour? (3) Do cultural differences exist in communicative variables of challenging behaviour? Naturalistic observations were used to investigate challenging behaviour in children with autism. A total of 32 (17 Australian and 15 Taiwanese) children with autism who were non-verbal or had limited speech participated in the current study and each participant was videotaped for 2 h during his/her everyday school routines. Sixteen out of 32 children had challenging behaviour. Challenging behaviour was used for requesting and rejecting communicative functions. A paired-samples t-test revealed that no significant differences existed in the frequency of occurrence between request and reject. Challenging behaviour was directed to adults and peers. A paired-samples t-test revealed that challenging behaviour was directed to adults significantly more frequently than to peers. Communicative partners showed different responses (e.g. deny, no response, delivered, removed, acknowledge) to challenging behaviour. A repeated-measures analysis of variance (ANOVA) revealed a main effect for partner response. Deny was the most common response. Challenging behaviour occurred across a variety of classroom activities (e.g. academic activities, morning circle, morning tea, lunch, free time). A repeated-measures ANOVA revealed a main effect for activity. Challenging behaviour occurred most often during academic activities. A set of correlation analyses indicated a significant correlation existed between the use of graphic symbols and the amount of challenging behaviour. A series of Mann-Whitney U-tests revealed significant differences between Australian and Taiwanese children on the amount of challenging behaviour, communicative functions and partners. A Chi-squared test revealed that there were significantly more Australian children with autism who displayed challenging behaviour than Taiwanese children. The current study shows that a high proportion of children with autism with severe speech impairments used challenging behaviour as a form of expressive communication in their school environments. The findings from the present study may have implications for practitioners who work with children with autism.

Enterocyte fatty acid-binding proteins (FABPs): different functions of liver and intestinal FABPs in the intestine.

PubMed

Gajda, Angela M; Storch, Judith

2015-02-01

Fatty acid-binding proteins (FABP) are highly abundant cytosolic proteins that are expressed in most mammalian tissues. In the intestinal enterocyte, both liver- (LFABP; FABP1) and intestinal FABPs (IFABP; FABP2) are expressed. These proteins display high-affinity binding for long-chain fatty acids (FA) and other hydrophobic ligands; thus, they are believed to be involved with uptake and trafficking of lipids in the intestine. In vitro studies have identified differences in ligand-binding stoichiometry and specificity, and in mechanisms of FA transfer to membranes, and it has been hypothesized that LFABP and IFABP have different functions in the enterocyte. Studies directly comparing LFABP- and IFABP-null mice have revealed markedly different phenotypes, indicating that these proteins indeed have different functions in intestinal lipid metabolism and whole body energy homeostasis. In this review, we discuss the evolving knowledge of the functions of LFABP and IFABP in the intestinal enterocyte. Copyright © 2014 Elsevier Ltd. All rights reserved.

Same-sex attraction, social relationships, psychosocial functioning, and school performance in early adolescence.

PubMed

Bos, Henny M W; Sandfort, Theo G M; de Bruyn, Eddy H; Hakvoort, Esther M

2008-01-01

The authors examined whether 13- to 15-year-old adolescents who experience feelings of same-sex attraction (SSA) differ from those without such feelings in the quality of relationships with parents, peers, and class mentors and in psychosocial functioning (health status and school performance). The authors also assessed whether differences in psychosocial functioning resulted from differences in the quality of social relationships. Data were collected from 866 Dutch high school students (mean age 13.61 years) by means of a computer-based questionnaire. Of the participants, 74 (8.5%) reported having feelings of SSA. The participants with SSA rated the quality of their relationships with their fathers and their peers lower than did those without SSA. Participants with SSA also had poorer mental health (higher levels of depression and lower levels of self-esteem) and lower school performance. A mediation analysis revealed that differences in psychosocial functioning resulted from differences in the quality of the same-sex attracted youths' social relationships, especially with fathers and peers. Copyright (c) 2008 APA.

Specific cerebral activation due to visual erotic stimuli in male-to-female transsexuals compared with male and female controls: an fMRI study.

PubMed

Gizewski, Elke R; Krause, Eva; Schlamann, Marc; Happich, Friederike; Ladd, Mark E; Forsting, Michael; Senf, Wolfgang

2009-02-01

Transsexuals harbor the strong feeling of having been born to the wrong sex. There is a continuing controversial discussion of whether or not transsexualism has a biological representation. Differences between males and females in terms of functional imaging during erotic stimuli have been previously described, revealing gender-specific results. Therefore, we postulated that male-to-female (MTF) transsexuals may show specific cerebral activation differing from their biological gender. Cerebral activation patterns during viewing of erotic film excerpts in functional magnetic resonance imaging (fMRI). Twelve male and 12 female heterosexual volunteers and 12 MTF transsexuals before any treatment viewed erotic film excerpts during fMRI. Additionally, subjective rating of sexual arousal was assessed. Statistics were performed using the Statistical Parametric Mapping software. Significantly enhanced activation for men compared with women was revealed in brain areas involved in erotic processing, i.e., the thalamus, the amygdala, and the orbitofrontal and insular cortex, whereas no specific activation for women was found. When comparing MTF transsexuals with male volunteers, activation patterns similar to female volunteers being compared with male volunteers were revealed. Sexual arousal was assessed using standard rating scales and did not differ significantly for the three groups. We revealed a cerebral activation pattern in MTF transsexuals compared with male controls similar to female controls compared with male controls during viewing of erotic stimuli, indicating a tendency of female-like cerebral processing in transsexualism.

Exploring the Yeast Acetylome Using Functional Genomics

PubMed Central

Duffy, Supipi Kaluarachchi; Friesen, Helena; Baryshnikova, Anastasia; Lambert, Jean-Philippe; Chong, Yolanda T.; Figeys, Daniel; Andrews, Brenda

2014-01-01

SUMMARY Lysine acetylation is a dynamic posttranslational modification with a well-defined role in regulating histones. The impact of acetylation on other cellular functions remains relatively uncharacterized. We explored the budding yeast acetylome with a functional genomics approach, assessing the effects of gene overexpression in the absence of lysine deacetylases (KDACs). We generated a network of 463 synthetic dosage lethal (SDL) interactions involving class I and II KDACs, revealing many cellular pathways regulated by different KDACs. A biochemical survey of genes interacting with the KDAC RPD3 identified 72 proteins acetylated in vivo. In-depth analysis of one of these proteins, Swi4, revealed a role for acetylation in G1-specific gene expression. Acetylation of Swi4 regulates interaction with its partner Swi6, both components of the SBF transcription factor. This study expands our view of the yeast acetylome, demonstrates the utility of functional genomic screens for exploring enzymatic pathways, and provides functional information that can be mined for future studies. PMID:22579291

Different functional modes of BAR domain proteins in formation and plasticity of mammalian postsynapses.

PubMed

Kessels, Michael M; Qualmann, Britta

2015-09-01

A plethora of cell biological processes involve modulations of cellular membranes. By using extended lipid-binding interfaces, some proteins have the power to shape membranes by attaching to them. Among such membrane shapers, the superfamily of Bin-Amphiphysin-Rvs (BAR) domain proteins has recently taken center stage. Extensive structural work on BAR domains has revealed a common curved fold that can serve as an extended membrane-binding interface to modulate membrane topologies and has allowed the grouping of the BAR domain superfamily into subfamilies with structurally slightly distinct BAR domain subtypes (N-BAR, BAR, F-BAR and I-BAR). Most BAR superfamily members are expressed in the mammalian nervous system. Neurons are elaborately shaped and highly compartmentalized cells. Therefore, analyses of synapse formation and of postsynaptic reorganization processes (synaptic plasticity) - a basis for learning and memory formation - has unveiled important physiological functions of BAR domain superfamily members. These recent advances, furthermore, have revealed that the functions of BAR domain proteins include different aspects. These functions are influenced by the often complex domain organization of BAR domain proteins. In this Commentary, we review these recent insights and propose to classify BAR domain protein functions into (1) membrane shaping, (2) physical integration, (3) action through signaling components, and (4) suppression of other BAR domain functions. © 2015. Published by The Company of Biologists Ltd.

Gene Expression Profiling Reveals Functional Specialization along the Intestinal Tract of a Carnivorous Teleostean Fish (Dicentrarchus labrax)

PubMed Central

Calduch-Giner, Josep A.; Sitjà-Bobadilla, Ariadna; Pérez-Sánchez, Jaume

2016-01-01

High-quality sequencing reads from the intestine of European sea bass were assembled, annotated by similarity against protein reference databases and combined with nucleotide sequences from public and private databases. After redundancy filtering, 24,906 non-redundant annotated sequences encoding 15,367 different gene descriptions were obtained. These annotated sequences were used to design a custom, high-density oligo-microarray (8 × 15 K) for the transcriptomic profiling of anterior (AI), middle (MI), and posterior (PI) intestinal segments. Similar molecular signatures were found for AI and MI segments, which were combined in a single group (AI-MI) whereas the PI outstood separately, with more than 1900 differentially expressed genes with a fold-change cutoff of 2. Functional analysis revealed that molecular and cellular functions related to feed digestion and nutrient absorption and transport were over-represented in AI-MI segments. By contrast, the initiation and establishment of immune defense mechanisms became especially relevant in PI, although the microarray expression profiling validated by qPCR indicated that these functional changes are gradual from anterior to posterior intestinal segments. This functional divergence occurred in association with spatial transcriptional changes in nutrient transporters and the mucosal chemosensing system via G protein-coupled receptors. These findings contribute to identify key indicators of gut functions and to compare different fish feeding strategies and immune defense mechanisms acquired along the evolution of teleosts. PMID:27610085

Gene Expression Profiling Reveals Functional Specialization along the Intestinal Tract of a Carnivorous Teleostean Fish (Dicentrarchus labrax).

PubMed

Calduch-Giner, Josep A; Sitjà-Bobadilla, Ariadna; Pérez-Sánchez, Jaume

2016-01-01

High-quality sequencing reads from the intestine of European sea bass were assembled, annotated by similarity against protein reference databases and combined with nucleotide sequences from public and private databases. After redundancy filtering, 24,906 non-redundant annotated sequences encoding 15,367 different gene descriptions were obtained. These annotated sequences were used to design a custom, high-density oligo-microarray (8 × 15 K) for the transcriptomic profiling of anterior (AI), middle (MI), and posterior (PI) intestinal segments. Similar molecular signatures were found for AI and MI segments, which were combined in a single group (AI-MI) whereas the PI outstood separately, with more than 1900 differentially expressed genes with a fold-change cutoff of 2. Functional analysis revealed that molecular and cellular functions related to feed digestion and nutrient absorption and transport were over-represented in AI-MI segments. By contrast, the initiation and establishment of immune defense mechanisms became especially relevant in PI, although the microarray expression profiling validated by qPCR indicated that these functional changes are gradual from anterior to posterior intestinal segments. This functional divergence occurred in association with spatial transcriptional changes in nutrient transporters and the mucosal chemosensing system via G protein-coupled receptors. These findings contribute to identify key indicators of gut functions and to compare different fish feeding strategies and immune defense mechanisms acquired along the evolution of teleosts.

Epitope mapping of the domains of human angiotensin converting enzyme.

PubMed

Kugaevskaya, Elena V; Kolesanova, Ekaterina F; Kozin, Sergey A; Veselovsky, Alexander V; Dedinsky, Ilya R; Elisseeva, Yulia E

2006-06-01

Somatic angiotensin converting enzyme (sACE), contains in its single chain two homologous domains (called N- and C-domains), each bearing a functional zinc-dependent active site. The present study aims to define the differences between two sACE domains and to localize experimentally revealed antigenic determinants (B-epitopes) in the recently determined three-dimensional structure of testicular tACE. The predicted linear antigenic determinants of human sACE were determined by peptide scanning ("PEPSCAN") approach. Essential difference was demonstrated between locations of the epitopes in the N- and C-domains. Comparison of arrangement of epitopes in the human domains with the corresponding sequences of some mammalian sACEs enabled to classify the revealed antigenic determinants as variable or conserved areas. The location of antigenic determinants with respect to various structural elements and to functionally important sites of the human sACE C-domain was estimated. The majority of antigenic sites of the C-domain were located at the irregular elements and at the boundaries of secondary structure elements. The data show structural differences between the sACE domains. The experimentally revealed antigenic determinants were in agreement with the recently determined crystal tACE structure. New potential applications are open to successfully produce mono-specific and group-specific antipeptide antibodies.

Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage.

PubMed

Chen, Lin-xing; Hu, Min; Huang, Li-nan; Hua, Zheng-shuang; Kuang, Jia-liang; Li, Sheng-jin; Shu, Wen-sheng

2015-07-01

The microbial communities in acid mine drainage have been extensively studied to reveal their roles in acid generation and adaption to this environment. Lacking, however, are integrated community- and organism-wide comparative gene transcriptional analyses that could reveal the response and adaptation mechanisms of these extraordinary microorganisms to different environmental conditions. In this study, comparative metagenomics and metatranscriptomics were performed on microbial assemblages collected from four geochemically distinct acid mine drainage (AMD) sites. Taxonomic analysis uncovered unexpectedly high microbial biodiversity of these extremely acidophilic communities, and the abundant taxa of Acidithiobacillus, Leptospirillum and Acidiphilium exhibited high transcriptional activities. Community-wide comparative analyses clearly showed that the AMD microorganisms adapted to the different environmental conditions via regulating the expression of genes involved in multiple in situ functional activities, including low-pH adaptation, carbon, nitrogen and phosphate assimilation, energy generation, environmental stress resistance, and other functions. Organism-wide comparative analyses of the active taxa revealed environment-dependent gene transcriptional profiles, especially the distinct strategies used by Acidithiobacillus ferrivorans and Leptospirillum ferrodiazotrophum in nutrients assimilation and energy generation for survival under different conditions. Overall, these findings demonstrate that the gene transcriptional profiles of AMD microorganisms are closely related to the site physiochemical characteristics, providing clues into the microbial response and adaptation mechanisms in the oligotrophic, extremely acidic environments.

Metagenomic analysis of the microbiota in the highly compartmented hindguts of six wood- or soil-feeding higher termites.

PubMed

Rossmassler, Karen; Dietrich, Carsten; Thompson, Claire; Mikaelyan, Aram; Nonoh, James O; Scheffrahn, Rudolf H; Sillam-Dussès, David; Brune, Andreas

2015-11-26

Termites are important contributors to carbon and nitrogen cycling in tropical ecosystems. Higher termites digest lignocellulose in various stages of humification with the help of an entirely prokaryotic microbiota housed in their compartmented intestinal tract. Previous studies revealed fundamental differences in community structure between compartments, but the functional roles of individual lineages in symbiotic digestion are mostly unknown. Here, we conducted a highly resolved analysis of the gut microbiota in six species of higher termites that feed on plant material at different levels of humification. Combining amplicon sequencing and metagenomics, we assessed similarities in community structure and functional potential between the major hindgut compartments (P1, P3, and P4). Cluster analysis of the relative abundances of orthologous gene clusters (COGs) revealed high similarities among wood- and litter-feeding termites and strong differences to humivorous species. However, abundance estimates of bacterial phyla based on 16S rRNA genes greatly differed from those based on protein-coding genes. Community structure and functional potential of the microbiota in individual gut compartments are clearly driven by the digestive strategy of the host. The metagenomics libraries obtained in this study provide the basis for future studies that elucidate the fundamental differences in the symbiont-mediated breakdown of lignocellulose and humus by termites of different feeding groups. The high proportion of uncultured bacterial lineages in all samples calls for a reference-independent approach for the correct taxonomic assignment of protein-coding genes.

Linking biological soil crust diversity to ecological functions

NASA Astrophysics Data System (ADS)

Glaser, Karin; Borchhardt, Nadine; Schulz, Karoline; Mikhailyuk, Tatiana; Baumann, Karen; Leinweber, Peter; Ulf, Karsten

2016-04-01

Biological soil crusts (BSCs) are an association of different microorganisms and soil particles in the top millimeters of the soil. They are formed by algae, cyanobacteria, microfungi, bacteria, bryophytes and lichens in various compositions. Our aim was to determine and compare the biodiversity of all occurring organisms in biogeographically different habitats, ranging from polar (both Arctic and Antarctic), subpolar (Scandinavia), temperate (Germany) to dry regions (Chile). The combination of microscopy and molecular techniques (next-generation sequencing) revealed highly diverse crust communities, whose composition clustered by region and correlates with habitat characteristics such as water content. The BSC biodiversity was then linked to the ecological function of the crusts. The functional role of the BSCs in the biogeochemical cycles of carbon, nitrogen and phosphorous is evaluated using an array of state of the art soil chemistry methods including Py-FIMS (pyrolysis field ionization mass spectrometry) and XANES (x-ray absorbance near edge structure). Total P as well as P fractions were quantified in all BSCs, adjacent soil underneath and comparable nearby soil of BSC-free areas revealing a remarkable accumulation of total phosphorous and a distinct pattern of P fractions in the crust. Further, we observed an indication of a different P-speciation composition in the crust compared with BSC-free soil. The data allow answering the question whether BSCs act as sink or source for these compounds, and how biodiversity controls the biogeochemical function of BSCs.

Metabolomics analysis reveals the metabolic and functional roles of flavonoids in light-sensitive tea leaves.

PubMed

Zhang, Qunfeng; Liu, Meiya; Ruan, Jianyun

2017-03-20

As the predominant secondary metabolic pathway in tea plants, flavonoid biosynthesis increases with increasing temperature and illumination. However, the concentration of most flavonoids decreases greatly in light-sensitive tea leaves when they are exposed to light, which further improves tea quality. To reveal the metabolism and potential functions of flavonoids in tea leaves, a natural light-sensitive tea mutant (Huangjinya) cultivated under different light conditions was subjected to metabolomics analysis. The results showed that chlorotic tea leaves accumulated large amounts of flavonoids with ortho-dihydroxylated B-rings (e.g., catechin gallate, quercetin and its glycosides etc.), whereas total flavonoids (e.g., myricetrin glycoside, epigallocatechin gallate etc.) were considerably reduced, suggesting that the flavonoid components generated from different metabolic branches played different roles in tea leaves. Furthermore, the intracellular localization of flavonoids and the expression pattern of genes involved in secondary metabolic pathways indicate a potential photoprotective function of dihydroxylated flavonoids in light-sensitive tea leaves. Our results suggest that reactive oxygen species (ROS) scavenging and the antioxidation effects of flavonoids help chlorotic tea plants survive under high light stress, providing new evidence to clarify the functional roles of flavonoids, which accumulate to high levels in tea plants. Moreover, flavonoids with ortho-dihydroxylated B-rings played a greater role in photo-protection to improve the acclimatization of tea plants.

Evidence for a π-junction in Nb/F/Nb' trilayers from superfluid density measurements

NASA Astrophysics Data System (ADS)

Lemberger, Thomas; Hinton, Michael; Steers, Stanley; Peters, Bryan; Yang, Fengyuan

Two-coil measurements of the sheet superfluid density of Nb/NiV/Nb' trilayers reveal the transition temperatures and volume superfluid densities of both Nb layers, as functions of the thickness, dF, of the intervening ferromagnetic (F) Ni0.96V0.04 layer. The upper transition occurs when the thicker Nb layer goes superconducting and superfluid first appears. Fitting the high-temperature superfluid density to an appropriate functional form reveals the presence of a lower ``transition'' where additional superfluid appears. This event is really a crossover, but the difference is irrelevant here. There is a surprising minimum in superfluid densities of both Nb layers at dF ~ 30 Å, followed by a slow rise. This behavior suggests that a π phase difference between the Nb layers develops at dF ~ 30 Å and continues to larger F thickness. Supported in part by NSF Grant DMR-0805227.

Functional relevance of neurotransmitter receptor heteromers in the central nervous system.

PubMed

Ferré, Sergi; Ciruela, Francisco; Woods, Amina S; Lluis, Carme; Franco, Rafael

2007-09-01

The existence of neurotransmitter receptor heteromers is becoming broadly accepted and their functional significance is being revealed. Heteromerization of neurotransmitter receptors produces functional entities that possess different biochemical characteristics with respect to the individual components of the heteromer. Neurotransmitter receptor heteromers can function as processors of computations that modulate cell signaling. Thus, the quantitative or qualitative aspects of the signaling generated by stimulation of any of the individual receptor units in the heteromer are different from those obtained during coactivation. Furthermore, recent studies demonstrate that some neurotransmitter receptor heteromers can exert an effect as processors of computations that directly modulate both pre- and postsynaptic neurotransmission. This is illustrated by the analysis of striatal receptor heteromers that control striatal glutamatergic neurotransmission.

Generational Differences in Work Values between Parents and Children and between Boys and Girls across Grade Levels 6, 9, 10, and 12

ERIC Educational Resources Information Center

Wijting, Jan P.; And Others

1978-01-01

Cross-sectional comparison of elementary and secondary school children and parents examined changes in work values and relationships between children's and parents' work values as a function of age and sex. Revealed support for hypothesized differences in children's values and for convergence of sex differences in values at later ages. (Author)

Individual differences in mathematical competence predict parietal brain activation during mental calculation.

PubMed

Grabner, Roland H; Ansari, Daniel; Reishofer, Gernot; Stern, Elsbeth; Ebner, Franz; Neuper, Christa

2007-11-01

Functional neuroimaging studies have revealed that parietal brain circuits subserve arithmetic problem solving and that their recruitment dynamically changes as a function of training and development. The present study investigated whether the brain activation during mental calculation is also modulated by individual differences in mathematical competence. Twenty-five adult students were selected from a larger pool based on their performance on standardized tests of intelligence and arithmetic and divided into groups of individuals with relatively lower and higher mathematical competence. These groups did not differ in their non-numerical intelligence or age. In an fMRI block-design, participants had to verify the correctness of single-digit and multi-digit multiplication problems. Analyses revealed that the individuals with higher mathematical competence displayed stronger activation of the left angular gyrus while solving both types of arithmetic problems. Additional correlational analyses corroborated the association between individual differences in mathematical competence and angular gyrus activation, even when variability in task performance was controlled for. These findings demonstrate that the recruitment of the left angular gyrus during arithmetic problem solving underlies individual differences in mathematical ability and suggests a stronger reliance on automatic, language-mediated processes in more competent individuals.

The complex and specific pMHC interactions with diverse HIV-1 TCR clonotypes reveal a structural basis for alterations in CTL function

NASA Astrophysics Data System (ADS)

Xia, Zhen; Chen, Huabiao; Kang, Seung-Gu; Huynh, Tien; Fang, Justin W.; Lamothe, Pedro A.; Walker, Bruce D.; Zhou, Ruhong

2014-02-01

Immune control of viral infections is modulated by diverse T cell receptor (TCR) clonotypes engaging peptide-MHC class I complexes on infected cells, but the relationship between TCR structure and antiviral function is unclear. Here we apply in silico molecular modeling with in vivo mutagenesis studies to investigate TCR-pMHC interactions from multiple CTL clonotypes specific for a well-defined HIV-1 epitope. Our molecular dynamics simulations of viral peptide-HLA-TCR complexes, based on two independent co-crystal structure templates, reveal that effective and ineffective clonotypes bind to the terminal portions of the peptide-MHC through similar salt bridges, but their hydrophobic side-chain packings can be very different, which accounts for the major part of the differences among these clonotypes. Non-specific hydrogen bonding to viral peptide also accommodates greater epitope variants. Furthermore, free energy perturbation calculations for point mutations on the viral peptide KK10 show excellent agreement with in vivo mutagenesis assays, with new predictions confirmed by additional experiments. These findings indicate a direct structural basis for heterogeneous CTL antiviral function.

Learning about learning: Mining human brain sub-network biomarkers from fMRI data

PubMed Central

Dereli, Nazli; Dang, Xuan-Hong; Bassett, Danielle S.; Wymbs, Nicholas F.; Grafton, Scott T.; Singh, Ambuj K.

2017-01-01

Modeling the brain as a functional network can reveal the relationship between distributed neurophysiological processes and functional interactions between brain structures. Existing literature on functional brain networks focuses mainly on a battery of network properties in “resting state” employing, for example, modularity, clustering, or path length among regions. In contrast, we seek to uncover functionally connected subnetworks that predict or correlate with cohort differences and are conserved within the subjects within a cohort. We focus on differences in both the rate of learning as well as overall performance in a sensorimotor task across subjects and develop a principled approach for the discovery of discriminative subgraphs of functional connectivity based on imaging acquired during practice. We discover two statistically significant subgraph regions: one involving multiple regions in the visual cortex and another involving the parietal operculum and planum temporale. High functional coherence in the former characterizes sessions in which subjects take longer to perform the task, while high coherence in the latter is associated with high learning rate (performance improvement across trials). Our proposed methodology is general, in that it can be applied to other cognitive tasks, to study learning or to differentiate between healthy patients and patients with neurological disorders, by revealing the salient interactions among brain regions associated with the observed global state. The discovery of such significant discriminative subgraphs promises a better data-driven understanding of the dynamic brain processes associated with high-level cognitive functions. PMID:29016686

Learning about learning: Mining human brain sub-network biomarkers from fMRI data.

PubMed

Bogdanov, Petko; Dereli, Nazli; Dang, Xuan-Hong; Bassett, Danielle S; Wymbs, Nicholas F; Grafton, Scott T; Singh, Ambuj K

2017-01-01

Modeling the brain as a functional network can reveal the relationship between distributed neurophysiological processes and functional interactions between brain structures. Existing literature on functional brain networks focuses mainly on a battery of network properties in "resting state" employing, for example, modularity, clustering, or path length among regions. In contrast, we seek to uncover functionally connected subnetworks that predict or correlate with cohort differences and are conserved within the subjects within a cohort. We focus on differences in both the rate of learning as well as overall performance in a sensorimotor task across subjects and develop a principled approach for the discovery of discriminative subgraphs of functional connectivity based on imaging acquired during practice. We discover two statistically significant subgraph regions: one involving multiple regions in the visual cortex and another involving the parietal operculum and planum temporale. High functional coherence in the former characterizes sessions in which subjects take longer to perform the task, while high coherence in the latter is associated with high learning rate (performance improvement across trials). Our proposed methodology is general, in that it can be applied to other cognitive tasks, to study learning or to differentiate between healthy patients and patients with neurological disorders, by revealing the salient interactions among brain regions associated with the observed global state. The discovery of such significant discriminative subgraphs promises a better data-driven understanding of the dynamic brain processes associated with high-level cognitive functions.

The Association between Sweet Taste Function, Anthropometry, and Dietary Intake in Adults.

PubMed

Low, Julia Y Q; Lacy, Kathleen E; McBride, Robert; Keast, Russell S J

2016-04-23

Variation in ability to detect, recognize, and perceive sweetness may influence food consumption, and eventually chronic nutrition-related conditions such as overweight and obesity. The aim of this study was to investigate the associations between sweet taste function, anthropometry, and dietary intake in adults. Participants' (n = 60; mean age in years = 26, SD = ±7.8) sweet taste function for a range of sweeteners (glucose, fructose, sucrose, sucralose, erythritol, and Rebaudioside A) was assessed by measuring detection and recognition thresholds and sweetness intensity. Height, weight, and waist circumference were also measured, and participants also completed a Food Frequency Questionnaire. There was large inter-individual variation in detection, recognition and sweetness intensity measures. Pearson's correlation coefficient revealed no robust correlations between measures of sweet taste function, anthropometry, and dietary intake, with the exception of suprathreshold intensity, which was moderately correlated with total energy intake (r = 0.23-0.40). One-way analysis of variance revealed no significant differences between the most and least sensitive participants in terms of BMI, waist circumference, and dietary intake for all measures of sweet taste function and sweeteners (all p > 0.01). When stratified into BMI categories, there were no significant differences in any measure of sweet taste function between the normal weight and overweight/obese participants (all p > 0.01). Results show that that sweet taste function is not associated with anthropometry and sweetness intensity measures are the most appropriate measure when assessing links between sweet taste and food consumption.

The Association between Sweet Taste Function, Anthropometry, and Dietary Intake in Adults

PubMed Central

Low, Julia Y. Q.; Lacy, Kathleen E.; McBride, Robert; Keast, Russell S. J.

2016-01-01

Variation in ability to detect, recognize, and perceive sweetness may influence food consumption, and eventually chronic nutrition-related conditions such as overweight and obesity. The aim of this study was to investigate the associations between sweet taste function, anthropometry, and dietary intake in adults. Participants’ (n = 60; mean age in years = 26, SD = ±7.8) sweet taste function for a range of sweeteners (glucose, fructose, sucrose, sucralose, erythritol, and Rebaudioside A) was assessed by measuring detection and recognition thresholds and sweetness intensity. Height, weight, and waist circumference were also measured, and participants also completed a Food Frequency Questionnaire. There was large inter-individual variation in detection, recognition and sweetness intensity measures. Pearson’s correlation coefficient revealed no robust correlations between measures of sweet taste function, anthropometry, and dietary intake, with the exception of suprathreshold intensity, which was moderately correlated with total energy intake (r = 0.23–0.40). One-way analysis of variance revealed no significant differences between the most and least sensitive participants in terms of BMI, waist circumference, and dietary intake for all measures of sweet taste function and sweeteners (all p > 0.01). When stratified into BMI categories, there were no significant differences in any measure of sweet taste function between the normal weight and overweight/obese participants (all p > 0.01). Results show that that sweet taste function is not associated with anthropometry and sweetness intensity measures are the most appropriate measure when assessing links between sweet taste and food consumption. PMID:27120614

Aberrant striatal functional connectivity in children with autism.

PubMed

Di Martino, Adriana; Kelly, Clare; Grzadzinski, Rebecca; Zuo, Xi-Nian; Mennes, Maarten; Mairena, Maria Angeles; Lord, Catherine; Castellanos, F Xavier; Milham, Michael P

2011-05-01

Models of autism spectrum disorders (ASD) as neural disconnection syndromes have been predominantly supported by examinations of abnormalities in corticocortical networks in adults with autism. A broader body of research implicates subcortical structures, particularly the striatum, in the physiopathology of autism. Resting state functional magnetic resonance imaging has revealed detailed maps of striatal circuitry in healthy and psychiatric populations and vividly captured maturational changes in striatal circuitry during typical development. Using resting state functional magnetic resonance imaging, we examined striatal functional connectivity (FC) in 20 children with ASD and 20 typically developing children between the ages of 7.6 and 13.5 years. Whole-brain voxelwise statistical maps quantified within-group striatal FC and between-group differences for three caudate and three putamen seeds for each hemisphere. Children with ASD mostly exhibited prominent patterns of ectopic striatal FC (i.e., functional connectivity present in ASD but not in typically developing children), with increased functional connectivity between nearly all striatal subregions and heteromodal associative and limbic cortex previously implicated in the physiopathology of ASD (e.g., insular and right superior temporal gyrus). Additionally, we found striatal functional hyperconnectivity with the pons, thus expanding the scope of functional alterations implicated in ASD. Secondary analyses revealed ASD-related hyperconnectivity between the pons and insula cortex. Examination of FC of striatal networks in children with ASD revealed abnormalities in circuits involving early developing areas, such as the brainstem and insula, with a pattern of increased FC in ectopic circuits that likely reflects developmental derangement rather than immaturity of functional circuits. Copyright © 2011 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

A dual-function fluorescent probe for monitoring the degrees of hypoxia in living cells via the imaging of nitroreductase and adenosine triphosphate.

PubMed

Fang, Yu; Shi, Wen; Hu, Yiming; Li, Xiaohua; Ma, Huimin

2018-05-24

A new dual-function fluorescent probe is developed for detecting nitroreductase (NTR) and adenosine triphosphate (ATP) with different responses. Imaging application of the probe reveals that intracellular NTR and ATP display an adverse changing trend during a hypoxic process and ATP can serve as a new sign for cell hypoxia.

Optical mapping of brain activation in gambling disorders

NASA Astrophysics Data System (ADS)

Yuan, Zhen; Lin, Xiaohong

2018-02-01

In this study, fNIRS was utilized to identify the brain activation difference between pathological gamblers (PGs) and heathy controls (HCs). We inspected the hemodynamic changes in the prefrontal cortex using fNIRS recordings during the completion of executive function and decision making tasks. Our finding revealed that the PG and HC groups exhibited significant differences in brain activation.

Different Brain Wave Patterns and Cortical Control Abilities in Relation to Different Creative Potentials

ERIC Educational Resources Information Center

Li, Ying-Han; Tseng, Chao-Yuan; Tsai, Arthur Chih-Hsin; Huang, Andrew Chih-Wei; Lin, Wei-Lun

2016-01-01

Contemporary understanding of brain functions provides a way to probe into the mystery of creativity. However, the prior evidence regarding the relationship between creativity and brain wave patterns reveals inconsistent conclusions. One possible reason might be that the means of selecting creative individuals in the past has varied in each study.…

Local loss and spatial homogenization of plant diversity reduce ecosystem multifunctionality.

PubMed

Hautier, Yann; Isbell, Forest; Borer, Elizabeth T; Seabloom, Eric W; Harpole, W Stanley; Lind, Eric M; MacDougall, Andrew S; Stevens, Carly J; Adler, Peter B; Alberti, Juan; Bakker, Jonathan D; Brudvig, Lars A; Buckley, Yvonne M; Cadotte, Marc; Caldeira, Maria C; Chaneton, Enrique J; Chu, Chengjin; Daleo, Pedro; Dickman, Christopher R; Dwyer, John M; Eskelinen, Anu; Fay, Philip A; Firn, Jennifer; Hagenah, Nicole; Hillebrand, Helmut; Iribarne, Oscar; Kirkman, Kevin P; Knops, Johannes M H; La Pierre, Kimberly J; McCulley, Rebecca L; Morgan, John W; Pärtel, Meelis; Pascual, Jesus; Price, Jodi N; Prober, Suzanne M; Risch, Anita C; Sankaran, Mahesh; Schuetz, Martin; Standish, Rachel J; Virtanen, Risto; Wardle, Glenda M; Yahdjian, Laura; Hector, Andy

2018-01-01

Biodiversity is declining in many local communities while also becoming increasingly homogenized across space. Experiments show that local plant species loss reduces ecosystem functioning and services, but the role of spatial homogenization of community composition and the potential interaction between diversity at different scales in maintaining ecosystem functioning remains unclear, especially when many functions are considered (ecosystem multifunctionality). We present an analysis of eight ecosystem functions measured in 65 grasslands worldwide. We find that more diverse grasslands-those with both species-rich local communities (α-diversity) and large compositional differences among localities (β-diversity)-had higher levels of multifunctionality. Moreover, α- and β-diversity synergistically affected multifunctionality, with higher levels of diversity at one scale amplifying the contribution to ecological functions at the other scale. The identity of species influencing ecosystem functioning differed among functions and across local communities, explaining why more diverse grasslands maintained greater functionality when more functions and localities were considered. These results were robust to variation in environmental drivers. Our findings reveal that plant diversity, at both local and landscape scales, contributes to the maintenance of multiple ecosystem services provided by grasslands. Preserving ecosystem functioning therefore requires conservation of biodiversity both within and among ecological communities.

Hierarchical organization of brain functional networks during visual tasks.

PubMed

Zhuo, Zhao; Cai, Shi-Min; Fu, Zhong-Qian; Zhang, Jie

2011-09-01

The functional network of the brain is known to demonstrate modular structure over different hierarchical scales. In this paper, we systematically investigated the hierarchical modular organizations of the brain functional networks that are derived from the extent of phase synchronization among high-resolution EEG time series during a visual task. In particular, we compare the modular structure of the functional network from EEG channels with that of the anatomical parcellation of the brain cortex. Our results show that the modular architectures of brain functional networks correspond well to those from the anatomical structures over different levels of hierarchy. Most importantly, we find that the consistency between the modular structures of the functional network and the anatomical network becomes more pronounced in terms of vision, sensory, vision-temporal, motor cortices during the visual task, which implies that the strong modularity in these areas forms the functional basis for the visual task. The structure-function relationship further reveals that the phase synchronization of EEG time series in the same anatomical group is much stronger than that of EEG time series from different anatomical groups during the task and that the hierarchical organization of functional brain network may be a consequence of functional segmentation of the brain cortex.

The development of young siblings of children with autism from 4 to 54 months.

PubMed

Gamliel, Ifat; Yirmiya, Nurit; Sigman, Marian

2007-01-01

Cognitive and language skills of 39 siblings of children with autism (SIBS-A) and 39 siblings of typically developing children (SIBS-TD) at ages 4, 14, 24, 36, and 54 months were compared. Twelve of the 39 SIBS-A revealed a delay in cognition and/or language (including one child diagnosed with autism) compared to only two SIBS-TD. Developmental trajectories revealed that the cognitive differences disappeared by age 54 months, but some differences in language ability remained. Thus, most SIBS-A were well-functioning, but some revealed cognitive and/or language difficulties during the preschool years. Even these siblings by and large caught up by the age of 54 months, with receptive and expressive language abilities remaining an area of difficulty for some earlier identified siblings.

Impact of Plant Functional Types on Coherence Between Precipitation and Soil Moisture: A Wavelet Analysis

NASA Astrophysics Data System (ADS)

Liu, Qi; Hao, Yonghong; Stebler, Elaine; Tanaka, Nobuaki; Zou, Chris B.

2017-12-01

Mapping the spatiotemporal patterns of soil moisture within heterogeneous landscapes is important for resource management and for the understanding of hydrological processes. A critical challenge in this mapping is comparing remotely sensed or in situ observations from areas with different vegetation cover but subject to the same precipitation regime. We address this challenge by wavelet analysis of multiyear observations of soil moisture profiles from adjacent areas with contrasting plant functional types (grassland, woodland, and encroached) and precipitation. The analysis reveals the differing soil moisture patterns and dynamics between plant functional types. The coherence at high-frequency periodicities between precipitation and soil moisture generally decreases with depth but this is much more pronounced under woodland compared to grassland. Wavelet analysis provides new insights on soil moisture dynamics across plant functional types and is useful for assessing differences and similarities in landscapes with heterogeneous vegetation cover.

Discriminating Among Probability Weighting Functions Using Adaptive Design Optimization

PubMed Central

Cavagnaro, Daniel R.; Pitt, Mark A.; Gonzalez, Richard; Myung, Jay I.

2014-01-01

Probability weighting functions relate objective probabilities and their subjective weights, and play a central role in modeling choices under risk within cumulative prospect theory. While several different parametric forms have been proposed, their qualitative similarities make it challenging to discriminate among them empirically. In this paper, we use both simulation and choice experiments to investigate the extent to which different parametric forms of the probability weighting function can be discriminated using adaptive design optimization, a computer-based methodology that identifies and exploits model differences for the purpose of model discrimination. The simulation experiments show that the correct (data-generating) form can be conclusively discriminated from its competitors. The results of an empirical experiment reveal heterogeneity between participants in terms of the functional form, with two models (Prelec-2, Linear in Log Odds) emerging as the most common best-fitting models. The findings shed light on assumptions underlying these models. PMID:24453406

Short report: the effect of expertise in hiking on recognition memory for mountain scenes.

PubMed

Kawamura, Satoru; Suzuki, Sae; Morikawa, Kazunori

2007-10-01

The nature of an expert memory advantage that does not depend on stimulus structure or chunking was examined, using more ecologically valid stimuli in the context of a more natural activity than previously studied domains. Do expert hikers and novice hikers see and remember mountain scenes differently? In the present experiment, 18 novice hikers and 17 expert hikers were presented with 60 photographs of scenes from hiking trails. These scenes differed in the degree of functional aspects that implied some action possibilities or dangers. The recognition test revealed that the memory performance of experts was significantly superior to that of novices for scenes with highly functional aspects. The memory performance for the scenes with few functional aspects did not differ between novices and experts. These results suggest that experts pay more attention to, and thus remember better, scenes with functional meanings than do novices.

Functional sequencing read annotation for high precision microbiome analysis

PubMed Central

Zhu, Chengsheng; Miller, Maximilian; Marpaka, Srinayani; Vaysberg, Pavel; Rühlemann, Malte C; Wu, Guojun; Heinsen, Femke-Anouska; Tempel, Marie; Zhao, Liping; Lieb, Wolfgang; Franke, Andre; Bromberg, Yana

2018-01-01

Abstract The vast majority of microorganisms on Earth reside in often-inseparable environment-specific communities—microbiomes. Meta-genomic/-transcriptomic sequencing could reveal the otherwise inaccessible functionality of microbiomes. However, existing analytical approaches focus on attributing sequencing reads to known genes/genomes, often failing to make maximal use of available data. We created faser (functional annotation of sequencing reads), an algorithm that is optimized to map reads to molecular functions encoded by the read-correspondent genes. The mi-faser microbiome analysis pipeline, combining faser with our manually curated reference database of protein functions, accurately annotates microbiome molecular functionality. mi-faser’s minutes-per-microbiome processing speed is significantly faster than that of other methods, allowing for large scale comparisons. Microbiome function vectors can be compared between different conditions to highlight environment-specific and/or time-dependent changes in functionality. Here, we identified previously unseen oil degradation-specific functions in BP oil-spill data, as well as functional signatures of individual-specific gut microbiome responses to a dietary intervention in children with Prader–Willi syndrome. Our method also revealed variability in Crohn's Disease patient microbiomes and clearly distinguished them from those of related healthy individuals. Our analysis highlighted the microbiome role in CD pathogenicity, demonstrating enrichment of patient microbiomes in functions that promote inflammation and that help bacteria survive it. PMID:29194524

Retinotopic patterns of functional connectivity between V1 and large-scale brain networks during resting fixation

PubMed Central

Griffis, Joseph C.; Elkhetali, Abdurahman S.; Burge, Wesley K.; Chen, Richard H.; Bowman, Anthony D.; Szaflarski, Jerzy P.; Visscher, Kristina M.

2016-01-01

Psychophysical and neurobiological evidence suggests that central and peripheral vision are specialized for different functions. This specialization of function might be expected to lead to differences in the large-scale functional interactions of early cortical areas that represent central and peripheral visual space. Here, we characterize differences in whole-brain functional connectivity among sectors in primary visual cortex (V1) corresponding to central, near-peripheral, and far-peripheral vision during resting fixation. Importantly, our analyses reveal that eccentricity sectors in V1 have different functional connectivity with non-visual areas associated with large-scale brain networks. Regions associated with the fronto-parietal control network are most strongly connected with central sectors of V1, regions associated with the cingulo-opercular control network are most strongly connected with near-peripheral sectors of V1, and regions associated with the default mode and auditory networks are most strongly connected with far-peripheral sectors of V1. Additional analyses suggest that similar patterns are present during eyes-closed rest. These results suggest that different types of visual information may be prioritized by large-scale brain networks with distinct functional profiles, and provide insights into how the small-scale functional specialization within early visual regions such as V1 relates to the large-scale organization of functionally distinct whole-brain networks. PMID:27554527

Diversity and interactions of microbial functional genes under differing environmental conditions: insights from a membrane bioreactor and an oxidation ditch.

PubMed

Xia, Yu; Hu, Man; Wen, Xianghua; Wang, Xiaohui; Yang, Yunfeng; Zhou, Jizhong

2016-01-08

The effect of environmental conditions on the diversity and interactions of microbial communities has caused tremendous interest in microbial ecology. Here, we found that with identical influents but differing operational parameters (mainly mixed liquor suspended solid (MLSS) concentrations, solid retention time (SRT) and dissolved oxygen (DO) concentrations), two full-scale municipal wastewater treatment systems applying oxidation ditch (OD) and membrane bioreactor (MBR) processes harbored a majority of shared genes (87.2%) but had different overall functional gene structures as revealed by two datasets of 12-day time-series generated by a functional gene array-GeoChip 4.2. Association networks of core carbon, nitrogen and phosphorus cycling genes in each system based on random matrix theory (RMT) showed different topological properties and the MBR nodes showed an indication of higher connectivity. MLSS and DO were shown to be effective in shaping functional gene structures of the systems by statistical analyses. Higher MLSS concentrations resulting in decreased resource availability of the MBR system were thought to promote positive interactions of important functional genes. Together, these findings show the differences of functional potentials of some bioprocesses caused by differing environmental conditions and suggest that higher stress of resource limitation increased positive gene interactions in the MBR system.

Diversity and interactions of microbial functional genes under differing environmental conditions: insights from a membrane bioreactor and an oxidation ditch

NASA Astrophysics Data System (ADS)

Xia, Yu; Hu, Man; Wen, Xianghua; Wang, Xiaohui; Yang, Yunfeng; Zhou, Jizhong

2016-01-01

The effect of environmental conditions on the diversity and interactions of microbial communities has caused tremendous interest in microbial ecology. Here, we found that with identical influents but differing operational parameters (mainly mixed liquor suspended solid (MLSS) concentrations, solid retention time (SRT) and dissolved oxygen (DO) concentrations), two full-scale municipal wastewater treatment systems applying oxidation ditch (OD) and membrane bioreactor (MBR) processes harbored a majority of shared genes (87.2%) but had different overall functional gene structures as revealed by two datasets of 12-day time-series generated by a functional gene array-GeoChip 4.2. Association networks of core carbon, nitrogen and phosphorus cycling genes in each system based on random matrix theory (RMT) showed different topological properties and the MBR nodes showed an indication of higher connectivity. MLSS and DO were shown to be effective in shaping functional gene structures of the systems by statistical analyses. Higher MLSS concentrations resulting in decreased resource availability of the MBR system were thought to promote positive interactions of important functional genes. Together, these findings show the differences of functional potentials of some bioprocesses caused by differing environmental conditions and suggest that higher stress of resource limitation increased positive gene interactions in the MBR system.

Diversity and interactions of microbial functional genes under differing environmental conditions: insights from a membrane bioreactor and an oxidation ditch

PubMed Central

Xia, Yu; Hu, Man; Wen, Xianghua; Wang, Xiaohui; Yang, Yunfeng; Zhou, Jizhong

2016-01-01

The effect of environmental conditions on the diversity and interactions of microbial communities has caused tremendous interest in microbial ecology. Here, we found that with identical influents but differing operational parameters (mainly mixed liquor suspended solid (MLSS) concentrations, solid retention time (SRT) and dissolved oxygen (DO) concentrations), two full-scale municipal wastewater treatment systems applying oxidation ditch (OD) and membrane bioreactor (MBR) processes harbored a majority of shared genes (87.2%) but had different overall functional gene structures as revealed by two datasets of 12-day time-series generated by a functional gene array-GeoChip 4.2. Association networks of core carbon, nitrogen and phosphorus cycling genes in each system based on random matrix theory (RMT) showed different topological properties and the MBR nodes showed an indication of higher connectivity. MLSS and DO were shown to be effective in shaping functional gene structures of the systems by statistical analyses. Higher MLSS concentrations resulting in decreased resource availability of the MBR system were thought to promote positive interactions of important functional genes. Together, these findings show the differences of functional potentials of some bioprocesses caused by differing environmental conditions and suggest that higher stress of resource limitation increased positive gene interactions in the MBR system. PMID:26743465

Functional implications of Major Histocompatibility (MH) variation using estuarine fish populations.

PubMed

Cohen, Sarah; Tirindelli, Joëlle; Gomez-Chiarri, Marta; Nacci, Diane

2006-12-01

Recently, there has been a dramatic expansion of studies of major histocompatibility complex (MHC) variation aimed at discovering functional differences in immunity across wild populations of diverse vertebrate species. Some species with relatively low genetic diversity or under strong directional selection by pathogens have revealed fascinating cases of MHC allelic disease linkage. More generally in genetically diverse species, however, these linkages may be hard to find. In this paper, we review approaches for assessing functional variation in MHC and discuss their potential use for discovering smaller-scale intraspecific spatial and temporal patterns of MHC variation. Then, we describe and illustrate an approach using the structural model to produce a population composite of variation in antigen-binding regions by mapping population-specific substitutions onto functional regions of the molecule. We are producing models of variation in major histocompatibility (MH) loci for populations of non-migratory fish (killifish, Fundulus heteroclitus) resident at sites that vary dramatically in environmental quality. We discuss the goal of relating MH population variation to functional differences in disease susceptibility such as those inferred by observations of parasitic infection and direct measurement of bacterial challenges in the laboratory. Our study has focused on relatively well-studied killifish populations, including those resident in a highly disturbed, chemically contaminated estuary and nearby less contaminated sites. Population-specific genetic changes at MHC antigen-binding loci are described, and evidence relevant to functional implications of these changes is reviewed. Population-specific patterns of variation in antigen-binding regions in combination with a range of assessments of immune function will provide a powerful new approach to reveal functional changes in MHC.

A new methodology based on functional principal component analysis to study postural stability post-stroke.

PubMed

Sánchez-Sánchez, M Luz; Belda-Lois, Juan-Manuel; Mena-Del Horno, Silvia; Viosca-Herrero, Enrique; Igual-Camacho, Celedonia; Gisbert-Morant, Beatriz

2018-05-05

A major goal in stroke rehabilitation is the establishment of more effective physical therapy techniques to recover postural stability. Functional Principal Component Analysis provides greater insight into recovery trends. However, when missing values exist, obtaining functional data presents some difficulties. The purpose of this study was to reveal an alternative technique for obtaining the Functional Principal Components without requiring the conversion to functional data beforehand and to investigate this methodology to determine the effect of specific physical therapy techniques in balance recovery trends in elderly subjects with hemiplegia post-stroke. A randomized controlled pilot trial was developed. Thirty inpatients post-stroke were included. Control and target groups were treated with the same conventional physical therapy protocol based on functional criteria, but specific techniques were added to the target group depending on the subjects' functional level. Postural stability during standing was quantified by posturography. The assessments were performed once a month from the moment the participants were able to stand up to six months post-stroke. The target group showed a significant improvement in postural control recovery trend six months after stroke that was not present in the control group. Some of the assessed parameters revealed significant differences between treatment groups (P < 0.05). The proposed methodology allows Functional Principal Component Analysis to be performed when data is scarce. Moreover, it allowed the dynamics of recovery of two different treatment groups to be determined, showing that the techniques added in the target group increased postural stability compared to the base protocol. Copyright © 2018 Elsevier Ltd. All rights reserved.

Linking Resting-State Networks in the Prefrontal Cortex to Executive Function: A Functional Near Infrared Spectroscopy Study.

PubMed

Zhao, Jia; Liu, Jiangang; Jiang, Xin; Zhou, Guifei; Chen, Guowei; Ding, Xiao P; Fu, Genyue; Lee, Kang

2016-01-01

Executive function (EF) plays vital roles in our everyday adaptation to the ever-changing environment. However, limited existing studies have linked EF to the resting-state brain activity. The functional connectivity in the resting state between the sub-regions of the brain can reveal the intrinsic neural mechanisms involved in cognitive processing of EF without disturbance from external stimuli. The present study investigated the relations between the behavioral executive function (EF) scores and the resting-state functional network topological properties in the Prefrontal Cortex (PFC). We constructed complex brain functional networks in the PFC from 90 healthy young adults using functional near infrared spectroscopy (fNIRS). We calculated the correlations between the typical network topological properties (regional topological properties and global topological properties) and the scores of both the Total EF and components of EF measured by computer-based Cambridge Neuropsychological Test Automated Battery (CANTAB). We found that the Total EF scores were positively correlated with regional properties in the right dorsal superior frontal gyrus (SFG), whereas the opposite pattern was found in the right triangular inferior frontal gyrus (IFG). Different EF components were related to different regional properties in various PFC areas, such as planning in the right middle frontal gyrus (MFG), working memory mainly in the right MFG and triangular IFG, short-term memory in the left dorsal SFG, and task switch in the right MFG. In contrast, there were no significant findings for global topological properties. Our findings suggested that the PFC plays an important role in individuals' behavioral performance in the executive function tasks. Further, the resting-state functional network can reveal the intrinsic neural mechanisms involved in behavioral EF abilities.

Multimodal MRI reveals structural connectivity differences in 22q11 deletion syndrome related to impaired spatial working memory.

PubMed

O'Hanlon, Erik; Howley, Sarah; Prasad, Sarah; McGrath, Jane; Leemans, Alexander; McDonald, Colm; Garavan, Hugh; Murphy, Kieran C

2016-12-01

Impaired spatial working memory is a core cognitive deficit observed in people with 22q11 Deletion syndrome (22q11DS) and has been suggested as a candidate endophenotype for schizophrenia. However, to date, the neuroanatomical mechanisms describing its structural and functional underpinnings in 22q11DS remain unclear. We quantitatively investigate the cognitive processes and associated neuroanatomy of spatial working memory in people with 22q11DS compared to matched controls. We examine whether there are significant between-group differences in spatial working memory using task related fMRI, Voxel based morphometry and white matter fiber tractography. Multimodal magnetic resonance imaging employing functional, diffusion and volumetric techniques were used to quantitatively assess the cognitive and neuroanatomical features of spatial working memory processes in 22q11DS. Twenty-six participants with genetically confirmed 22q11DS aged between 9 and 52 years and 26 controls aged between 8 and 46 years, matched for age, gender, and handedness were recruited. People with 22q11DS have significant differences in spatial working memory functioning accompanied by a gray matter volume reduction in the right precuneus. Gray matter volume was significantly correlated with task performance scores in these areas. Tractography revealed extensive differences along fibers between task-related cortical activations with pronounced differences localized to interhemispheric commissural fibers within the parietal section of the corpus callosum. Abnormal spatial working memory in 22q11DS is associated with aberrant functional activity in conjunction with gray and white matter structural abnormalities. These anomalies in discrete brain regions may increase susceptibility to the development of psychiatric disorders such as schizophrenia. Hum Brain Mapp 37:4689-4705, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

The Microbiome of Seriola lalandi of Wild and Aquaculture Origin Reveals Differences in Composition and Potential Function.

PubMed

Ramírez, Carolina; Romero, Jaime

2017-01-01

Seriola lalandi is an economically important species that is globally distributed in temperate and subtropical marine waters. Aquaculture production of this species has had problems associated with intensive fish farming, such as disease outbreaks or nutritional deficiencies causing high mortalities. Intestinal microbiota has been involved in many processes that benefit the host, such as disease control, stimulation of the immune response, and the promotion of nutrient metabolism, among others. However, little is known about the potential functionality of the microbiota and the differences in the composition between wild and aquacultured fish. Here, we assayed the V4-region of the 16S rRNA gene using high-throughput sequencing. Our results showed that there are significant differences between S. lalandi of wild and aquaculture origin (ANOSIM and PERMANOVA, P < 0.05). At the genus level, a total of 13 genera were differentially represented between the two groups, all of which have been described as beneficial microorganisms that have an antagonistic effect against pathogenic bacteria, improve immunological parameters and growth performance, and contribute to nutrition. Additionally, the changes in the presumptive functions of the intestinal microbiota of yellowtail were examined by predicting the metagenomes using PICRUSt. The most abundant functional categories were those corresponding to the metabolism of cofactors and vitamins, amino acid metabolism and carbohydrate metabolism, revealing differences in the contribution of the microbiota depending on the origin of the animals. To our knowledge, this is the first study to characterize and compare the intestinal microbiota of S. lalandi of wild and aquaculture origin using high-throughput sequencing.

Plant Abiotic Stress Proteomics: The Major Factors Determining Alterations in Cellular Proteome

PubMed Central

Kosová, Klára; Vítámvás, Pavel; Urban, Milan O.; Prášil, Ilja T.; Renaut, Jenny

2018-01-01

HIGHLIGHTS: Major environmental and genetic factors determining stress-related protein abundance are discussed.Major aspects of protein biological function including protein isoforms and PTMs, cellular localization and protein interactions are discussed.Functional diversity of protein isoforms and PTMs is discussed. Abiotic stresses reveal profound impacts on plant proteomes including alterations in protein relative abundance, cellular localization, post-transcriptional and post-translational modifications (PTMs), protein interactions with other protein partners, and, finally, protein biological functions. The main aim of the present review is to discuss the major factors determining stress-related protein accumulation and their final biological functions. A dynamics of stress response including stress acclimation to altered ambient conditions and recovery after the stress treatment is discussed. The results of proteomic studies aimed at a comparison of stress response in plant genotypes differing in stress adaptability reveal constitutively enhanced levels of several stress-related proteins (protective proteins, chaperones, ROS scavenging- and detoxification-related enzymes) in the tolerant genotypes with respect to the susceptible ones. Tolerant genotypes can efficiently adjust energy metabolism to enhanced needs during stress acclimation. Stress tolerance vs. stress susceptibility are relative terms which can reflect different stress-coping strategies depending on the given stress treatment. The role of differential protein isoforms and PTMs with respect to their biological functions in different physiological constraints (cellular compartments and interacting partners) is discussed. The importance of protein functional studies following high-throughput proteome analyses is presented in a broader context of plant biology. In summary, the manuscript tries to provide an overview of the major factors which have to be considered when interpreting data from proteomic studies on stress-treated plants. PMID:29472941

Differences in Brain Structure and Function in Older Adults with Self-Reported Disabling and Non-Disabling Chronic Low Back Pain

PubMed Central

Buckalew, Neilly; Haut, Marc W.; Aizenstein, Howard; Morrow, Lisa; Perera, Subashan; Kuwabara, Hiroto; Weiner, Debra K.

2010-01-01

Objective The primary aim of this pilot study was to identify structural and functional brain differences in older adults with self-reported disabling chronic low back pain (CLBP) compared with those who reported non-disabling CLBP. Design Cross-sectional. Participants Sixteen cognitively intact older adults, eight with disabling CLBP and eight with non-disabling. Exclusions were psychiatric or neurological disorders, substance abuse, opioid use, or diabetes mellitus. Methods Participants underwent: structural and functional brain MRI; neuropsychological assessment using the Repeatable Battery for the Assessment of Neuropsychological Status, Trail Making Tests A and B; and physical performance assessment using the Short Physical Performance Battery. Results In the disabled group there was significantly lower white matter (WM) integrity (P < 0.05) of the splenium of the corpus callosum. This group also demonstrated activation of the right medial prefrontal cortex at rest whereas the non-disabled demonstrated activation of the left lateral prefrontal cortex. Combined groups analysis revealed a strong positive correlation (rs = 0.80, P < 0.0002) between WM integrity of the left centrum semiovale with gait-speed. Secondary analysis revealed a strong negative correlation between total months of CLBP and WM integrity of the SCC (rs = −0.59, P < 0.02). Conclusions Brain structure and function is different in older adults with disabling CLBP compared to those with non-disabling CLBP. Deficits in brain morphology combining groups are associated with pain duration and poor physical function. Our findings suggest brain structure and function may play a key role in chronic-pain-related-disability and may be important treatment targets. PMID:20609128

Functional and evolutionary relationships between bacteriorhodopsin and halorhodopsin in the archaebacterium, halobacterium halobium

NASA Technical Reports Server (NTRS)

Lanyi, J. K.

1986-01-01

The archaebacteria occupy a unique place in phylogenetic trees constructed from analyses of sequences from key informational macromolecules, and their study continues to yield interesting ideas on the early evolution and divergence of biological forms. It is now known that the halobacteria among these species contain various retinal-proteins, resembling eukaryotic rhodopsins, but with different functions. Two of these pigments, located in the cytoplasmic membranes of the bacteria, are bacteriorhodopsin (a light-driven proton pump) and halorhodopsin (a light-driven chloride pump). Comparison of these systems is expected to reveal structure/function relationships in these simple (primitive?) energy transducing membrane components and evolutionary relationships which had produced the structural features which allow the divergent functions. Findings indicate that very different primary structures are needed for these proteins to accomplish their different functions. Indeed, analysis of partial amino acid sequences from halo-opsin shows already that few if any long segments exist which are homologous to bacterio-opsin. Either these proteins diverged a very long time ago to allow for the observed differences, or the evolutionary clock in the halobacteria runs faster than usual.

Comparison of Saccharomyces cerevisiae F-BAR domain structures reveals a conserved inositol phosphate binding site.

PubMed

Moravcevic, Katarina; Alvarado, Diego; Schmitz, Karl R; Kenniston, Jon A; Mendrola, Jeannine M; Ferguson, Kathryn M; Lemmon, Mark A

2015-02-03

F-BAR domains control membrane interactions in endocytosis, cytokinesis, and cell signaling. Although they are generally thought to bind curved membranes containing negatively charged phospholipids, numerous functional studies argue that differences in lipid-binding selectivities of F-BAR domains are functionally important. Here, we compare membrane-binding properties of the Saccharomyces cerevisiae F-BAR domains in vitro and in vivo. Whereas some F-BAR domains (such as Bzz1p and Hof1p F-BARs) bind equally well to all phospholipids, the F-BAR domain from the RhoGAP Rgd1p preferentially binds phosphoinositides. We determined X-ray crystal structures of F-BAR domains from Hof1p and Rgd1p, the latter bound to an inositol phosphate. The structures explain phospholipid-binding selectivity differences and reveal an F-BAR phosphoinositide binding site that is fully conserved in a mammalian RhoGAP called Gmip and is partly retained in certain other F-BAR domains. Our findings reveal previously unappreciated determinants of F-BAR domain lipid-binding specificity and provide a basis for its prediction from sequence. Copyright © 2015 Elsevier Ltd. All rights reserved.

Comparison of Saccharomyces cerevisiae F-BAR Domain Structures Reveals a Conserved Inositol Phosphate Binding Site

DOE PAGES

Moravcevic, Katarina; Alvarado, Diego; Schmitz, Karl R.; ...

2015-01-22

F-BAR domains control membrane interactions in endocytosis, cytokinesis, and cell signaling. Although they are generally thought to bind curved membranes containing negatively charged phospholipids, numerous functional studies argue that differences in lipid-binding selectivities of F-BAR domains are functionally important. Here in this paper, we compare membrane-binding properties of the Saccharomyces cerevisiae F-BAR domains in vitro and in vivo. Whereas some F-BAR domains (such as Bzz1p and Hof1p F-BARs) bind equally well to all phospholipids, the F-BAR domain from the RhoGAP Rgd1p preferentially binds phosphoinositides. We determined X-ray crystal structures of F-BAR domains from Hof1p and Rgd1p, the latter bound tomore » an inositol phosphate. The structures explain phospholipid-binding selectivity differences and reveal an F-BAR phosphoinositide binding site that is fully conserved in a mammalian RhoGAP called Gmip and is partly retained in certain other F-BAR domains. In conclusion, our findings reveal previously unappreciated determinants of F-BAR domain lipid-binding specificity and provide a basis for its prediction from sequence.« less

Electrical-pulse-induced resistivity modulation in Pt/TiO2-δ/Pt multilayer device related to nanoionics-based neuromorphic function

NASA Astrophysics Data System (ADS)

Kawamura, Kinya; Tsuchiya, Takashi; Takayanagi, Makoto; Terabe, Kazuya; Higuchi, Tohru

2017-06-01

Resistivity modulation behavior in Pt/TiO2-δ/Pt multilayer devices was investigated in terms of nanoionics-based neuromorphic function. The current relaxation behavior, which corresponds to short-term and long-term memorization in neuromorphic function, was analyzed using electrical pulses. In contrast to the huge difference in ionic conductivity for bulk crystal materials of TiO2-δ and WO3, the difference in the relaxation behavior was small. Rutherford backscattering spectrometry and hydrogen forward scattering spectrometry revealed that the TiO2-δ thin film contained 5.6 at. % of protons. This indicates that the neuromorphic function in TiO2-δ-based devices is caused by extrinsic proton transport, presumably through the grain boundary.

Temperature regulates methane production through the function centralization of microbial community in anaerobic digestion.

PubMed

Lin, Qiang; De Vrieze, Jo; He, Guihua; Li, Xiangzhen; Li, Jiabao

2016-09-01

Temperature is crucial for the performance of anaerobic digestion process. In this study of anaerobic digestion of swine manure, the relationship between the microbial gene expression and methane production at different temperatures (25-55°C) was revealed through metatranscriptomic analysis. Daily methane production and total biogas production increased with temperature up to 50°C, but decreased at 55°C. The functional gene expression showed great variation at different temperatures. The function centralization (opposite to alpha-diversity), assessed by the least proportions of functional pathways contributing for at least 50% of total reads positively correlated to methane production. Temperature regulated methane production probably through reducing the diversity of functional pathways, but enhancing central functional pathways, so that most of cellular activities and resource were invested in methanogenesis and related pathways, enhancing the efficiency of conversion of substrates to methane. This research demonstrated the importance of function centralization for efficient system functioning. Copyright © 2016 Elsevier Ltd. All rights reserved.

Solution structure of CXCL5--a novel chemokine and adipokine implicated in inflammation and obesity.

PubMed

Sepuru, Krishna Mohan; Poluri, Krishna Mohan; Rajarathnam, Krishna

2014-01-01

The chemokine CXCL5 is selectively expressed in highly specialized cells such as epithelial type II cells in the lung and white adipose tissue macrophages in muscle, where it mediates diverse functions from combating microbial infections by regulating neutrophil trafficking to promoting obesity by inhibiting insulin signaling. Currently very little is known regarding the structural basis of how CXCL5 mediates its novel functions. Towards this missing knowledge, we have solved the solution structure of the CXCL5 dimer by NMR spectroscopy. CXCL5 is a member of a subset of seven CXCR2-activating chemokines (CAC) that are characterized by the highly conserved ELR motif in the N-terminal tail. The structure shows that CXCL5 adopts the typical chemokine fold, but also reveals several distinct differences in the 30 s loop and N-terminal residues; not surprisingly, crosstalk between N-terminal and 30 s loop residues have been implicated as a major determinant of receptor activity. CAC function also involves binding to highly sulfated glycosaminoglycans (GAG), and the CXCL5 structure reveals a distinct distribution of positively charged residues, suggesting that differences in GAG interactions also influence function. The availability of the structure should now facilitate the design of experiments to better understand the molecular basis of various CXCL5 functions, and also serve as a template for the design of inhibitors for use in a clinical setting.

Magneto-optical effects in semimetallic Bi 1–xSb x (x=0.015)

DOE PAGES

Dordevic, S. V.; Wolf, M. S.; Stojilovic, N.; ...

2012-09-12

We report the results of infrared and magneto-optical spectroscopy study on electrodynamic response of bismuth doped with 1.5% of antimony. The spectra are presented for temperatures down to 4.2 K, and in magnetic fields as high as 18 T. The results reveal strong magneto-optical activity, similar to pure bismuth, however there are some differences introduced by antimony doping. Analysis of optical functions reveals that the two type of charge carriers respond differently to external magnetic field. Finally, when the system enters the extreme quantum regime, both the inter- and intraband Landau Level transition are observed in the spectra.

Gender differences in lateralization of mismatch negativity in dichotic listening tasks.

PubMed

Ikezawa, Satoru; Nakagome, Kazuyuki; Mimura, Masaru; Shinoda, Junko; Itoh, Kenji; Homma, Ikuo; Kamijima, Kunitoshi

2008-04-01

With the aim of investigating gender differences in the functional lateralization subserving preattentive processing of language stimuli, we compared auditory mismatch negativities (MMNs) using dichotic listening tasks. Forty-four healthy volunteers, including 23 males and 21 females, participated in the study. MMNs generated by pure-tone and phonetic stimuli were compared, to check for the existence of language-specific gender differences in lateralization. Both EEG amplitude and scalp current density (SCD) data were analyzed. With phonetic MMNs, EEG findings revealed significantly larger amplitude in females than males, especially in the right hemisphere, while SCD findings revealed left hemisphere dominance and contralateral dominance in males alone. With pure-tone MMNs, no significant gender differences in hemispheric lateralization appeared in either EEG or SCD findings. While males exhibited left-lateralized activation with phonetic MMNs, females exhibited more bilateral activity. Further, the contralateral dominance of the SCD distribution associated with the ear receiving deviant stimuli in males indicated that ipsilateral input as well as interhemispheric transfer across the corpus callosum to the ipsilateral side was more suppressed in males than in females. The findings of the present study suggest that functional lateralization subserving preattentive detection of phonetic change differs between the genders. These results underscore the significance of considering the gender differences in the study of MMN, especially when phonetic stimulus is adopted. Moreover, they support the view of Voyer and Flight [Voyer, D., Flight, J., 2001. Gender differences in laterality on a dichotic task: the influence of report strategies. Cortex 37, 345-362.] in that the gender difference in hemispheric lateralization of language function is observed in a well-managed-attention condition, which fits the condition adopted in the MMN measurement; subjects are required to focus attention to a distraction task and thereby ignore the phonetic stimuli that elicit MMN.

Influence of Cognitive Functioning on Age-Related Performance Declines in Visuospatial Sequence Learning.

PubMed

Krüger, Melanie; Hinder, Mark R; Puri, Rohan; Summers, Jeffery J

2017-01-01

Objectives: The aim of this study was to investigate how age-related performance differences in a visuospatial sequence learning task relate to age-related declines in cognitive functioning. Method: Cognitive functioning of 18 younger and 18 older participants was assessed using a standardized test battery. Participants then undertook a perceptual visuospatial sequence learning task. Various relationships between sequence learning and participants' cognitive functioning were examined through correlation and factor analysis. Results: Older participants exhibited significantly lower performance than their younger counterparts in the sequence learning task as well as in multiple cognitive functions. Factor analysis revealed two independent subsets of cognitive functions associated with performance in the sequence learning task, related to either the processing and storage of sequence information (first subset) or problem solving (second subset). Age-related declines were only found for the first subset of cognitive functions, which also explained a significant degree of the performance differences in the sequence learning task between age-groups. Discussion: The results suggest that age-related performance differences in perceptual visuospatial sequence learning can be explained by declines in the ability to process and store sequence information in older adults, while a set of cognitive functions related to problem solving mediates performance differences independent of age.

Multifunctional RNA Nanoparticles

PubMed Central

2015-01-01

Our recent advancements in RNA nanotechnology introduced novel nanoscaffolds (nanorings); however, the potential of their use for biomedical applications was never fully revealed. As presented here, besides functionalization with multiple different short interfering RNAs for combinatorial RNA interference (e.g., against multiple HIV-1 genes), nanorings also allow simultaneous embedment of assorted RNA aptamers, fluorescent dyes, proteins, as well as recently developed RNA–DNA hybrids aimed to conditionally activate multiple split functionalities inside cells. PMID:25267559

On the universality of Marangoni-driven spreading

NASA Astrophysics Data System (ADS)

Visser, Claas; van Capelleveen, Bram; Koldeweij, Robin; Lohse, Detlef

2017-11-01

When two liquids of different surface tensions come into contact, the liquid with lower surface tension spreads over the other. Here we measure the dynamics of this Marangoni-driven spreading in the drop-drop geometry, revealing universal behavior with respect to the control parameters as well as other geometries (such as spreading over a flat interface). The distance L over which the low-surface-tension liquid has covered the high-surface-tension droplet is measured as a function of time t, surface tension difference between the liquids Δσ , and viscosity η, revealing power-law behavior L(t) tα . The exponent α is discussed for the early and late spreading regimes. Spreading inhibition is observed at high viscosity, for which the threshold is discussed. Finally, we show that our results collapse onto a single curve of dimensionless L(t) as a function of dimensionless time, which also captures previous results for different geometries, surface tension modifiers, and miscibility. As this curve spans 7 orders of magnitude, Marangoni-induced spreading can be considered a universal phenomenon for many practically encountered liquid-liquid systems.

Imagine All the People: How the Brain Creates and Uses Personality Models to Predict Behavior

PubMed Central

Hassabis, Demis; Spreng, R. Nathan; Rusu, Andrei A.; Robbins, Clifford A.; Mar, Raymond A.; Schacter, Daniel L.

2014-01-01

The behaviors of other people are often central to envisioning the future. The ability to accurately predict the thoughts and actions of others is essential for successful social interactions, with far-reaching consequences. Despite its importance, little is known about how the brain represents people in order to predict behavior. In this functional magnetic resonance imaging study, participants learned the unique personality of 4 protagonists and imagined how each would behave in different scenarios. The protagonists' personalities were composed of 2 traits: Agreeableness and Extraversion. Which protagonist was being imagined was accurately inferred based solely on activity patterns in the medial prefrontal cortex using multivariate pattern classification, providing novel evidence that brain activity can reveal whom someone is thinking about. Lateral temporal and posterior cingulate cortex discriminated between different degrees of agreeableness and extraversion, respectively. Functional connectivity analysis confirmed that regions associated with trait-processing and individual identities were functionally coupled. Activity during the imagination task, and revealed by functional connectivity, was consistent with the default network. Our results suggest that distinct regions code for personality traits, and that the brain combines these traits to represent individuals. The brain then uses this “personality model” to predict the behavior of others in novel situations. PMID:23463340

Metagenomic analysis of the microbiota in the highly compartmented hindguts of six wood- or soil-feeding higher termites

DOE PAGES

Rossmassler, Karen; Dietrich, Carsten; Thompson, Claire; ...

2015-11-26

Termites are important contributors to carbon and nitrogen cycling in tropical ecosystems. Higher termites digest lignocellulose in various stages of humification with the help of an entirely prokaryotic microbiota housed in their compartmented intestinal tract. Previous studies revealed fundamental differences in community structure between compartments, but the functional roles of individual lineages in symbiotic digestion are mostly unknown. Furthermore, we conducted a highly resolved analysis of the gut microbiota in six species of higher termites that feed on plant material at different levels of humification. Combining amplicon sequencing and metagenomics, we assessed similarities in community structure and functional potential betweenmore » the major hindgut compartments (P1, P3, and P4). Cluster analysis of the relative abundances of orthologous gene clusters (COGs) revealed high similarities among woodand litter-feeding termites and strong differences to humivorous species. However, abundance estimates of bacterial phyla based on 16S rRNA genes greatly differed from those based on protein-coding genes. In conclusion, the community structure and functional potential of the microbiota in individual gut compartments are clearly driven by the digestive strategy of the host. The metagenomics libraries obtained in this study provide the basis for future studies that elucidate the fundamental differences in the symbiont-mediated breakdown of lignocellulose and humus by termites of different feeding groups. The high proportion of uncultured bacterial lineages in all samples calls for a reference-independent approach for the correct taxonomic assignment of protein-coding genes.« less

Metagenomic analysis of the microbiota in the highly compartmented hindguts of six wood- or soil-feeding higher termites

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

Rossmassler, Karen; Dietrich, Carsten; Thompson, Claire

Termites are important contributors to carbon and nitrogen cycling in tropical ecosystems. Higher termites digest lignocellulose in various stages of humification with the help of an entirely prokaryotic microbiota housed in their compartmented intestinal tract. Previous studies revealed fundamental differences in community structure between compartments, but the functional roles of individual lineages in symbiotic digestion are mostly unknown. Furthermore, we conducted a highly resolved analysis of the gut microbiota in six species of higher termites that feed on plant material at different levels of humification. Combining amplicon sequencing and metagenomics, we assessed similarities in community structure and functional potential betweenmore » the major hindgut compartments (P1, P3, and P4). Cluster analysis of the relative abundances of orthologous gene clusters (COGs) revealed high similarities among woodand litter-feeding termites and strong differences to humivorous species. However, abundance estimates of bacterial phyla based on 16S rRNA genes greatly differed from those based on protein-coding genes. In conclusion, the community structure and functional potential of the microbiota in individual gut compartments are clearly driven by the digestive strategy of the host. The metagenomics libraries obtained in this study provide the basis for future studies that elucidate the fundamental differences in the symbiont-mediated breakdown of lignocellulose and humus by termites of different feeding groups. The high proportion of uncultured bacterial lineages in all samples calls for a reference-independent approach for the correct taxonomic assignment of protein-coding genes.« less

Provenance effect on carbon assimilation, photochemistry and leaf morphology in Mediterranean Cistus species under chilling stress.

PubMed

Puglielli, G; Cuevas Román, F J; Catoni, R; Moreno Rojas, J M; Gratani, L; Varone, L

2017-07-01

The potential resilience of shrub species to environmental change deserves attention in those areas threatened by climate change, such as the Mediterranean Basin. We asked if leaves produced under different climate conditions through the winter season to spring can highlight the leaf traits involved in determining potential resilience of three Cistus spp. to changing environmental conditions and to what extent intraspecific differences affect such a response. We analysed carbon assimilation, maximum quantum efficiency of PSII photochemistry (F v /F m ) and leaf morphological control of the photosynthetic process in leaves formed through the winter season into spring in C. creticus subsp. eriocephalus (CE), C. salvifolius (CS) and C. monspeliensis (CM) grown from seed of different provenances under common garden conditions. Intraspecific differences were found in F v /F m for CE and CS. Carbon assimilation-related parameters were not affected by provenance. Moreover, our analysis highlighted that the functional relationships investigated can follow seasonal changes and revealed patterns originating from species-specific differences in LMA arising during the favourable period. Cistus spp. have great ability to modify the structure and function of their leaves in the mid-term in order to cope with changing environmental conditions. The F v /F m response to chilling reveals that susceptibility to photoinhibition is a trait under selection in Cistus species. Concerning carbon assimilation, differing ability to control stomatal opening was highlighted between species. Moreover, seasonal changes of the functional relationships investigated can have predictable consequences on species leaf turnover strategies. © 2017 German Botanical Society and The Royal Botanical Society of the Netherlands.

Structural variations in prefrontal cortex mediate the relationship between early childhood stress and spatial working memory

PubMed Central

Hanson, Jamie L.; Chung, Moo K.; Avants, Brian B.; Rudolph, Karen D.; Shirtcliff, Elizabeth A.; Gee, James C.; Davidson, Richard J.; Pollak, Seth D.

2012-01-01

A large corpus of research indicates exposure to stress impairs cognitive abilities, specifically executive functioning dependent on the prefrontal cortex (PFC). We collected structural MRI scans (n=61), well-validated assessments of executive functioning, and detailed interviews assessing stress exposure in humans, to examine whether cumulative life stress affected brain morphometry and one type of executive functioning, spatial working memory, during adolescence—a critical time of brain development and reorganization. Analysis of variations in brain structure revealed that cumulative life stress and spatial working memory were related to smaller volumes in the PFC, specifically prefrontal gray and white matter between the anterior cingulate and the frontal poles. Mediation analyses revealed that individual differences in prefrontal volumes accounted for the association between cumulative life stress and spatial working memory. These results suggest that structural changes in the PFC may serve as a mediating mechanism through which greater cumulative life stress engenders decrements in cognitive functioning. PMID:22674267

C-RAF function at the genome-wide transcriptome level: A systematic view.

PubMed

Huang, Ying; Zhang, Xin-Yu; An, Su; Yang, Yang; Liu, Ying; Hao, Qian; Guo, Xiao-Xi; Xu, Tian-Rui

2018-05-20

C-RAF was the first member of the RAF kinase family to be discovered. Since its discovery, C-RAF has been found to regulate many fundamental cell processes, such as cell proliferation, cell death, and metabolism. However, the majority of these functions are achieved through interactions with different proteins; the genes regulated by C-RAF in its active or inactive state remain unclear. In the work, we used RNA-seq analysis to study the global transcriptomes of C-RAF bearing or C-RAF knockout cells in quiescent or EGF activated states. We identified 3353 genes that are promoted or suppressed by C-RAF. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed that these genes are involved in drug addiction, cardiomyopathy, autoimmunity, and regulation of cell metabolism. Our results provide a panoramic view of C-RAF function, including known and novel functions, and have revealed potential targets for elucidating the role of C-RAF. Copyright © 2018 Elsevier B.V. All rights reserved.

Cognitive aspects of sexual functioning: differences between East Asian-Canadian and Euro-Canadian women.

PubMed

Morton, Heather; Gorzalka, Boris B

2013-11-01

The purpose of this study was to investigate the sexual beliefs of female undergraduates, as well as the thoughts they experience during sexual experiences. The study aimed to determine potential differences in these variables between East Asian-Canadians and Euro-Canadians, as well as the influence of acculturation on these variables. In addition, the relationships between sexual beliefs, automatic thoughts, and specific aspects of sexual functioning were examined. Euro-Canadian (n = 77) and East Asian-Canadian (n = 123) undergraduate women completed the Sexual Dysfunctional Beliefs Questionnaire, the Sexual Modes Questionnaire, the Female Sexual Function Index, and the Vancouver Index of Acculturation. East Asian women endorsed almost all sexual beliefs assessed in this study more than did Euro-Canadian women, and endorsement of these beliefs was associated with acculturation. In addition, East Asian-Canadian and Euro-Canadian women differed in the frequency of experiencing negative automatic thoughts. Results also revealed associations between difficulties in sexual functioning, and both sexual beliefs and automatic thoughts. Together, these results provide preliminary support for the hypothesis that differences in cognitive aspects of sexuality may underlie the differences in sexual functioning previously observed between these two groups.

The functional anatomy of suggested limb paralysis.

PubMed

Deeley, Quinton; Oakley, David A; Toone, Brian; Bell, Vaughan; Walsh, Eamonn; Marquand, Andre F; Giampietro, Vincent; Brammer, Michael J; Williams, Steven C R; Mehta, Mitul A; Halligan, Peter W

2013-02-01

Suggestions of limb paralysis in highly hypnotically suggestible subjects have been employed to successfully model conversion disorders, revealing similar patterns of brain activation associated with attempted movement of the affected limb. However, previous studies differ with regard to the executive regions involved during involuntary inhibition of the affected limb. This difference may have arisen as previous studies did not control for differences in hypnosis depth between conditions and/or include subjective measures to explore the experience of suggested paralysis. In the current study we employed functional magnetic resonance imaging (fMRI) to examine the functional anatomy of left and right upper limb movements in eight healthy subjects selected for high hypnotic suggestibility during (i) hypnosis (NORMAL) and (ii) attempted movement following additional left upper limb paralysis suggestions (PARALYSIS). Contrast of left upper limb motor function during NORMAL relative to PARALYSIS conditions revealed greater activation of contralateral M1/S1 and ipsilateral cerebellum, consistent with the engagement of these regions in the completion of movements. By contrast, two significant observations were noted in PARALYSIS relative to NORMAL conditions. In conjunction with reports of attempts to move the paralysed limb, greater supplementary motor area (SMA) activation was observed, a finding consistent with the role of SMA in motor intention and planning. The anterior cingulate cortex (ACC, BA 24) was also significantly more active in PARALYSIS relative to NORMAL conditions - suggesting that ACC (BA 24) may be implicated in involuntary, as well as voluntary inhibition of prepotent motor responses. Copyright © 2012 Elsevier Ltd. All rights reserved.

Root Exudation of Phytochemicals in Arabidopsis Follows Specific Patterns That Are Developmentally Programmed and Correlate with Soil Microbial Functions

PubMed Central

Sugiyama, Akifumi; Manter, Daniel K.; Vivanco, Jorge M.

2013-01-01

Plant roots constantly secrete compounds into the soil to interact with neighboring organisms presumably to gain certain functional advantages at different stages of development. Accordingly, it has been hypothesized that the phytochemical composition present in the root exudates changes over the course of the lifespan of a plant. Here, root exudates of in vitro grown Arabidopsis plants were collected at different developmental stages and analyzed using GC-MS. Principle component analysis revealed that the composition of root exudates varied at each developmental stage. Cumulative secretion levels of sugars and sugar alcohols were higher in early time points and decreased through development. In contrast, the cumulative secretion levels of amino acids and phenolics increased over time. The expression in roots of genes involved in biosynthesis and transportation of compounds represented in the root exudates were consistent with patterns of root exudation. Correlation analyses were performed of the in vitro root exudation patterns with the functional capacity of the rhizosphere microbiome to metabolize these compounds at different developmental stages of Arabidopsis grown in natural soils. Pyrosequencing of rhizosphere mRNA revealed strong correlations (p<0.05) between microbial functional genes involved in the metabolism of carbohydrates, amino acids and secondary metabolites with the corresponding compounds released by the roots at particular stages of plant development. In summary, our results suggest that the root exudation process of phytochemicals follows a developmental pattern that is genetically programmed. PMID:23383346

Differential Dynamic Engagement within 24 SH3 Domain: Peptide Complexes Revealed by Co-Linear Chemical Shift Perturbation Analysis

PubMed Central

Stollar, Elliott J.; Lin, Hong; Davidson, Alan R.; Forman-Kay, Julie D.

2012-01-01

There is increasing evidence for the functional importance of multiple dynamically populated states within single proteins. However, peptide binding by protein-protein interaction domains, such as the SH3 domain, has generally been considered to involve the full engagement of peptide to the binding surface with minimal dynamics and simple methods to determine dynamics at the binding surface for multiple related complexes have not been described. We have used NMR spectroscopy combined with isothermal titration calorimetry to comprehensively examine the extent of engagement to the yeast Abp1p SH3 domain for 24 different peptides. Over one quarter of the domain residues display co-linear chemical shift perturbation (CCSP) behavior, in which the position of a given chemical shift in a complex is co-linear with the same chemical shift in the other complexes, providing evidence that each complex exists as a unique dynamic rapidly inter-converting ensemble. The extent the specificity determining sub-surface of AbpSH3 is engaged as judged by CCSP analysis correlates with structural and thermodynamic measurements as well as with functional data, revealing the basis for significant structural and functional diversity amongst the related complexes. Thus, CCSP analysis can distinguish peptide complexes that may appear identical in terms of general structure and percent peptide occupancy but have significant local binding differences across the interface, affecting their ability to transmit conformational change across the domain and resulting in functional differences. PMID:23251481

The evolution of pattern camouflage strategies in waterfowl and game birds.

PubMed

Marshall, Kate L A; Gluckman, Thanh-Lan

2015-05-01

Visual patterns are common in animals. A broad survey of the literature has revealed that different patterns have distinct functions. Irregular patterns (e.g., stipples) typically function in static camouflage, whereas regular patterns (e.g., stripes) have a dual function in both motion camouflage and communication. Moreover, irregular and regular patterns located on different body regions ("bimodal" patterning) can provide an effective compromise between camouflage and communication and/or enhanced concealment via both static and motion camouflage. Here, we compared the frequency of these three pattern types and traced their evolutionary history using Bayesian comparative modeling in aquatic waterfowl (Anseriformes: 118 spp.), which typically escape predators by flight, and terrestrial game birds (Galliformes: 170 spp.), which mainly use a "sit and hide" strategy to avoid predation. Given these life histories, we predicted that selection would favor regular patterning in Anseriformes and irregular or bimodal patterning in Galliformes and that pattern function complexity should increase over the course of evolution. Regular patterns were predominant in Anseriformes whereas regular and bimodal patterns were most frequent in Galliformes, suggesting that patterns with multiple functions are broadly favored by selection over patterns with a single function in static camouflage. We found that the first patterns to evolve were either regular or bimodal in Anseriformes and either irregular or regular in Galliformes. In both orders, irregular patterns could evolve into regular patterns but not the reverse. Our hypothesis of increasing complexity in pattern camouflage function was supported in Galliformes but not in Anseriformes. These results reveal a trajectory of pattern evolution linked to increasing function complexity in Galliformes although not in Anseriformes, suggesting that both ecology and function complexity can have a profound influence on pattern evolution.

The evolution of pattern camouflage strategies in waterfowl and game birds

PubMed Central

Marshall, Kate L A; Gluckman, Thanh-Lan

2015-01-01

Visual patterns are common in animals. A broad survey of the literature has revealed that different patterns have distinct functions. Irregular patterns (e.g., stipples) typically function in static camouflage, whereas regular patterns (e.g., stripes) have a dual function in both motion camouflage and communication. Moreover, irregular and regular patterns located on different body regions (“bimodal” patterning) can provide an effective compromise between camouflage and communication and/or enhanced concealment via both static and motion camouflage. Here, we compared the frequency of these three pattern types and traced their evolutionary history using Bayesian comparative modeling in aquatic waterfowl (Anseriformes: 118 spp.), which typically escape predators by flight, and terrestrial game birds (Galliformes: 170 spp.), which mainly use a “sit and hide” strategy to avoid predation. Given these life histories, we predicted that selection would favor regular patterning in Anseriformes and irregular or bimodal patterning in Galliformes and that pattern function complexity should increase over the course of evolution. Regular patterns were predominant in Anseriformes whereas regular and bimodal patterns were most frequent in Galliformes, suggesting that patterns with multiple functions are broadly favored by selection over patterns with a single function in static camouflage. We found that the first patterns to evolve were either regular or bimodal in Anseriformes and either irregular or regular in Galliformes. In both orders, irregular patterns could evolve into regular patterns but not the reverse. Our hypothesis of increasing complexity in pattern camouflage function was supported in Galliformes but not in Anseriformes. These results reveal a trajectory of pattern evolution linked to increasing function complexity in Galliformes although not in Anseriformes, suggesting that both ecology and function complexity can have a profound influence on pattern evolution. PMID:26045950

Long-term psychosocial consequences of surgical congenital malformations.

PubMed

Diseth, Trond H; Emblem, Ragnhild

2017-10-01

Surgical congenital malformations often represent years of treatment, large number of hospital stays, treatment procedures, and long-term functional sequels affecting patients' psychosocial functioning. Both functional defects and psychosocial difficulties that occur commonly in childhood may pass through adolescence on to adulthood. This overview presents reports published over the past 3 decades to elucidate the long-term psychosocial consequences of surgical congenital malformations. Literature searches conducted on PubMed database revealed that less than 1% of all the records of surgical congenital malformations described long-term psychosocial consequences, but with diverse findings. This inconsistency may be due to methodological differences or deficiencies; especially in study design, patient sampling, and methods. Most of the studies revealed that the functional deficits may have great impact on patients' mental health, psychosocial functioning, and QoL; both short- and long-term negative consequences. Factors other than functional problems, e.g., repeated anesthesia, multiple hospitalization, traumatic treatment procedures, and parental dysfunctioning, may also predict long-term mental health and psychosocial functioning. Through multidisciplinary approach, pediatric surgeons should also be aware of deficits in emotional and psychosocial functioning. To achieve overall optimal psychosocial functioning, the challenge is to find a compromise between physically optimal treatment procedures and procedures that are not psychologically detrimental. Copyright © 2017. Published by Elsevier Inc.

Does double-row rotator cuff repair improve functional outcome of patients compared with single-row technique? A systematic review.

PubMed

DeHaan, Alexander M; Axelrad, Thomas W; Kaye, Elizabeth; Silvestri, Lorenzo; Puskas, Brian; Foster, Timothy E

2012-05-01

The advantage of single-row versus double-row arthroscopic rotator cuff repair techniques has been a controversial issue in sports medicine and shoulder surgery. There is biomechanical evidence that double-row techniques are superior to single-row techniques; however, there is no clinical evidence that the double-row technique provides an improved functional outcome. When compared with single-row rotator cuff repair, double-row fixation, although biomechanically superior, has no clinical benefit with respect to retear rate or improved functional outcome. Systematic review. The authors reviewed prospective studies of level I or II clinical evidence that compared the efficacy of single- and double-row rotator cuff repairs. Functional outcome scores included the American Shoulder and Elbow Surgeons (ASES) shoulder scale, the Constant shoulder score, and the University of California, Los Angeles (UCLA) shoulder rating scale. Radiographic failures and complications were also analyzed. A test of heterogeneity for patient demographics was also performed to determine if there were differences in the patient profiles across the included studies. Seven studies fulfilled our inclusion criteria. The test of heterogeneity across these studies showed no differences. The functional ASES, Constant, and UCLA outcome scores revealed no difference between single- and double-row rotator cuff repairs. The total retear rate, which included both complete and partial retears, was 43.1% for the single-row repair and 27.2% for the double-row repair (P = .057), representing a trend toward higher failures in the single-row group. Through a comprehensive literature search and meta-analysis of current arthroscopic rotator cuff repairs, we found that the single-row repairs did not differ from the double-row repairs in functional outcome scores. The double-row repairs revealed a trend toward a lower radiographic proven retear rate, although the data did not reach statistical significance. There may be a concerning trend toward higher retear rates in patients undergoing a single-row repair, but further studies are required.

Proteomics profiling of interactome dynamics by colocalisation analysis (COLA).

PubMed

Mardakheh, Faraz K; Sailem, Heba Z; Kümper, Sandra; Tape, Christopher J; McCully, Ryan R; Paul, Angela; Anjomani-Virmouni, Sara; Jørgensen, Claus; Poulogiannis, George; Marshall, Christopher J; Bakal, Chris

2016-12-20

Localisation and protein function are intimately linked in eukaryotes, as proteins are localised to specific compartments where they come into proximity of other functionally relevant proteins. Significant co-localisation of two proteins can therefore be indicative of their functional association. We here present COLA, a proteomics based strategy coupled with a bioinformatics framework to detect protein-protein co-localisations on a global scale. COLA reveals functional interactions by matching proteins with significant similarity in their subcellular localisation signatures. The rapid nature of COLA allows mapping of interactome dynamics across different conditions or treatments with high precision.

Effects of water flow regulation on ecosystem functioning in a Mediterranean river network assessed by wood decomposition.

PubMed

Abril, Meritxell; Muñoz, Isabel; Casas-Ruiz, Joan P; Gómez-Gener, Lluís; Barceló, Milagros; Oliva, Francesc; Menéndez, Margarita

2015-06-01

Mediterranean rivers are extensively modified by flow regulation practises along their courses. An important part of the river impoundment in this area is related to the presence of small dams constructed mainly for water abstraction purposes. These projects drastically modified the ecosystem morphology, transforming lotic into lentic reaches and increasing their alternation along the river. Hydro-morphologial differences between these reaches indicate that flow regulation can trigger important changes in the ecosystem functioning. Decomposition of organic matter is an integrative process and this complexity makes it a good indicator of changes in the ecosystem. The aim of this study was to assess the effect caused by flow regulation on ecosystem functioning at the river network scale, using wood decomposition as a functional indicator. We studied the mass loss from wood sticks during three months in different lotic and lentic reaches located along a Mediterranean river basin, in both winter and summer. Additionally, we identified the environmental factors affecting decomposition rates along the river orders. The results revealed differences in decomposition rates between sites in both seasons that were principally related to the differences between stream orders. The rates were mainly related to temperature, nutrient concentrations (NO2(-), NO3(2-)) and water residence time. High-order streams with higher temperature and nutrient concentrations exhibited higher decomposition rates compared with low-order streams. The effect of the flow regulation on the decomposition rates only appeared to be significant in high orders, especially in winter, when the hydrological characteristics of lotic and lentic habitats widely varied. Lotic reaches with lower water residence time exhibited greater decomposition rates compared with lentic reaches probably due to more physical abrasion and differences in the microbial assemblages. Overall, our study revealed that in high orders the reduction of flow caused by flow regulation affects the wood decomposition indicating changes in ecosystem functioning. Copyright © 2015 Elsevier B.V. All rights reserved.

Raman fingerprints of amyloid structures.

PubMed

Flynn, Jessica D; Lee, Jennifer C

2018-06-21

Structural differences in pathological and functional amyloid fibrils have been investigated by Raman microspectroscopy. Second-derivative analyses of amide-I and amide-III bands distinguish parallel in-register β-sheets from a β-solenoid. Further, spatially resolved Raman spectra reveal molecular heterogeneity in amyloid structures.

Abnormal functional specialization within medial prefrontal cortex in high-functioning autism: a multi-voxel similarity analysis

PubMed Central

Meuwese, Julia D.I.; Towgood, Karren J.; Frith, Christopher D.; Burgess, Paul W.

2009-01-01

Multi-voxel pattern analyses have proved successful in ‘decoding’ mental states from fMRI data, but have not been used to examine brain differences associated with atypical populations. We investigated a group of 16 (14 males) high-functioning participants with autism spectrum disorder (ASD) and 16 non-autistic control participants (12 males) performing two tasks (spatial/verbal) previously shown to activate medial rostral prefrontal cortex (mrPFC). Each task manipulated: (i) attention towards perceptual versus self-generated information and (ii) reflection on another person's mental state (‘mentalizing'versus ‘non-mentalizing’) in a 2 × 2 design. Behavioral performance and group-level fMRI results were similar between groups. However, multi-voxel similarity analyses revealed strong differences. In control participants, the spatial distribution of activity generalized significantly between task contexts (spatial/verbal) when examining the same function (attention/mentalizing) but not when comparing different functions. This pattern was disrupted in the ASD group, indicating abnormal functional specialization within mrPFC, and demonstrating the applicability of multi-voxel pattern analysis to investigations of atypical populations. PMID:19174370

Differences conception prospective students teacher about limit of function based gender

NASA Astrophysics Data System (ADS)

Usman, Juniati, Dwi; Siswono, Tatag Yuli Eko

2017-08-01

Gender is one of the interesting topics and has continuity to be explored in mathematics education research. The purpose of this study to explore difference on conceptions of students teaching program by gender. It specialized on conception of understanding, representating, and mental images about limit function. This research conducting qualitative explorative method approach. The subject consisted of one man and one woman from the group of highly skilled student and has gone through semester V. Based on data that had been analyzed proved that male student has an understanding about limit function shared by explaining this material using illustrations, while female student explained it through verbal explanation. Due to representating aspect, it revealed that both of male and female students have similarity such as using verbal explanation, graphs, symbols, and tables to representating about limit function. Analyzing Mental image aspect, researcher got that male student using word "to converge" to explained about limit function, while female student using word "to approach". So, there are differences conceptions about limit function between male and female student.

Applying an Integrative Framework of Executive Function to Preschoolers With Specific Language Impairment.

PubMed

Kapa, Leah L; Plante, Elena; Doubleday, Kevin

2017-08-16

The first goal of this research was to compare verbal and nonverbal executive function abilities between preschoolers with and without specific language impairment (SLI). The second goal was to assess the group differences on 4 executive function components in order to determine if the components may be hierarchically related as suggested within a developmental integrative framework of executive function. This study included 26 4- and 5-year-olds diagnosed with SLI and 26 typically developing age- and sex-matched peers. Participants were tested on verbal and nonverbal measures of sustained selective attention, working memory, inhibition, and shifting. The SLI group performed worse compared with typically developing children on both verbal and nonverbal measures of sustained selective attention and working memory, the verbal inhibition task, and the nonverbal shifting task. Comparisons of standardized group differences between executive function measures revealed a linear increase with the following order: working memory, inhibition, shifting, and sustained selective attention. The pattern of results suggests that preschoolers with SLI have deficits in executive functioning compared with typical peers, and deficits are not limited to verbal tasks. A significant linear relationship between group differences across executive function components supports the possibility of a hierarchical relationship between executive function skills.

Dual role of wingless signaling in stem-like hematopoietic precursor maintenance in Drosophila.

PubMed

Sinenko, Sergey A; Mandal, Lolitika; Martinez-Agosto, Julian A; Banerjee, Utpal

2009-05-01

In Drosophila, blood development occurs in a specialized larval hematopoietic organ, the lymph gland (LG), within which stem-like hemocyte precursors or prohemocytes differentiate to multiple blood cell types. Here we show that components of the Wingless (Wg) signaling pathway are expressed in prohemocytes. Loss- and gain-of-function analysis indicates that canonical Wg signaling is required for maintenance of prohemocytes and negatively regulates their differentiation. Wg signals locally in a short-range fashion within different compartments of the LG. In addition, Wg signaling positively regulates the proliferation and maintenance of cells that function as a hematopoietic niche in Drosophila, the posterior signaling center (PSC), and in the proliferation of crystal cells. Our studies reveal a conserved function of Wg signaling in the maintenance of stem-like blood progenitors and reveal an involvement of this pathway in the regulation of hemocyte differentiation through its action in the hematopoietic niche.

Computational gene expression profiling under salt stress reveals patterns of co-expression

PubMed Central

Sanchita; Sharma, Ashok

2016-01-01

Plants respond differently to environmental conditions. Among various abiotic stresses, salt stress is a condition where excess salt in soil causes inhibition of plant growth. To understand the response of plants to the stress conditions, identification of the responsible genes is required. Clustering is a data mining technique used to group the genes with similar expression. The genes of a cluster show similar expression and function. We applied clustering algorithms on gene expression data of Solanum tuberosum showing differential expression in Capsicum annuum under salt stress. The clusters, which were common in multiple algorithms were taken further for analysis. Principal component analysis (PCA) further validated the findings of other cluster algorithms by visualizing their clusters in three-dimensional space. Functional annotation results revealed that most of the genes were involved in stress related responses. Our findings suggest that these algorithms may be helpful in the prediction of the function of co-expressed genes. PMID:26981411

Phospho-selective mechanisms of arrestin conformations and functions revealed by unnatural amino acid incorporation and 19F-NMR

PubMed Central

Yang, Fan; Yu, Xiao; Liu, Chuan; Qu, Chang-Xiu; Gong, Zheng; Liu, Hong-Da; Li, Fa-Hui; Wang, Hong-Mei; He, Dong-Fang; Yi, Fan; Song, Chen; Tian, Chang-Lin; Xiao, Kun-Hong; Wang, Jiang-Yun; Sun, Jin-Peng

2015-01-01

Specific arrestin conformations are coupled to distinct downstream effectors, which underlie the functions of many G-protein-coupled receptors (GPCRs). Here, using unnatural amino acid incorporation and fluorine-19 nuclear magnetic resonance (19F-NMR) spectroscopy, we demonstrate that distinct receptor phospho-barcodes are translated to specific β-arrestin-1 conformations and direct selective signalling. With its phosphate-binding concave surface, β-arrestin-1 ‘reads' the message in the receptor phospho-C-tails and distinct phospho-interaction patterns are revealed by 19F-NMR. Whereas all functional phosphopeptides interact with a common phosphate binding site and induce the movements of finger and middle loops, different phospho-interaction patterns induce distinct structural states of β-arrestin-1 that are coupled to distinct arrestin functions. Only clathrin recognizes and stabilizes GRK2-specific β-arrestin-1 conformations. The identified receptor-phospho-selective mechanism for arrestin conformation and the spacing of the multiple phosphate-binding sites in the arrestin enable arrestin to recognize plethora phosphorylation states of numerous GPCRs, contributing to the functional diversity of receptors. PMID:26347956

Motor learning in a complex balance task and associated neuroplasticity: a comparison between endurance athletes and nonathletes.

PubMed

Seidel, Oliver; Carius, Daniel; Kenville, Rouven; Ragert, Patrick

2017-09-01

Studies suggested that motor expertise is associated with functional and structural brain alterations, which positively affect sensorimotor performance and learning capabilities. The purpose of the present study was to unravel differences in motor skill learning and associated functional neuroplasticity between endurance athletes (EA) and nonathletes (NA). For this purpose, participants had to perform a multimodal balance task (MBT) training on 2 sessions, which were separated by 1 wk. Before and after MBT training, a static balance task (SBT) had to be performed. MBT-induced functional neuroplasticity and neuromuscular alterations were assessed by means of functional near-infrared spectroscopy (fNIRS) and electromyography (EMG) during SBT performance. We hypothesized that EA would showed superior initial SBT performance and stronger MBT-induced improvements in SBT learning rates compared with NA. On a cortical level, we hypothesized that MBT training would lead to differential learning-dependent functional changes in motor-related brain regions [such as primary motor cortex (M1)] during SBT performance. In fact, EA showed superior initial SBT performance, whereas learning rates did not differ between groups. On a cortical level, fNIRS recordings (time × group interaction) revealed a stronger MBT-induced decrease in left M1 and inferior parietal lobe (IPL) for deoxygenated hemoglobin in EA. Even more interesting, learning rates were correlated with fNIRS changes in right M1/IPL. On the basis of these findings, we provide novel evidence for superior MBT training-induced functional neuroplasticity in highly trained athletes. Future studies should investigate these effects in different sports disciplines to strengthen previous work on experience-dependent neuroplasticity. NEW & NOTEWORTHY Motor expertise is associated with functional/structural brain plasticity. How such neuroplastic reorganization translates into altered motor learning processes remains elusive. We investigated endurance athletes (EA) and nonathletes (NA) in a multimodal balance task (MBT). EA showed superior static balance performance (SBT), whereas MBT-induced SBT improvements did not differ between groups. Functional near-infrared spectroscopy recordings revealed a differential MBT training-induced decrease of deoxygenated hemoglobin in left primary motor cortex and inferior parietal lobe between groups. Copyright © 2017 the American Physiological Society.

Functional Basis of Microorganism Classification.

PubMed

Zhu, Chengsheng; Delmont, Tom O; Vogel, Timothy M; Bromberg, Yana

2015-08-01

Correctly identifying nearest "neighbors" of a given microorganism is important in industrial and clinical applications where close relationships imply similar treatment. Microbial classification based on similarity of physiological and genetic organism traits (polyphasic similarity) is experimentally difficult and, arguably, subjective. Evolutionary relatedness, inferred from phylogenetic markers, facilitates classification but does not guarantee functional identity between members of the same taxon or lack of similarity between different taxa. Using over thirteen hundred sequenced bacterial genomes, we built a novel function-based microorganism classification scheme, functional-repertoire similarity-based organism network (FuSiON; flattened to fusion). Our scheme is phenetic, based on a network of quantitatively defined organism relationships across the known prokaryotic space. It correlates significantly with the current taxonomy, but the observed discrepancies reveal both (1) the inconsistency of functional diversity levels among different taxa and (2) an (unsurprising) bias towards prioritizing, for classification purposes, relatively minor traits of particular interest to humans. Our dynamic network-based organism classification is independent of the arbitrary pairwise organism similarity cut-offs traditionally applied to establish taxonomic identity. Instead, it reveals natural, functionally defined organism groupings and is thus robust in handling organism diversity. Additionally, fusion can use organism meta-data to highlight the specific environmental factors that drive microbial diversification. Our approach provides a complementary view to cladistic assignments and holds important clues for further exploration of microbial lifestyles. Fusion is a more practical fit for biomedical, industrial, and ecological applications, as many of these rely on understanding the functional capabilities of the microbes in their environment and are less concerned with phylogenetic descent.

Functional Basis of Microorganism Classification

PubMed Central

Zhu, Chengsheng; Delmont, Tom O.; Vogel, Timothy M.; Bromberg, Yana

2015-01-01

Correctly identifying nearest “neighbors” of a given microorganism is important in industrial and clinical applications where close relationships imply similar treatment. Microbial classification based on similarity of physiological and genetic organism traits (polyphasic similarity) is experimentally difficult and, arguably, subjective. Evolutionary relatedness, inferred from phylogenetic markers, facilitates classification but does not guarantee functional identity between members of the same taxon or lack of similarity between different taxa. Using over thirteen hundred sequenced bacterial genomes, we built a novel function-based microorganism classification scheme, functional-repertoire similarity-based organism network (FuSiON; flattened to fusion). Our scheme is phenetic, based on a network of quantitatively defined organism relationships across the known prokaryotic space. It correlates significantly with the current taxonomy, but the observed discrepancies reveal both (1) the inconsistency of functional diversity levels among different taxa and (2) an (unsurprising) bias towards prioritizing, for classification purposes, relatively minor traits of particular interest to humans. Our dynamic network-based organism classification is independent of the arbitrary pairwise organism similarity cut-offs traditionally applied to establish taxonomic identity. Instead, it reveals natural, functionally defined organism groupings and is thus robust in handling organism diversity. Additionally, fusion can use organism meta-data to highlight the specific environmental factors that drive microbial diversification. Our approach provides a complementary view to cladistic assignments and holds important clues for further exploration of microbial lifestyles. Fusion is a more practical fit for biomedical, industrial, and ecological applications, as many of these rely on understanding the functional capabilities of the microbes in their environment and are less concerned with phylogenetic descent. PMID:26317871

To Stroop or Not to Stroop: Sex-Related Differences in Brain-Behavior Associations During Early Childhood

PubMed Central

Cuevas, Kimberly; Calkins, Susan D.; Bell, Martha Ann

2015-01-01

Executive functions (EFs) are linked with optimal cognitive and social-emotional development. Despite behavioral evidence of sex differences in early childhood EF, little is known about potential sex differences in corresponding brain-behavior associations. The present study examined changes in 4-year-olds’ 6–9 Hz EEG power in response to increased executive processing demands (i.e., “Stroop-like” vs. “non-Stroop” day-night tasks). Although there were no sex differences in task performance, an examination of multiple scalp electrode sites revealed that boys exhibited more widespread changes in EEG power as compared to girls. Further, multiple regression analyses controlling for maternal education and non-EF performance indicated that individual differences in boys’ and girls’ EF performance were associated with different frontal neural correlates (i.e., different frontal scalp sites and different measures of EEG power). These data reveal valuable information concerning sex differences in the neural systems underlying executive processing during early childhood. PMID:26681615

Gene Set−Based Integrative Analysis Revealing Two Distinct Functional Regulation Patterns in Four Common Subtypes of Epithelial Ovarian Cancer

PubMed Central

Chang, Chia-Ming; Chuang, Chi-Mu; Wang, Mong-Lien; Yang, Yi-Ping; Chuang, Jen-Hua; Yang, Ming-Jie; Yen, Ming-Shyen; Chiou, Shih-Hwa; Chang, Cheng-Chang

2016-01-01

Clear cell (CCC), endometrioid (EC), mucinous (MC) and high-grade serous carcinoma (SC) are the four most common subtypes of epithelial ovarian carcinoma (EOC). The widely accepted dualistic model of ovarian carcinogenesis divided EOCs into type I and II categories based on the molecular features. However, this hypothesis has not been experimentally demonstrated. We carried out a gene set-based analysis by integrating the microarray gene expression profiles downloaded from the publicly available databases. These quantified biological functions of EOCs were defined by 1454 Gene Ontology (GO) term and 674 Reactome pathway gene sets. The pathogenesis of the four EOC subtypes was investigated by hierarchical clustering and exploratory factor analysis. The patterns of functional regulation among the four subtypes containing 1316 cases could be accurately classified by machine learning. The results revealed that the ERBB and PI3K-related pathways played important roles in the carcinogenesis of CCC, EC and MC; while deregulation of cell cycle was more predominant in SC. The study revealed that two different functional regulation patterns exist among the four EOC subtypes, which were compatible with the type I and II classifications proposed by the dualistic model of ovarian carcinogenesis. PMID:27527159

Cobalt coordination and clustering in alpha-Co(OH)(2) revealed by synchrotron X-ray total scattering.

PubMed

Neilson, James R; Kurzman, Joshua A; Seshadri, Ram; Morse, Daniel E

2010-09-03

Structures of layered metal hydroxides are not well described by traditional crystallography. Total scattering from a synthesis-controlled subset of these materials, as described here, reveals that different cobalt coordination polyhedra cluster within each layer on short length scales, offering new insights and approaches for understanding the properties of these and related layered materials. Structures related to that of brucite [Mg(OH)(2)] are ubiquitous in the mineral world and offer a variety of useful functions ranging from catalysis and ion-exchange to sequestration and energy transduction, including applications in batteries. However, it has been difficult to resolve the atomic structure of these layered compounds because interlayer disorder disrupts the long-range periodicity necessary for diffraction-based structure determination. For this reason, traditional unit-cell-based descriptions have remained inaccurate. Here we apply, for the first time to such layered hydroxides, synchrotron X-ray total scattering methods-analyzing both the Bragg and diffuse components-to resolve the intralayer structure of three different alpha-cobalt hydroxides, revealing the nature and distribution of metal site coordination. The different compounds with incorporated chloride ions have been prepared with kinetic control of hydrolysis to yield different ratios of octahedrally and tetrahedrally coordinated cobalt ions within the layers, as confirmed by total scattering. Real-space analyses indicate local clustering of polyhedra within the layers, manifested in the weighted average of different ordered phases with fixed fractions of tetrahedrally coordinated cobalt sites. These results, hidden from an averaged unit-cell description, reveal new structural characteristics that are essential to understanding the origin of fundamental material properties such as color, anion exchange capacity, and magnetic behavior. Our results also provide further insights into the detailed mechanisms of aqueous hydrolysis chemistry of hydrated metal salts. We emphasize the power of the methods used here for establishing structure-property correlations in functional materials with related layered structures.

Lack of species-specific difference in pulmonary function when using mouse versus human plasma in a mouse model of hemorrhagic shock.

PubMed

Peng, Zhanglong; Pati, Shibani; Fontaine, Magali J; Hall, Kelly; Herrera, Anthony V; Kozar, Rosemary A

2016-11-01

Clinical studies have demonstrated that the early and empiric use of plasma improves survival after hemorrhagic shock. We have demonstrated in rodent models of hemorrhagic shock that resuscitation with plasma is protective to the lungs compared with lactated Ringer's solution. As our long-term objective is to determine the molecular mechanisms that modulate plasma's protective effects in injured bleeding patients, we have used human plasma in a mouse model of hemorrhagic shock. The goal of the current experiments is to determine if there are significant adverse effects on lung injury when using human versus mouse plasma in an established murine model of hemorrhagic shock and laparotomy. Mice underwent laparotomy and 90 minutes of hemorrhagic shock to a mean arterial pressure (MAP) of 35 ± 5 mm Hg followed by resuscitation at 1× shed blood using either mouse fresh frozen plasma (FFP), human FFP, or human lyophilized plasma. Mean arterial pressure was recorded during shock and for the first 30 minutes of resuscitation. After 3 hours, animals were killed, and lungs collected for analysis. There was a significant increase in early MAP when mouse FFP was used to resuscitate animals compared with human FFP or human lyophilized plasma. However, despite these differences, analysis of the mouse lungs revealed no significant differences in pulmonary histopathology, lung permeability, or lung edema between all three plasma groups. Analysis of neutrophil infiltration in the lungs revealed that mouse FFP decreased neutrophil influx as measured by neutrophil staining; however, myeloperoxidase immunostaining revealed no significant differences in between groups. The study of human plasma in a mouse model of hemorrhagic shock is feasible but does reveal some differences compared with mouse plasma-based resuscitation in physiologic measures such as MAP postresuscitation. Measures of end organ function such as lung injury appear to be comparable in this acute model of hemorrhagic shock and resuscitation.

Structural adaptations to diverse fighting styles in sexually selected weapons

PubMed Central

McCullough, Erin L.; Tobalske, Bret W.; Emlen, Douglas J.

2014-01-01

The shapes of sexually selected weapons differ widely among species, but the drivers of this diversity remain poorly understood. Existing explanations suggest weapon shapes reflect structural adaptations to different fighting styles, yet explicit tests of this hypothesis are lacking. We constructed finite element models of the horns of different rhinoceros beetle species to test whether functional specializations for increased performance under species-specific fighting styles could have contributed to the diversification of weapon form. We find that horns are both stronger and stiffer in response to species-typical fighting loads and that they perform more poorly under atypical fighting loads, which suggests weapons are structurally adapted to meet the functional demands of fighting. Our research establishes a critical link between weapon form and function, revealing one way male–male competition can drive the diversification of animal weapons. PMID:25201949

Structural adaptations to diverse fighting styles in sexually selected weapons.

PubMed

McCullough, Erin L; Tobalske, Bret W; Emlen, Douglas J

2014-10-07

The shapes of sexually selected weapons differ widely among species, but the drivers of this diversity remain poorly understood. Existing explanations suggest weapon shapes reflect structural adaptations to different fighting styles, yet explicit tests of this hypothesis are lacking. We constructed finite element models of the horns of different rhinoceros beetle species to test whether functional specializations for increased performance under species-specific fighting styles could have contributed to the diversification of weapon form. We find that horns are both stronger and stiffer in response to species-typical fighting loads and that they perform more poorly under atypical fighting loads, which suggests weapons are structurally adapted to meet the functional demands of fighting. Our research establishes a critical link between weapon form and function, revealing one way male-male competition can drive the diversification of animal weapons.

Sparse dictionary learning of resting state fMRI networks.

PubMed

Eavani, Harini; Filipovych, Roman; Davatzikos, Christos; Satterthwaite, Theodore D; Gur, Raquel E; Gur, Ruben C

2012-07-02

Research in resting state fMRI (rsfMRI) has revealed the presence of stable, anti-correlated functional subnetworks in the brain. Task-positive networks are active during a cognitive process and are anti-correlated with task-negative networks, which are active during rest. In this paper, based on the assumption that the structure of the resting state functional brain connectivity is sparse, we utilize sparse dictionary modeling to identify distinct functional sub-networks. We propose two ways of formulating the sparse functional network learning problem that characterize the underlying functional connectivity from different perspectives. Our results show that the whole-brain functional connectivity can be concisely represented with highly modular, overlapping task-positive/negative pairs of sub-networks.

Neural correlates of social exclusion across ages: A coordinate-based meta-analysis of functional MRI studies.

PubMed

Vijayakumar, Nandita; Cheng, Theresa W; Pfeifer, Jennifer H

2017-06-01

Given the recent surge in functional neuroimaging studies on social exclusion, the current study employed activation likelihood estimation (ALE) based meta-analyses to identify brain regions that have consistently been implicated across different experimental paradigms used to investigate exclusion. We also examined the neural correlates underlying Cyberball, the most commonly used paradigm to study exclusion, as well as differences in exclusion-related activation between developing (7-18 years of age, from pre-adolescence up to late adolescence) and emerging adult (broadly defined as undergraduates, including late adolescence and young adulthood) samples. Results revealed involvement of the bilateral medial prefrontal and posterior cingulate cortices, right precuneus and left ventrolateral prefrontal cortex across the different paradigms used to examine social exclusion; similar activation patterns were identified when restricting the analysis to Cyberball studies. Investigations into age-related effects revealed that ventrolateral prefrontal activations identified in the full sample were driven by (i.e. present in) developmental samples, while medial prefrontal activations were driven by emerging adult samples. In addition, the right ventral striatum was implicated in exclusion, but only in developmental samples. Subtraction analysis revealed significantly greater activation likelihood in striatal and ventrolateral prefrontal clusters in the developmental samples as compared to emerging adults, though the opposite contrast failed to identify any significant regions. Findings integrate the knowledge accrued from functional neuroimaging studies on social exclusion to date, highlighting involvement of lateral prefrontal regions implicated in regulation and midline structures involved in social cognitive and self-evaluative processes across experimental paradigms and ages, as well as limbic structures in developing samples specifically. Copyright © 2017 Elsevier Inc. All rights reserved.

Resolving Microzooplankton Functional Groups In A Size-Structured Planktonic Model

NASA Astrophysics Data System (ADS)

Taniguchi, D.; Dutkiewicz, S.; Follows, M. J.; Jahn, O.; Menden-Deuer, S.

2016-02-01

Microzooplankton are important marine grazers, often consuming a large fraction of primary productivity. They consist of a great diversity of organisms with different behaviors, characteristics, and rates. This functional diversity, and its consequences, are not currently reflected in large-scale ocean ecological simulations. How should these organisms be represented, and what are the implications for their biogeography? We develop a size-structured, trait-based model to characterize a diversity of microzooplankton functional groups. We compile and examine size-based laboratory data on the traits, revealing some patterns with size and functional group that we interpret with mechanistic theory. Fitting the model to the data provides parameterizations of key rates and properties, which we employ in a numerical ocean model. The diversity of grazing preference, rates, and trophic strategies enables the coexistence of different functional groups of micro-grazers under various environmental conditions, and the model produces testable predictions of the biogeography.

Distinct hippocampal functional networks revealed by tractography-based parcellation.

PubMed

Adnan, Areeba; Barnett, Alexander; Moayedi, Massieh; McCormick, Cornelia; Cohn, Melanie; McAndrews, Mary Pat

2016-07-01

Recent research suggests the anterior and posterior hippocampus form part of two distinct functional neural networks. Here we investigate the structural underpinnings of this functional connectivity difference using diffusion-weighted imaging-based parcellation. Using this technique, we substantiated that the hippocampus can be parcellated into distinct anterior and posterior segments. These structurally defined segments did indeed show different patterns of resting state functional connectivity, in that the anterior segment showed greater connectivity with temporal and orbitofrontal cortex, whereas the posterior segment was more highly connected to medial and lateral parietal cortex. Furthermore, we showed that the posterior hippocampal connectivity to memory processing regions, including the dorsolateral prefrontal cortex, parahippocampal, inferior temporal and fusiform gyri and the precuneus, predicted interindividual relational memory performance. These findings provide important support for the integration of structural and functional connectivity in understanding the brain networks underlying episodic memory.

Dynamic Functional Connectivity States Between the Dorsal and Ventral Sensorimotor Networks Revealed by Dynamic Conditional Correlation Analysis of Resting-State Functional Magnetic Resonance Imaging.

PubMed

Syed, Maleeha F; Lindquist, Martin A; Pillai, Jay J; Agarwal, Shruti; Gujar, Sachin K; Choe, Ann S; Caffo, Brian; Sair, Haris I

2017-12-01

Functional connectivity in resting-state functional magnetic resonance imaging (rs-fMRI) has received substantial attention since the initial findings of Biswal et al. Traditional network correlation metrics assume that the functional connectivity in the brain remains stationary over time. However, recent studies have shown that robust temporal fluctuations of functional connectivity among as well as within functional networks exist, challenging this assumption. In this study, these dynamic correlation differences were investigated between the dorsal and ventral sensorimotor networks by applying the dynamic conditional correlation model to rs-fMRI data of 20 healthy subjects. k-Means clustering was used to determine an optimal number of discrete connectivity states (k = 10) of the sensorimotor system across all subjects. Our analysis confirms the existence of differences in dynamic correlation between the dorsal and ventral networks, with highest connectivity found within the ventral motor network.

The secretory pathway: exploring yeast diversity.

PubMed

Delic, Marizela; Valli, Minoska; Graf, Alexandra B; Pfeffer, Martin; Mattanovich, Diethard; Gasser, Brigitte

2013-11-01

Protein secretion is an essential process for living organisms. In eukaryotes, this encompasses numerous steps mediated by several hundred cellular proteins. The core functions of translocation through the endoplasmic reticulum membrane, primary glycosylation, folding and quality control, and vesicle-mediated secretion are similar from yeasts to higher eukaryotes. However, recent research has revealed significant functional differences between yeasts and mammalian cells, and even among diverse yeast species. This review provides a current overview of the canonical protein secretion pathway in the model yeast Saccharomyces cerevisiae, highlighting differences to mammalian cells as well as currently unresolved questions, and provides a genomic comparison of the S. cerevisiae pathway to seven other yeast species where secretion has been investigated due to their attraction as protein production platforms, or for their relevance as pathogens. The analysis of Candida albicans, Candida glabrata, Kluyveromyces lactis, Pichia pastoris, Hansenula polymorpha, Yarrowia lipolytica, and Schizosaccharomyces pombe reveals that many - but not all - secretion steps are more redundant in S. cerevisiae due to duplicated genes, while some processes are even absent in this model yeast. Recent research obviates that even where homologous genes are present, small differences in protein sequence and/or differences in the regulation of gene expression may lead to quite different protein secretion phenotypes. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

There are differences in cerebral activation between females in distinct menstrual phases during viewing of erotic stimuli: A fMRI study.

PubMed

Gizewski, Elke R; Krause, Eva; Karama, Sherif; Baars, Anneke; Senf, Wolfgang; Forsting, Michael

2006-09-01

There is evidence that men experience more sexual arousal than women but also that women in mid-luteal phase experience more sexual arousal than women outside this phase. Recently, a few functional brain imaging studies have tackled the issue of gender differences as pertaining to reactions to erotica. The question of whether or not gender differences in reactions to erotica are maintained with women in different phases has not yet been answered from a functional brain imaging perspective. In order to examine this issue, functional MRI was performed in 22 male and 22 female volunteers. Subjects viewed erotic film excerpts alternating with emotionally neutral excerpts in a standard block-design paradigm. Arousal to erotic stimuli was evaluated using standard rating scales after scanning. Two-sample t-test with uncorrected P < 0.001 values for a priori determined region of interests involved in processing of erotic stimuli and with corrected P < 0.05 revealed gender differences: Comparing women in mid-luteal phase and during their menses, superior activation was revealed for women in mid-luteal phase in the anterior cingulate, left insula, and orbitofrontal cortex. A superior activation for men was found in the left thalamus, the bilateral amygdala, the anterior cingulate, the bilateral orbitofrontal, bilateral parahippocampal, and insular regions, which were maintained at a corrected P in the amygdala, the insula, and thalamus. There were no areas of significant superior activation for women neither in mid-luteal phase nor during their menses. Our results indicate that there are differences between women in the two cycle times in cerebral activity during viewing of erotic stimuli. Furthermore, gender differences with women in mid-luteal phases are similar to those in females outside the mid-luteal phase.

Functional Performance and Associations between Performance Tests and Neurological Assessment Differ in Men and Women with Parkinson's Disease.

PubMed

Medijainen, Kadri; Pääsuke, Mati; Lukmann, Aet; Taba, Pille

2015-01-01

Neurological assessment of a patient with Parkinson's disease (PD) is expected to reflect upon functional performance. As women are known to report more limitations even for same observed functional performance level, present study was designed to examine whether associations between neurological assessments and functional performance differ across genders. 14 men and 14 women with PD participated. Functional performance was assessed by measuring walking speeds on 10-meter walk test (10MWT) and by performing timed-up-and-go-test (TUG). Neurological assessment included Hoehn and Yahr Scale (HY), Movement Disorders Society Unified Parkinson's Disease Rating Scale (MDS-UPDRS), Schwab and England Activities of Daily Living Scale (S-E), and Mini Mental State Examination (MMSE). In women with PD, Kendall's tau-b correlation analyses revealed significant correlations between functional performance tests and neurological assessment measures, with the exception in MMSE. No corresponding associations were found for men, although they demonstrated better functional performance, as expected. Men in similar clinical stage of the PD perform better on functional tests than women. Disease severity reflects upon functional performance differently in men and women with PD. Results indicate that when interpreting the assessment results of both functional performance and neurological assessment tests, the gender of the patient should be taken into consideration.

Study of diffusion and local structure of sodium-silicate liquid: the molecular dynamic simulation

NASA Astrophysics Data System (ADS)

Hung, Pham Khac; Noritake, Fumiya; San, Luyen Thi; Van, To Ba; Vinh, Le The

2017-10-01

A systematic analysis on sodium-silicate melt with various silica contents was carried out. The simulation revealed two diffusion mechanisms occurred in the melt: the bond-breaking and hopping between sites. The local structure was analyzed through T-simplexes. It was revealed that T-clusters have a non-spherical shape and represent the diffusion channel, in which Na atoms are dominant, but no any O atoms are located. The SiO2-poor melt acquires a long channel. In contrast, the SiO2-rich melt consists of unconnected short channels. The simulation also revealed the immobile and mobile regions which differ in local structure and constituent composition. We propose a new CL-function to characterizing the spatial distribution of different atom component. The spatial distribution of mobile and immobile atoms is found quite different. In particular, the immobile atoms are concentrated in high-density regions possessing very large density of immobile atoms. The spatial distribution of mobile atoms in contrast is more homogeneous.

The complex and specific pMHC interactions with diverse HIV-1 TCR clonotypes reveal a structural basis for alterations in CTL function

PubMed Central

Xia, Zhen; Chen, Huabiao; Kang, Seung-gu; Huynh, Tien; Fang, Justin W.; Lamothe, Pedro A.; Walker, Bruce D.; Zhou, Ruhong

2014-01-01

Immune control of viral infections is modulated by diverse T cell receptor (TCR) clonotypes engaging peptide-MHC class I complexes on infected cells, but the relationship between TCR structure and antiviral function is unclear. Here we apply in silico molecular modeling with in vivo mutagenesis studies to investigate TCR-pMHC interactions from multiple CTL clonotypes specific for a well-defined HIV-1 epitope. Our molecular dynamics simulations of viral peptide-HLA-TCR complexes, based on two independent co-crystal structure templates, reveal that effective and ineffective clonotypes bind to the terminal portions of the peptide-MHC through similar salt bridges, but their hydrophobic side-chain packings can be very different, which accounts for the major part of the differences among these clonotypes. Non-specific hydrogen bonding to viral peptide also accommodates greater epitope variants. Furthermore, free energy perturbation calculations for point mutations on the viral peptide KK10 show excellent agreement with in vivo mutagenesis assays, with new predictions confirmed by additional experiments. These findings indicate a direct structural basis for heterogeneous CTL antiviral function. PMID:24522437

Death Anxiety as a Function of Aging Anxiety

ERIC Educational Resources Information Center

Benton, Jeremy P.; Christopher, Andrew N.; Walter, Mark I.

2007-01-01

To assess how different facets of aging anxiety contributed to the prediction of tangible and existential death anxiety, 167 Americans of various Christian denominations completed a battery of questionnaires. Multiple regression analyses, controlling for demographic variables and previously demonstrated predictors of death anxiety, revealed that…

Three Types of Cortical L5 Neurons that Differ in Brain-Wide Connectivity and Function

PubMed Central

Kim, Euiseok J.; Juavinett, Ashley L.; Kyubwa, Espoir M.; Jacobs, Matthew W.; Callaway, Edward M.

2015-01-01

SUMMARY Cortical layer 5 (L5) pyramidal neurons integrate inputs from many sources and distribute outputs to cortical and subcortical structures. Previous studies demonstrate two L5 pyramid types: cortico-cortical (CC) and cortico-subcortical (CS). We characterize connectivity and function of these cell types in mouse primary visual cortex and reveal a new subtype. Unlike previously described L5 CC and CS neurons, this new subtype does not project to striatum [cortico-cortical, non-striatal (CC-NS)] and has distinct morphology, physiology and visual responses. Monosynaptic rabies tracing reveals that CC neurons preferentially receive input from higher visual areas, while CS neurons receive more input from structures implicated in top-down modulation of brain states. CS neurons are also more direction-selective and prefer faster stimuli than CC neurons. These differences suggest distinct roles as specialized output channels, with CS neurons integrating information and generating responses more relevant to movement control and CC neurons being more important in visual perception. PMID:26671462

Three Types of Cortical Layer 5 Neurons That Differ in Brain-wide Connectivity and Function.

PubMed

Kim, Euiseok J; Juavinett, Ashley L; Kyubwa, Espoir M; Jacobs, Matthew W; Callaway, Edward M

2015-12-16

Cortical layer 5 (L5) pyramidal neurons integrate inputs from many sources and distribute outputs to cortical and subcortical structures. Previous studies demonstrate two L5 pyramid types: cortico-cortical (CC) and cortico-subcortical (CS). We characterize connectivity and function of these cell types in mouse primary visual cortex and reveal a new subtype. Unlike previously described L5 CC and CS neurons, this new subtype does not project to striatum [cortico-cortical, non-striatal (CC-NS)] and has distinct morphology, physiology, and visual responses. Monosynaptic rabies tracing reveals that CC neurons preferentially receive input from higher visual areas, while CS neurons receive more input from structures implicated in top-down modulation of brain states. CS neurons are also more direction-selective and prefer faster stimuli than CC neurons. These differences suggest distinct roles as specialized output channels, with CS neurons integrating information and generating responses more relevant to movement control and CC neurons being more important in visual perception. Copyright © 2015 Elsevier Inc. All rights reserved.

Ab initio density functional theory investigation of structural and electronic properties of double-walled silicon carbide nanotubes

NASA Astrophysics Data System (ADS)

Moradian, Rostam; Behzad, Somayeh; Chegel, Raad

2009-12-01

By using ab initio density functional theory, the structural and electronic properties of (n,n)@(11,11) double-walled silicon carbide nanotubes (SiCNTs) are investigated. Our calculations reveal the existence of an energetically favorable double-walled nanotube whose interwall distance is about 4.3 Å. Interwall spacing and curvature difference are found to be essential for the electronic states around the Fermi level.

Barb geometry of asymmetrical feathers reveals a transitional morphology in the evolution of avian flight

PubMed Central

Feo, Teresa J.; Field, Daniel J.; Prum, Richard O.

2015-01-01

The geometry of feather barbs (barb length and barb angle) determines feather vane asymmetry and vane rigidity, which are both critical to a feather's aerodynamic performance. Here, we describe the relationship between barb geometry and aerodynamic function across the evolutionary history of asymmetrical flight feathers, from Mesozoic taxa outside of modern avian diversity (Microraptor, Archaeopteryx, Sapeornis, Confuciusornis and the enantiornithine Eopengornis) to an extensive sample of modern birds. Contrary to previous assumptions, we find that barb angle is not related to vane-width asymmetry; instead barb angle varies with vane function, whereas barb length variation determines vane asymmetry. We demonstrate that barb geometry significantly differs among functionally distinct portions of flight feather vanes, and that cutting-edge leading vanes occupy a distinct region of morphospace characterized by small barb angles. This cutting-edge vane morphology is ubiquitous across a phylogenetically and functionally diverse sample of modern birds and Mesozoic stem birds, revealing a fundamental aerodynamic adaptation that has persisted from the Late Jurassic. However, in Mesozoic taxa stemward of Ornithurae and Enantiornithes, trailing vane barb geometry is distinctly different from that of modern birds. In both modern birds and enantiornithines, trailing vanes have larger barb angles than in comparatively stemward taxa like Archaeopteryx, which exhibit small trailing vane barb angles. This discovery reveals a previously unrecognized evolutionary transition in flight feather morphology, which has important implications for the flight capacity of early feathered theropods such as Archaeopteryx and Microraptor. Our findings suggest that the fully modern avian flight feather, and possibly a modern capacity for powered flight, evolved crownward of Confuciusornis, long after the origin of asymmetrical flight feathers, and much later than previously recognized. PMID:25673687

Look beyond one's own nose: combination of information from publicly available sources reveals an association of GATA4 polymorphisms with plasma triglycerides.

PubMed

Lamina, Claudia; Coassin, Stefan; Illig, Thomas; Kronenberg, Florian

2011-12-01

GATA4iKO mice exhibit impeded triglyceride absorption from intestine and decreased plasma triglyceride levels. Data in humans are lacking. We hypothesized that triglyceride levels might also be regulated by polymorphisms in the GATA4 gene in humans. We used publicly available data from different sources to evaluate this hypothesis. Our approach is a more often applicable advance to uncover associations and their functional implications which would have been otherwise missed by standard genome-wide association studies (GWAS). We used the publicly available GWAS results from 137 SNPs in the GATA4 region for triglyceride levels. We embedded these results into the comprehensive functional genomics data provided in the UCSC Genome Browser including among others information on regulatory elements and interspecies conservation. A concise graphical presentation is proposed together with an R function for automatic data preparation. This process is presented in an educational manner using a screencast to become most useful for other researchers. We observed several polymorphisms in and around the GATA4 gene which have a significant influence on plasma triglyceride levels with the lowest p-value at SNP rs1466785 (Bonferroni-corrected p-value = 1.76e-5). The bioinformatic evaluation of this locus in publicly available functional genomics data provided converging evidence for the presence of a transcriptional regulator downstream of GATA4. The combination of different sources of data has revealed an association of GATA4 with triglyceride levels in humans. Our evaluation exemplifies how an integrative analysis including both statistical and biological perspectives can shed new light on available association data and reveals novel candidate genes, which are otherwise hidden in the noisy region below genome-wide significance. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Unraveling Core Functional Microbiota in Traditional Solid-State Fermentation by High-Throughput Amplicons and Metatranscriptomics Sequencing.

PubMed

Song, Zhewei; Du, Hai; Zhang, Yan; Xu, Yan

2017-01-01

Fermentation microbiota is specific microorganisms that generate different types of metabolites in many productions. In traditional solid-state fermentation, the structural composition and functional capacity of the core microbiota determine the quality and quantity of products. As a typical example of food fermentation, Chinese Maotai-flavor liquor production involves a complex of various microorganisms and a wide variety of metabolites. However, the microbial succession and functional shift of the core microbiota in this traditional food fermentation remain unclear. Here, high-throughput amplicons (16S rRNA gene amplicon sequencing and internal transcribed space amplicon sequencing) and metatranscriptomics sequencing technologies were combined to reveal the structure and function of the core microbiota in Chinese soy sauce aroma type liquor production. In addition, ultra-performance liquid chromatography and headspace-solid phase microextraction-gas chromatography-mass spectrometry were employed to provide qualitative and quantitative analysis of the major flavor metabolites. A total of 10 fungal and 11 bacterial genera were identified as the core microbiota. In addition, metatranscriptomic analysis revealed pyruvate metabolism in yeasts (genera Pichia, Schizosaccharomyces, Saccharomyces , and Zygosaccharomyces ) and lactic acid bacteria (genus Lactobacillus ) classified into two stages in the production of flavor components. Stage I involved high-level alcohol (ethanol) production, with the genus Schizosaccharomyces serving as the core functional microorganism. Stage II involved high-level acid (lactic acid and acetic acid) production, with the genus Lactobacillus serving as the core functional microorganism. The functional shift from the genus Schizosaccharomyces to the genus Lactobacillus drives flavor component conversion from alcohol (ethanol) to acid (lactic acid and acetic acid) in Chinese Maotai-flavor liquor production. Our findings provide insight into the effects of the core functional microbiota in soy sauce aroma type liquor production and the characteristics of the fermentation microbiota under different environmental conditions.

Assessment of patient functional performance in different knee arthroplasty designs during unconstrained squat

PubMed Central

Verdini, Federica; Zara, Claudio; Leo, Tommaso; Mengarelli, Alessandro; Cardarelli, Stefano; Innocenti, Bernardo

2017-01-01

Summary Background In this paper, squat named by Authors unconstrained because performed without constrains related to feet position, speed, knee maximum angle to be reached, was tested as motor task revealing differences in functional performance after knee arthroplasty. It involves large joints ranges of motion, does not compromise joint safety and requires accurate control strategies to maintain balance. Methods Motion capture techniques were used to study squat on a healthy control group (CTR) and on three groups, each characterised by a specific knee arthroplasty design: a Total Knee Arthroplasty (TKA), a Mobile Bearing and a Fixed Bearing Unicompartmental Knee Arthroplasty (respectively MBUA and FBUA). Squat was analysed during descent, maintenance and ascent phase and described by speed, angular kinematics of lower and upper body, the Center of Pressure (CoP) trajectory and muscle activation timing of quadriceps and biceps femoris. Results Compared to CTR, for TKA and MBUA knee maximum flexion was lower, vertical speed during descent and ascent reduced and the duration of whole movement was longer. CoP mean distance was higher for all arthroplasty groups during descent as higher was, CoP mean velocity for MBUA and TKA during ascent and descent. Conclusions Unconstrained squat is able to reveal differences in the functional performance among control and arthroplasty groups and between different arthroplasty designs. Considering the similarity index calculated for the variables showing statistically significance, FBUA performance appears to be closest to that of the CTR group. Level of evidence III a. PMID:29387646

Psychosocial functioning in adolescents with complex partial seizures.

PubMed

Elliott, I

1992-03-01

This pilot study examined psychosocial functioning in adolescents (age 12.5-18.5 years) with complex partial seizures. Twenty-five subjects were divided into three groups: Group I (N = 11), medically treated with uncontrolled seizures; Group II (N = 6), medically managed with controlled seizures; and Group III (N = 8), epilepsy refractory to medical management with seizure control following surgery. Psychosocial functioning was measured using the "Adolescent Psychosocial Inventory" of Batzel and Dodrill. Findings revealed significant differences (F 4.80. p less than 0.02) in psychosocial functioning between the three groups. Group I showed the poorest overall adjustment; Group II, the best adjustment; Group III was better adjusted than Group I, but less than Group II. Significant difficulties were evident in the areas of school, interpersonal, emotional, seizure adjustment and overall psychosocial functioning in Group III. No problems were evident in Group II. School, emotional and overall adjustment were moderately problematic in Group III. Analysis of biological and demographic data revealed a significant association between increased numbers of medications and poorer psychosocial functioning (r = 58, p less than 0.02). The study results provide direction for clinic and community nurse specialists to set priorities with regard to assessment and supportive interventions.

Plant lectins: the ties that bind in root symbiosis and plant defense.

PubMed

De Hoff, Peter L; Brill, Laurence M; Hirsch, Ann M

2009-07-01

Lectins are a diverse group of carbohydrate-binding proteins that are found within and associated with organisms from all kingdoms of life. Several different classes of plant lectins serve a diverse array of functions. The most prominent of these include participation in plant defense against predators and pathogens and involvement in symbiotic interactions between host plants and symbiotic microbes, including mycorrhizal fungi and nitrogen-fixing rhizobia. Extensive biological, biochemical, and molecular studies have shed light on the functions of plant lectins, and a plethora of uncharacterized lectin genes are being revealed at the genomic scale, suggesting unexplored and novel diversity in plant lectin structure and function. Integration of the results from these different types of research is beginning to yield a more detailed understanding of the function of lectins in symbiosis, defense, and plant biology in general.

Gene Expression Architecture of Mouse Dorsal and Tail Skin Reveals Functional Differences in Inflammation and Cancer | Office of Cancer Genomics

Cancer.gov

Inherited germline polymorphisms can cause gene expression levels in normal tissues to differ substantially between individuals. We present an analysis of the genetic architecture of normal adult skin from 470 genetically unique mice, demonstrating the effect of germline variants, skin tissue location, and perturbation by exogenous inflammation or tumorigenesis on gene signaling pathways.

The Investigation and Analysis of Chinese University Students' Current Situation of Entrepreneurship and the Countermeasures--The Reflection from a Special Investigation in Pearl Delta in China

ERIC Educational Resources Information Center

Lifang, Li

2012-01-01

This research has chosen some students and undergraduates from 35 colleges and universities, which are national, local and professional colleges or universities with different entrepreneurship needs and different educational functions in the same area. The research reveals that the undergraduates or students are in strong desire of career…

Learning at different satiation levels reveals parallel functions for the cAMP-protein kinase A cascade in formation of long-term memory.

PubMed

Friedrich, Anke; Thomas, Ulf; Müller, Uli

2004-05-05

Learning and memory formation in intact animals is generally studied under defined parameters, including the control of feeding. We used associative olfactory conditioning of the proboscis extension response in honeybees to address effects of feeding status on processes of learning and memory formation. Comparing groups of animals with different but defined feeding status at the time of conditioning reveals new and characteristic features in memory formation. In animals fed 18 hr earlier, three-trial conditioning induces a stable memory that consists of different phases: a mid-term memory (MTM), translation-dependent early long-term memory (eLTM; 1-2 d), and a transcription-dependent late LTM (lLTM; > or =3 d). Additional feeding of a small amount of sucrose 4 hr before conditioning leads to a loss of all of these memory phases. Interestingly, the basal activity of the cAMP-dependent protein kinase A (PKA), a key player in LTM formation, differs in animals with different satiation levels. Pharmacological rescue of the low basal PKA activity in animals fed 4 hr before conditioning points to a specific function of cAMP-PKA cascade in mediating satiation-dependent memory formation. An increase in PKA activity during conditioning rescues only transcription-dependent lLTM; acquisition, MTM, and eLTM are still impaired. Thus, during conditioning, the cAMP-PKA cascade mediates the induction of the transcription-dependent lLTM, depending on the satiation level. This result provides the first evidence for a central and distinct function of the cAMP-PKA cascade connecting satiation level with learning.

Subtyping cognitive profiles in Autism Spectrum Disorder using a Functional Random Forest algorithm.

PubMed

Feczko, E; Balba, N M; Miranda-Dominguez, O; Cordova, M; Karalunas, S L; Irwin, L; Demeter, D V; Hill, A P; Langhorst, B H; Grieser Painter, J; Van Santen, J; Fombonne, E J; Nigg, J T; Fair, D A

2018-05-15

DSM-5 Autism Spectrum Disorder (ASD) comprises a set of neurodevelopmental disorders characterized by deficits in social communication and interaction and repetitive behaviors or restricted interests, and may both affect and be affected by multiple cognitive mechanisms. This study attempts to identify and characterize cognitive subtypes within the ASD population using our Functional Random Forest (FRF) machine learning classification model. This model trained a traditional random forest model on measures from seven tasks that reflect multiple levels of information processing. 47 ASD diagnosed and 58 typically developing (TD) children between the ages of 9 and 13 participated in this study. Our RF model was 72.7% accurate, with 80.7% specificity and 63.1% sensitivity. Using the random forest model, the FRF then measures the proximity of each subject to every other subject, generating a distance matrix between participants. This matrix is then used in a community detection algorithm to identify subgroups within the ASD and TD groups, and revealed 3 ASD and 4 TD putative subgroups with unique behavioral profiles. We then examined differences in functional brain systems between diagnostic groups and putative subgroups using resting-state functional connectivity magnetic resonance imaging (rsfcMRI). Chi-square tests revealed a significantly greater number of between group differences (p < .05) within the cingulo-opercular, visual, and default systems as well as differences in inter-system connections in the somato-motor, dorsal attention, and subcortical systems. Many of these differences were primarily driven by specific subgroups suggesting that our method could potentially parse the variation in brain mechanisms affected by ASD. Copyright © 2017. Published by Elsevier Inc.

Exceptionally tight membrane-binding may explain the key role of the synaptotagmin-7 C 2 A domain in asynchronous neurotransmitter release

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

Voleti, Rashmi; Tomchick, Diana R.; Südhof, Thomas C.

Synaptotagmins (Syts) act as Ca2+ sensors in neurotransmitter release by virtue of Ca2+-binding to their two C2 domains, but their mechanisms of action remain unclear. Puzzlingly, Ca2+-binding to the C2B domain appears to dominate Syt1 function in synchronous release, whereas Ca2+-binding to the C2A domain mediates Syt7 function in asynchronous release. Here we show that crystal structures of the Syt7 C2A domain and C2AB region, and analyses of intrinsic Ca2+-binding to the Syt7 C2 domains using isothermal titration calorimetry, did not reveal major differences that could explain functional differentiation between Syt7 and Syt1. However, using liposome titrations under Ca2+ saturatingmore » conditions, we show that the Syt7 C2A domain has a very high membrane affinity and dominates phospholipid binding to Syt7 in the presence or absence of L-α-phosphatidylinositol 4,5-diphosphate (PIP2). For Syt1, the two Ca2+-saturated C2 domains have similar affinities for membranes lacking PIP2, but the C2B domain dominates binding to PIP2-containing membranes. Mutagenesis revealed that the dramatic differences in membrane affinity between the Syt1 and Syt7 C2A domains arise in part from apparently conservative residue substitutions, showing how striking biochemical and functional differences can result from the cumulative effects of subtle residue substitutions. Viewed together, our results suggest that membrane affinity may be a key determinant of the functions of Syt C2 domains in neurotransmitter release.« less

Chloroplast digestion and the development of functional kleptoplasty in juvenile Elysia timida (Risso, 1818) as compared to short-term and non-chloroplast-retaining sacoglossan slugs

PubMed Central

Wägele, Heike

2017-01-01

Sacoglossan sea slugs are the only metazoans known to perform functional kleptoplasty, the sequestration and retention of functional chloroplasts within their digestive gland cells. Remarkably, a few species with this ability can survive starvation periods of 3–12 months likely due to their stolen chloroplasts. There are no reports of kleptoplast transfer from mother slug to either eggs or juveniles, demonstrating that each animal must independently acquire its kleptoplasts and develop the ability to maintain them within its digestive gland. We present here an investigation into the development of functional kleptoplasty in a long-term kleptoplast retaining species, Elysia timida. Laboratory-reared juvenile slugs of different post-metamorphic ages were placed in starvation and compared to 5 known short-term retaining slug species and 5 non-retaining slug species. The subsequent results indicate that functional kleptoplasty is not performed by E. timida until after 15 days post-metamorphosis and that by 25 days, these animals outlive many of the short-term retention species. Digestive activity was also monitored using lysosomal abundance as an indicator, revealing different patterns in starving juveniles versus adults. Starved juveniles were reintroduced to food to determine any differences in digestive activity when starvation ends, resulting in an increase in the number of kleptoplasts, but no overall change in lysosomal activity. By revealing some of the changes that occur during early development in these animals, which begin as non-kleptoplast-retaining and grow into long-term retaining slugs, this investigation provides a basis for future inquiries into the origin and development of this remarkable ability. PMID:29020043

Social Maturity and Executive Function Among Deaf Learners

PubMed Central

Marschark, Marc; Kronenberger, William G.; Rosica, Mark; Borgna, Georgianna; Convertino, Carol; Durkin, Andreana; Machmer, Elizabeth; Schmitz, Kathryn L.

2017-01-01

Two experiments examined relations among social maturity, executive function, language, and cochlear implant (CI) use among deaf high school and college students. Experiment 1 revealed no differences between deaf CI users, deaf nonusers, and hearing college students in measures of social maturity. However, deaf students (both CI users and nonusers) reported significantly greater executive function (EF) difficulties in several domains, and EF was related to social maturity. Experiment 2 found that deaf CI users and nonusers in high school did not differ from each other in social maturity or EF, but individuals who relied on sign language reported significantly more immature behaviors than deaf peers who used spoken language. EF difficulties again were associated with social maturity. The present results indicate that EF and social maturity are interrelated, but those relations vary in different deaf subpopulations. As with academic achievement, CI use appears to have little long-term impact on EF or social maturity. Results are discussed in terms of their convergence with findings related to incidental learning and functioning in several domains. PMID:27686092

Common molecular basis of the sentence comprehension network revealed by neurotransmitter receptor fingerprints.

PubMed

Zilles, Karl; Bacha-Trams, Maraike; Palomero-Gallagher, Nicola; Amunts, Katrin; Friederici, Angela D

2015-02-01

The language network is a well-defined large-scale neural network of anatomically and functionally interacting cortical areas. The successful language process requires the transmission of information between these areas. Since neurotransmitter receptors are key molecules of information processing, we hypothesized that cortical areas which are part of the same functional language network may show highly similar multireceptor expression pattern ("receptor fingerprint"), whereas those that are not part of this network should have different fingerprints. Here we demonstrate that the relation between the densities of 15 different excitatory, inhibitory and modulatory receptors in eight language-related areas are highly similar and differ considerably from those of 18 other brain regions not directly involved in language processing. Thus, the fingerprints of all cortical areas underlying a large-scale cognitive domain such as language is a characteristic, functionally relevant feature of this network and an important prerequisite for the underlying neuronal processes of language functions. Copyright © 2014 Elsevier Ltd. All rights reserved.

Common molecular basis of the sentence comprehension network revealed by neurotransmitter receptor fingerprints

PubMed Central

Zilles, Karl; Bacha-Trams, Maraike; Palomero-Gallagher, Nicola; Amunts, Katrin; Friederici, Angela D.

2015-01-01

The language network is a well-defined large-scale neural network of anatomically and functionally interacting cortical areas. The successful language process requires the transmission of information between these areas. Since neurotransmitter receptors are key molecules of information processing, we hypothesized that cortical areas which are part of the same functional language network may show highly similar multireceptor expression pattern (“receptor fingerprint”), whereas those that are not part of this network should have different fingerprints. Here we demonstrate that the relation between the densities of 15 different excitatory, inhibitory and modulatory receptors in eight language-related areas are highly similar and differ considerably from those of 18 other brain regions not directly involved in language processing. Thus, the fingerprints of all cortical areas underlying a large-scale cognitive domain such as language is a characteristic, functionally relevant feature of this network and an important prerequisite for the underlying neuronal processes of language functions. PMID:25243991

Developmental differences in relations between parent-reported executive function and unitized and non-unitized memory representations during childhood

PubMed Central

Blankenship, Sarah L.; Riggins, Tracy

2015-01-01

Previous research has documented an association between executive functioning (EF) and memory for bound details. However, it is unknown if this relation varies as a function of the type of bound information (i.e., unitized versus non-unitized) and whether this association changes as a function of age during childhood, when both EF and memory undergo rapid development. The current study sought to address these gaps by examining whether relations between parent-reported EF differed for unitized versus non-unitized memory representations and if these relations differed between children who were 4, 6, or 8 years of age. Results revealed that EF was selectively associated with non-unitized associative memory in 8-year-old children; no significant relations between EF and either memory condition were evident in 4- or 6-year-olds. These results suggest relations between EF and memory may be specific to non-unitized representations and that this association may emerge across childhood as both EF and memory abilities develop. PMID:26347683

Sex differences in functional activation patterns revealed by increased emotion processing demands.

PubMed

Hall, Geoffrey B C; Witelson, Sandra F; Szechtman, Henry; Nahmias, Claude

2004-02-09

Two [O(15)] PET studies assessed sex differences regional brain activation in the recognition of emotional stimuli. Study I revealed that the recognition of emotion in visual faces resulted in bilateral frontal activation in women, and unilateral right-sided activation in men. In study II, the complexity of the emotional face task was increased through tje addition of associated auditory emotional stimuli. Men again showed unilateral frontal activation, in this case to the left; whereas women did not show bilateral frontal activation, but showed greater limbic activity. These results suggest that when processing broader cross-modal emotional stimuli, men engage more in associative cognitive strategies while women draw more on primary emotional references.

End-to-side neurorraphy: a long-term study of neural regeneration in a rat model.

PubMed

Tarasidis, G; Watanabe, O; Mackinnon, S E; Strasberg, S R; Haughey, B H; Hunter, D A

1998-10-01

This study evaluated long-term reinnervation of an end-to-side neurorraphy and the resultant functional recovery in a rat model. The divided distal posterior tibial nerve was repaired to the side of an intact peroneal nerve. Control groups included a cut-and-repair of the posterior tibial nerve and an end-to-end repair of the peroneal nerve to the posterior tibial nerve. Evaluations included walking-track analysis, nerve conduction studies, muscle mass measurements, retrograde nerve tracing, and histologic evaluation. Walking tracks indicated poor recovery of posterior tibial nerve function in the experimental group. No significant difference in nerve conduction velocities was seen between the experimental and control groups. Gastrocnemius muscle mass measurements revealed no functional recovery in the experimental group. Similarly, retrograde nerve tracing revealed minimal motor neuron staining in the experimental group. However, some sensory staining was seen within the dorsal root ganglia of the end-to-side group. Histologic study revealed minimal myelinated axonal regeneration in the experimental group as compared with findings in the other groups. These results suggest that predominantly sensory regeneration occurs in an end-to-side neurorraphy at an end point of 6 months.

Time-Varying Networks of Inter-Ictal Discharging Reveal Epileptogenic Zone.

PubMed

Zhang, Luyan; Liang, Yi; Li, Fali; Sun, Hongbin; Peng, Wenjing; Du, Peishan; Si, Yajing; Song, Limeng; Yu, Liang; Xu, Peng

2017-01-01

The neuronal synchronous discharging may cause an epileptic seizure. Currently, most of the studies conducted to investigate the mechanism of epilepsy are based on EEGs or functional magnetic resonance imaging (fMRI) recorded during the ictal discharging or the resting-state, and few studies have probed into the dynamic patterns during the inter-ictal discharging that are much easier to record in clinical applications. Here, we propose a time-varying network analysis based on adaptive directed transfer function to uncover the dynamic brain network patterns during the inter-ictal discharging. In addition, an algorithm based on the time-varying outflow of information derived from the network analysis is developed to detect the epileptogenic zone. The analysis performed revealed the time-varying network patterns during different stages of inter-ictal discharging; the epileptogenic zone was activated prior to the discharge onset then worked as the source to propagate the activity to other brain regions. Consistence between the epileptogenic zones detected by our proposed approach and the actual epileptogenic zones proved that time-varying network analysis could not only reveal the underlying neural mechanism of epilepsy, but also function as a useful tool in detecting the epileptogenic zone based on the EEGs in the inter-ictal discharging.

Changes in reflectance anisotropy of wheat crop during different phenophases

NASA Astrophysics Data System (ADS)

Lunagaria, Manoj M.; Patel, Haridas R.

2017-04-01

The canopy structure of wheat changes significantly with growth stages and leads to changes in reflectance anisotropy. Bidirectional reflectance distribution function characterises the reflectance anisotropy of the targets, which can be approximated. Spectrodirectional reflectance measurements on wheat crop were acquired using a field goniometer system. The bidirectional reflectance spectra were acquired at 54 view angles to cover the hemispheric span up to 60° view zenith. The observations were made during early growth stages till maturity of the crop. The anisotropy was not constant for all wavelengths and anisotropic factors clearly revealed spectral dependence, which was more pronounced in near principal plane. In near infrared, wheat canopy expressed less reflectance anisotropy because of higher multiple scattering. The broad hotspot signature was noticeable in reflectance of canopy whenever view and solar angles were close. Distinct changes in bidirectional reflectance distribution function were observed during booting to flowering stages as the canopy achieves more uniformity, height and head emergence. The function clearly reveals bowl shape during heading to early milking growth stages of the crop. Late growth stages show less prominent gap and shadow effects. Anisotropy index revealed that wheat exhibits changes in reflectance anisotropy with phenological development and with spectral bands.

Comparison of the recovery patterns of language and cognitive functions in patients with post-traumatic language processing deficits and in patients with aphasia following a stroke.

PubMed

Vukovic, Mile; Vuksanovic, Jasmina; Vukovic, Irena

2008-01-01

In this study we investigated the recovery patterns of language and cognitive functions in patients with post-traumatic language processing deficits and in patients with aphasia following a stroke. The correlation of specific language functions and cognitive functions was analyzed in the acute phase and 6 months later. Significant recovery of the tested functions was observed in both groups. However, in patients with post-traumatic language processing deficits the degree of recovery of most language functions and some cognitive functions was higher. A significantly greater correlation was revealed within language and cognitive functions, as well as between language functions and other aspects of cognition in patients with post-traumatic language processing deficits than in patients with aphasia following a stroke. Our results show that patients with post-traumatic language processing deficits have a different recovery pattern and a different pattern of correlation between language and cognitive functions compared to patients with aphasia following a stroke. (1) Better understanding of the differences in recovery of language and cognitive functions in patients who have suffered strokes and those who have experienced traumatic brain injury. (2) Better understanding of the relationship between language and cognitive functions in patients with post-traumatic language processing deficits and in patients with aphasia following a stroke. (3) Better understanding of the factors influencing recovery.

Assessment of rock musician's efferent system functioning using contralateral suppression of otoacoustic emissions.

PubMed

Kumar, Prawin; Grover, Vibhu; Publius A, Sam; Sanju, Himanshu Kumar; Sinha, Sachchidanand

2016-12-01

Contralateral suppression of oto acoustic emission (OAE) is referred as activation of efferent system. Previous literature mentioned about the importance of contralateral suppression of OAEs as a tool to assess efferent system in different groups of population. There is dearth of literature to explore the efferent system function in experienced musicians exposed to rock music using TEOAEs and DPOAEs. Two groups of participant (14 rock musicians and 14 non-musicians) in the age range of 18-25 years were involved in the study. Contralateral suppression of TEOAEs and DPOAEs were measured using ILO (Version 6) in both groups. Descriptive statistics showed higher suppression of TEOAEs and DPOAEs in rock-musicians at most of the frequencies in comparison to non-musicians. For DPOAE measures, Mann Whitney U test results revealed significantly greater DPOAE suppression only at 1 kHz and 3 kHz in rock-musicians compared to non-musicians. For within group comparison, Kruskal Wallis test results revealed there were significant difference observed across most of the frequencies i.e. at 1 kHz, 3 kHz and 6 kHz. For TEOAE measures, Mann Whitney U test results revealed that only at 2 kHz, TEOAE suppression in rock-musician was significantly greater compared to non-musicians. Similarly, Kuskal Wallis test results revealed that within group there were no significant differences observed for most of the frequencies except 2 kHz. Based on the above finding, present study concludes that rock musicians are having better efferent system compared to non-musicians. No suppression effect at few frequencies probably indicates more vulnerability at those frequencies. Contralateral suppression of DPOAE shows more significant finding in comparison to contralateral suppression of TEOAEs in present study.

Authentic Discourse and the Survival English Curriculum.

ERIC Educational Resources Information Center

Cathcart, Ruth Larimer

1989-01-01

In-depth analysis of topic distribution, utterance functions, and structural and lexical elements in a doctor-patient interaction revealed significant differences between authentic discourse and English-as-a-Second-Language text discourse, suggesting a need for better collection of more authentic data, for a distributional analysis of…

Increased spatial granularity of left brain activation and unique age/gender signatures: a 4D frequency domain approach to cerebral lateralization at rest.

PubMed

Agcaoglu, O; Miller, R; Mayer, A R; Hugdahl, K; Calhoun, V D

2016-12-01

Cerebral lateralization is a well-studied topic. However, most of the research to date in functional magnetic resonance imaging (fMRI) has been carried out on hemodynamic fluctuations of voxels, networks, or regions of interest (ROIs). For example, cerebral differences can be revealed by comparing the temporal activation of an ROI in one hemisphere with the corresponding homotopic region in the other hemisphere. While this approach can reveal significant information about cerebral organization, it does not provide information about the full spatiotemporal organization of the hemispheres. The cerebral differences revealed in literature suggest that hemispheres have different spatiotemporal organization in the resting state. In this study, we evaluate cerebral lateralization in the 4D spatiotemporal frequency domain to compare the hemispheres in the context of general activation patterns at different spatial and temporal scales. We use a gender-balanced resting fMRI dataset comprising over 600 healthy subjects ranging in age from 12 to 71, that have previously been studied with a network specific voxel-wise and global analysis of lateralization (Agcaoglu, et al. NeuroImage, 2014). Our analysis elucidates significant differences in the spatiotemporal organization of brain activity between hemispheres, and generally more spatiotemporal fluctuation in the left hemisphere especially in the high spatial frequency bands, and more power in the right hemisphere in the low and middle spatial frequencies. Importantly, the identified effects are not visible in the context of a typical assessment of voxelwise, regional, or even global laterality, thus our study highlights the value of 4D spatiotemporal frequency domain analyses as a complementary and powerful tool for studying brain function.

Manganese- and 1-methyl-4-phenylpyridinium-induced neurotoxicity display differences in morphological, electrophysiological and genome-wide alterations: implications for idiopathic Parkinson's disease.

PubMed

Mythri, Rajeswara Babu; Raghunath, Narayana Reddy; Narwade, Santosh Chandrakant; Pandareesh, Mirazkar Dasharatha Rao; Sabitha, Kollarkandi Rajesh; Aiyaz, Mohamad; Chand, Bipin; Sule, Manas; Ghosh, Krittika; Kumar, Senthil; Shankarappa, Bhagyalakshmi; Soundararajan, Soundarya; Alladi, Phalguni Anand; Purushottam, Meera; Gayathri, Narayanappa; Deobagkar, Deepti Dileep; Laxmi, Thenkanidiyoor Rao; Srinivas Bharath, Muchukunte Mukunda

2017-11-01

Idiopathic Parkinson's disease and manganese-induced atypical parkinsonism are characterized by movement disorder and nigrostriatal pathology. Although clinical features, brain region involved and responsiveness to levodopa distinguish both, differences at the neuronal level are largely unknown. We studied the morphological, neurophysiological and molecular differences in dopaminergic neurons exposed to the Parkinson's disease toxin 1-methyl-4-phenylpyridinium ion (MPP + ) and manganese (Mn), followed by validation in the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine and Mn mouse models. Morphological analysis highlighted loss of neuronal processes in the MPP + and not the Mn model. Cellular network dynamics of dopaminergic neurons characterized by spike frequency and inter-spike intervals indicated major neuronal population (~ 93%) with slow discharge rates (0-5 Hz). While MPP + exposure suppressed the firing of these neurons, Mn neither suppressed nor elevated the neuronal activity. High-throughput transcriptomic analysis revealed up-regulation of 694 and 603 genes and down-regulation of 428 and 255 genes in the MPP + and Mn models respectively. Many differentially expressed genes were unique to either models and contributed to neuroinflammation, metabolic/mitochondrial function, apoptosis and nuclear function, synaptic plasticity, neurotransmission and cytoskeleton. Analysis of the Janus kinase-signal transducer and activator of transcription pathway with implications for neuritogenesis and neuronal proliferation revealed contrasting profile in both models. Genome-wide DNA methylomics revealed differences between both models and substantiated the epigenetic basis of the difference in the Janus kinase-signal transducer and activator of transcription pathway. We conclude that idiopathic Parkinson's disease and atypical parkinsonism have divergent neurotoxicological manifestation at the dopaminergic neuronal level with implications for pathobiology and evolution of novel therapeutics. Cover Image for this issue: doi. 10.1111/jnc.13821. © 2017 International Society for Neurochemistry.

Multiple Sex-Associated Regions and a Putative Sex Chromosome in Zebrafish Revealed by RAD Mapping and Population Genomics

PubMed Central

Anderson, Jennifer L.; Rodríguez Marí, Adriana; Braasch, Ingo; Amores, Angel; Hohenlohe, Paul; Batzel, Peter; Postlethwait, John H.

2012-01-01

Within vertebrates, major sex determining genes can differ among taxa and even within species. In zebrafish (Danio rerio), neither heteromorphic sex chromosomes nor single sex determination genes of large effect, like Sry in mammals, have yet been identified. Furthermore, environmental factors can influence zebrafish sex determination. Although progress has been made in understanding zebrafish gonad differentiation (e.g. the influence of germ cells on gonad fate), the primary genetic basis of zebrafish sex determination remains poorly understood. To identify genetic loci associated with sex, we analyzed F2 offspring of reciprocal crosses between Oregon *AB and Nadia (NA) wild-type zebrafish stocks. Genome-wide linkage analysis, using more than 5,000 sequence-based polymorphic restriction site associated (RAD-tag) markers and population genomic analysis of more than 30,000 single nucleotide polymorphisms in our *ABxNA crosses revealed a sex-associated locus on the end of the long arm of chr-4 for both cross families, and an additional locus in the middle of chr-3 in one cross family. Additional sequencing showed that two SNPs in dmrt1 previously suggested to be functional candidates for sex determination in a cross of ABxIndia wild-type zebrafish, are not associated with sex in our AB fish. Our data show that sex determination in zebrafish is polygenic and that different genes may influence sex determination in different strains or that different genes become more important under different environmental conditions. The association of the end of chr-4 with sex is remarkable because, unique in the karyotype, this chromosome arm shares features with known sex chromosomes: it is highly heterochromatic, repetitive, late replicating, and has reduced recombination. Our results reveal that chr-4 has functional and structural properties expected of a sex chromosome. PMID:22792396

Near-isogenic cotton germplasm lines that differ in fiber-bundle strength have temporal differences in fiber gene expression patterns as revealed by comparative high-throughput profiling.

PubMed

Hinchliffe, Doug J; Meredith, William R; Yeater, Kathleen M; Kim, Hee Jin; Woodward, Andrew W; Chen, Z Jeffrey; Triplett, Barbara A

2010-05-01

Gene expression profiles of developing cotton (Gossypium hirsutum L.) fibers from two near-isogenic lines (NILs) that differ in fiber-bundle strength, short-fiber content, and in fewer than two genetic loci were compared using an oligonucleotide microarray. Fiber gene expression was compared at five time points spanning fiber elongation and secondary cell wall (SCW) biosynthesis. Fiber samples were collected from field plots in a randomized, complete block design, with three spatially distinct biological replications for each NIL at each time point. Microarray hybridizations were performed in a loop experimental design that allowed comparisons of fiber gene expression profiles as a function of time between the two NILs. Overall, developmental expression patterns revealed by the microarray experiment agreed with previously reported cotton fiber gene expression patterns for specific genes. Additionally, genes expressed coordinately with the onset of SCW biosynthesis in cotton fiber correlated with gene expression patterns of other SCW-producing plant tissues. Functional classification and enrichment analysis of differentially expressed genes between the two NILs revealed that genes associated with SCW biosynthesis were significantly up-regulated in fibers of the high-fiber quality line at the transition stage of cotton fiber development. For independent corroboration of the microarray results, 15 genes were selected for quantitative reverse transcription PCR analysis of fiber gene expression. These analyses, conducted over multiple field years, confirmed the temporal difference in fiber gene expression between the two NILs. We hypothesize that the loci conferring temporal differences in fiber gene expression between the NILs are important regulatory sequences that offer the potential for more targeted manipulation of cotton fiber quality.

Phenotypic diversity of diploid and haploid Emiliania huxleyi cells and of cells in different growth phases revealed by comparative metabolomics.

PubMed

Mausz, Michaela A; Pohnert, Georg

2015-01-01

In phytoplankton a high species diversity of microalgae co-exists at a given time. But diversity is not only reflected by the species composition. Within these species different life phases as well as different metabolic states can cause additional diversity. One important example is the coccolithophore Emiliania huxleyi. Diploid cells play an important role in marine ecosystems since they can form massively abundant algal blooms but in addition the less abundant haploid life phase of E. huxleyi occurs in lower quantities. Both life phases may fulfill different functions in the plankton. We hypothesize that in addition to the functional diversity caused by this life phase transition the growth stage of cells can also influence the metabolic composition and thus the ecological impact of E. huxleyi. Here we introduce a metabolomic survey in dependence of life phases as well as different growth phases to reveal such changes. The comparative metabolomic approach is based on the extraction of intracellular metabolites from intact microalgae, derivatization and analysis by gas chromatography coupled to mass spectrometry (GC-MS). Automated data processing and statistical analysis using canonical analysis of principal coordinates (CAP) revealed unique metabolic profiles for each life phase. Concerning the correlations of metabolites to growth phases, complex patterns were observed. As for example the saccharide mannitol showed its highest concentration in the exponential phase, whereas fatty acids were correlated to stationary and sterols to declining phase. These results are indicative for specific ecological roles of these stages of E. huxleyi and are discussed in the context of previous physiological and ecological studies. Copyright © 2014 Elsevier GmbH. All rights reserved.

Global analysis of human duplicated genes reveals the relative importance of whole-genome duplicates originated in the early vertebrate evolution.

PubMed

Acharya, Debarun; Ghosh, Tapash C

2016-01-22

Gene duplication is a genetic mutation that creates functionally redundant gene copies that are initially relieved from selective pressures and may adapt themselves to new functions with time. The levels of gene duplication may vary from small-scale duplication (SSD) to whole genome duplication (WGD). Studies with yeast revealed ample differences between these duplicates: Yeast WGD pairs were functionally more similar, less divergent in subcellular localization and contained a lesser proportion of essential genes. In this study, we explored the differences in evolutionary genomic properties of human SSD and WGD genes, with the identifiable human duplicates coming from the two rounds of whole genome duplication occurred early in vertebrate evolution. We observed that these two groups of duplicates were also dissimilar in terms of their evolutionary and genomic properties. But interestingly, this is not like the same observed in yeast. The human WGDs were found to be functionally less similar, diverge more in subcellular level and contain a higher proportion of essential genes than the SSDs, all of which are opposite from yeast. Additionally, we explored that human WGDs were more divergent in their gene expression profile, have higher multifunctionality and are more often associated with disease, and are evolutionarily more conserved than human SSDs. Our study suggests that human WGD duplicates are more divergent and entails the adaptation of WGDs to novel and important functions that consequently lead to their evolutionary conservation in the course of evolution.

Investigation of phonon transport and thermal boundary conductance at the interface of functionalized SWCNT and poly (ether-ketone)

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

Huang, Haoxiang; Kumar, Satish, E-mail: satish.kumar@me.gatech.edu; Chen, Liang

2016-09-07

Carbon nanostructures such as carbon nanotube (CNT), graphene, and carbon fibers can be used as fillers in amorphous polymers to improve their thermal properties. In this study, the effect of covalent bonding of CNT with poly(ether ketone) (PEK) on interfacial thermal interactions is investigated using non-equilibrium molecular dynamics simulations. The number of covalent bonds between (20, 20) CNT and PEK is varied in the range of 0–80 (0%–6.25%), and the thermal boundary conductance is computed. The analysis reveals that covalent functionalization of CNT atoms can enhance the thermal boundary conductance by an order of magnitude compared to the non-functionalized CNT-PEKmore » interface at a high degree of CNT functionalization. Besides strengthening the thermal coupling, covalent functionalization is also shown to modify the phonon spectra of CNT. The transient spectral energy analysis shows that the crosslinks cause faster energy exchange from CNT to PEK in different frequency bands. The oxygen atom of hydroxyl group of PEK contributes energy transfer in the low frequency band, while aromatic and carbonyl carbon atoms play a more significant role in high frequency bands. In addition, by analyzing the relaxation time of the spectral temperature of different frequency bands of CNT, it is revealed that with increasing number of bonds, both lower frequency vibrational modes and higher frequency modes efficiently couple across the CNT-PEK interface and contribute in thermal energy transfer from CNT to the matrix.« less

Different Modulatory Mechanisms of Renal FXYD12 for Na+-K+-ATPase between Two Closely Related Medakas upon Salinity Challenge

PubMed Central

Yang, Wen-Kai; Kang, Chao-Kai; Hsu, An-Di; Lin, Chia-Hao; Lee, Tsung-Han

2016-01-01

Upon salinity challenge, the Na+-K+-ATPase (NKA) of fish kidney plays a crucial role in maintaining ion and water balance. Moreover, the FXYD protein family was found to be a regulator of NKA. Our preliminary results revealed that fxyd12 was highly expressed in the kidneys of the two closely related euryhaline medaka species (Oryzias dancena and O. latipes) from different natural habitats (brackish water and fresh water). In this study, we investigated the expression and association of renal FXYD12 and NKA α-subunit as well as potential functions of FXYD12 in the two medakas. These findings illustrated and compared the regulatory roles of FXYD12 for NKA in kidneys of the two medakas in response to salinity changes. In this study, at the mRNA and/or protein level, the expression patterns were similar for renal FXYD12 and NKA in the two medakas. However, different patterns of NKA activities and different interaction levels between FXYD12 and NKA were found in the kidneys of these two medakas. The results revealed that different strategies were used in the kidneys of the two medaka species upon salinity challenge. On the other hand, gene knockdown experiments demonstrated that the function of O. dancena FXYD12 allowed maintenance of a high level of NKA activity. The results of the present study indicated that the kidneys of the examined euryhaline medakas originating from brackish water and fresh water exhibited different modulatory mechanisms through which renal FXYD12 enhanced NKA activity to maintain internal homeostasis. Our findings broadened the knowledge of expression and functions of FXYD proteins, the modulators of NKA, in vertebrates. PMID:27194950

Multitrophic functional diversity predicts ecosystem functioning in experimental assemblages of estuarine consumers.

PubMed

Lefcheck, Jonathan S; Duffy, J Emmett

2015-11-01

The use of functional traits to explain how biodiversity affects ecosystem functioning has attracted intense interest, yet few studies have a priori altered functional diversity, especially in multitrophic communities. Here, we manipulated multivariate functional diversity of estuarine grazers and predators within multiple levels of species richness to test how species richness and functional diversity predicted ecosystem functioning in a multitrophic food web. Community functional diversity was a better predictor than species richness for the majority of ecosystem properties, based on generalized linear mixed-effects models. Combining inferences from eight traits into a single multivariate index increased prediction accuracy of these models relative to any individual trait. Structural equation modeling revealed that functional diversity of both grazers and predators was important in driving final biomass within trophic levels, with stronger effects observed for predators. We also show that different species drove different ecosystem responses, with evidence for both sampling effects and complementarity. Our study extends experimental investigations of functional trait diversity to a multilevel food web, and demonstrates that functional diversity can be more accurate and effective than species richness in predicting community biomass in a food web context.

Multi-slice MRI reveals heterogeneity in disease distribution along the length of muscle in Duchenne muscular dystrophy.

PubMed

Chrzanowski, Stephen M; Baligand, Celine; Willcocks, Rebecca J; Deol, Jasjit; Schmalfuss, Ilona; Lott, Donovan J; Daniels, Michael J; Senesac, Claudia; Walter, Glenn A; Vandenborne, Krista

2017-09-01

Duchenne muscular dystrophy (DMD) causes progressive pathologic changes to muscle secondary to a cascade of inflammation, lipid deposition, and fibrosis. Clinically, this manifests as progressive weakness, functional loss, and premature mortality. Though insult to whole muscle groups is well established, less is known about the relationship between intramuscular pathology and function. Differences of intramuscular heterogeneity across muscle length were assessed using an ordinal MRI grading scale in lower leg muscles of boys with DMD and correlated to patient's functional status. Cross sectional T 1 weighted MRI images with fat suppression were obtained from ambulatory boys with DMD. Six muscles (tibialis anterior, extensor digitorum longus, peroneus, soleus, medial and lateral gastrocnemii) were graded using an ordinal grading scale over 5 slice sections along the lower leg length. The scores from each slice were combined and results were compared to global motor function and age. Statistically greater differences of involvement were observed at the proximal ends of muscle compared to the midbellies. Multi-slice assessment correlated significantly to age and the Vignos functional scale, whereas single-slice assessment correlated to the Vignos functional scale only. Lastly, differential disease involvement of whole muscle groups and intramuscular heterogeneity were observed amongst similar age subjects. A multi-slice ordinal MRI grading scale revealed that muscles are not uniformly affected, with more advanced disease visible near the tendons in a primarily ambulatory population with DMD. A geographically comprehensive evaluation of the heterogeneously affected muscle in boys with DMD may more accurately assess disease involvement.

Genome-wide analysis of the Dof transcription factor gene family reveals soybean-specific duplicable and functional characteristics.

PubMed

Guo, Yong; Qiu, Li-Juan

2013-01-01

The Dof domain protein family is a classic plant-specific zinc-finger transcription factor family involved in a variety of biological processes. There is great diversity in the number of Dof genes in different plants. However, there are only very limited reports on the characterization of Dof transcription factors in soybean (Glycine max). In the present study, 78 putative Dof genes were identified from the whole-genome sequence of soybean. The predicted GmDof genes were non-randomly distributed within and across 19 out of 20 chromosomes and 97.4% (38 pairs) were preferentially retained duplicate paralogous genes located in duplicated regions of the genome. Soybean-specific segmental duplications contributed significantly to the expansion of the soybean Dof gene family. These Dof proteins were phylogenetically clustered into nine distinct subgroups among which the gene structure and motif compositions were considerably conserved. Comparative phylogenetic analysis of these Dof proteins revealed four major groups, similar to those reported for Arabidopsis and rice. Most of the GmDofs showed specific expression patterns based on RNA-seq data analyses. The expression patterns of some duplicate genes were partially redundant while others showed functional diversity, suggesting the occurrence of sub-functionalization during subsequent evolution. Comprehensive expression profile analysis also provided insights into the soybean-specific functional divergence among members of the Dof gene family. Cis-regulatory element analysis of these GmDof genes suggested diverse functions associated with different processes. Taken together, our results provide useful information for the functional characterization of soybean Dof genes by combining phylogenetic analysis with global gene-expression profiling.

Bcl2-associated Athanogene 3 Interactome Analysis Reveals a New Role in Modulating Proteasome Activity*

PubMed Central

Chen, Ying; Yang, Li-Na; Cheng, Li; Tu, Shun; Guo, Shu-Juan; Le, Huang-Ying; Xiong, Qian; Mo, Ran; Li, Chong-Yang; Jeong, Jun-Seop; Jiang, Lizhi; Blackshaw, Seth; Bi, Li-Jun; Zhu, Heng; Tao, Sheng-Ce; Ge, Feng

2013-01-01

Bcl2-associated athanogene 3 (BAG3), a member of the BAG family of co-chaperones, plays a critical role in regulating apoptosis, development, cell motility, autophagy, and tumor metastasis and in mediating cell adaptive responses to stressful stimuli. BAG3 carries a BAG domain, a WW domain, and a proline-rich repeat (PXXP), all of which mediate binding to different partners. To elucidate BAG3's interaction network at the molecular level, we employed quantitative immunoprecipitation combined with knockdown and human proteome microarrays to comprehensively profile the BAG3 interactome in humans. We identified a total of 382 BAG3-interacting proteins with diverse functions, including transferase activity, nucleic acid binding, transcription factors, proteases, and chaperones, suggesting that BAG3 is a critical regulator of diverse cellular functions. In addition, we characterized interactions between BAG3 and some of its newly identified partners in greater detail. In particular, bioinformatic analysis revealed that the BAG3 interactome is strongly enriched in proteins functioning within the proteasome-ubiquitination process and that compose the proteasome complex itself, suggesting that a critical biological function of BAG3 is associated with the proteasome. Functional studies demonstrated that BAG3 indeed interacts with the proteasome and modulates its activity, sustaining cell survival and underlying resistance to therapy through the down-modulation of apoptosis. Taken as a whole, this study expands our knowledge of the BAG3 interactome, provides a valuable resource for understanding how BAG3 affects different cellular functions, and demonstrates that biologically relevant data can be harvested using this kind of integrated approach. PMID:23824909

Latent binocular function in amblyopia.

PubMed

Chadnova, Eva; Reynaud, Alexandre; Clavagnier, Simon; Hess, Robert F

2017-11-01

Recently, psychophysical studies have shown that humans with amblyopia do have binocular function that is not normally revealed due to dominant suppressive interactions under normal viewing conditions. Here we use magnetoencephalography (MEG) combined with dichoptic visual stimulation to investigate the underlying binocular function in humans with amblyopia for stimuli that, because of their temporal properties, would be expected to bypass suppressive effects and to reveal any underlying binocular function. We recorded contrast response functions in visual cortical area V1 of amblyopes and normal observers using a steady state visually evoked responses (SSVER) protocol. We used stimuli that were frequency-tagged at 4Hz and 6Hz that allowed identification of the responses from each eye and were of a sufficiently high temporal frequency (>3Hz) to bypass suppression. To characterize binocular function, we compared dichoptic masking between the two eyes in normal and amblyopic participants as well as interocular phase differences in the two groups. We observed that the primary visual cortex responds less to the stimulation of the amblyopic eye compared to the fellow eye. The pattern of interaction in the amblyopic visual system however was not significantly different between the amblyopic and fellow eyes. However, the amblyopic suppressive interactions were lower than those observed in the binocular system of our normal observers. Furthermore, we identified an interocular processing delay of approximately 20ms in our amblyopic group. To conclude, when suppression is greatly reduced, such as the case with our stimulation above 3Hz, the amblyopic visual system exhibits a lack of binocular interactions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Functional modules by relating protein interaction networks and gene expression.

PubMed

Tornow, Sabine; Mewes, H W

2003-11-01

Genes and proteins are organized on the basis of their particular mutual relations or according to their interactions in cellular and genetic networks. These include metabolic or signaling pathways and protein interaction, regulatory or co-expression networks. Integrating the information from the different types of networks may lead to the notion of a functional network and functional modules. To find these modules, we propose a new technique which is based on collective, multi-body correlations in a genetic network. We calculated the correlation strength of a group of genes (e.g. in the co-expression network) which were identified as members of a module in a different network (e.g. in the protein interaction network) and estimated the probability that this correlation strength was found by chance. Groups of genes with a significant correlation strength in different networks have a high probability that they perform the same function. Here, we propose evaluating the multi-body correlations by applying the superparamagnetic approach. We compare our method to the presently applied mean Pearson correlations and show that our method is more sensitive in revealing functional relationships.

Functional modules by relating protein interaction networks and gene expression

PubMed Central

Tornow, Sabine; Mewes, H. W.

2003-01-01

Genes and proteins are organized on the basis of their particular mutual relations or according to their interactions in cellular and genetic networks. These include metabolic or signaling pathways and protein interaction, regulatory or co-expression networks. Integrating the information from the different types of networks may lead to the notion of a functional network and functional modules. To find these modules, we propose a new technique which is based on collective, multi-body correlations in a genetic network. We calculated the correlation strength of a group of genes (e.g. in the co-expression network) which were identified as members of a module in a different network (e.g. in the protein interaction network) and estimated the probability that this correlation strength was found by chance. Groups of genes with a significant correlation strength in different networks have a high probability that they perform the same function. Here, we propose evaluating the multi-body correlations by applying the superparamagnetic approach. We compare our method to the presently applied mean Pearson correlations and show that our method is more sensitive in revealing functional relationships. PMID:14576317

Detailed Wave Function Analysis for Multireference Methods: Implementation in the Molcas Program Package and Applications to Tetracene.

PubMed

Plasser, Felix; Mewes, Stefanie A; Dreuw, Andreas; González, Leticia

2017-11-14

High-level multireference computations on electronically excited and charged states of tetracene are performed, and the results are analyzed using an extensive wave function analysis toolbox that has been newly implemented in the Molcas program package. Aside from verifying the strong effect of dynamic correlation, this study reveals an unexpected critical influence of the atomic orbital basis set. It is shown that different polarized double-ζ basis sets produce significantly different results for energies, densities, and overall wave functions, with the best performance obtained for the atomic natural orbital (ANO) basis set by Pierloot et al. Strikingly, the ANO basis set not only reproduces the energies but also performs exceptionally well in terms of describing the diffuseness of the different states and of their attachment/detachment densities. This study, thus, not only underlines the fact that diffuse basis functions are needed for an accurate description of the electronic wave functions but also shows that, at least for the present example, it is enough to include them implicitly in the contraction scheme.

Similarity and diversity of translational GTPase factors EF-G, EF4, and BipA: From structure to function.

PubMed

Ero, Rya; Kumar, Veerendra; Chen, Yun; Gao, Yong-Gui

2016-12-01

EF-G, EF4, and BipA are members of the translation factor family of GTPases with a common ribosome binding mode and GTPase activation mechanism. However, topological variations of shared as well as unique domains ensure different roles played by these proteins during translation. Recent X-ray crystallography and cryo-electron microscopy studies have revealed the structural basis for the involvement of EF-G domain IV in securing the movement of tRNAs and mRNA during translocation as well as revealing how the unique C-terminal domains of EF4 and BipA interact with the ribosome and tRNAs contributing to the regulation of translation under certain conditions. EF-G, EF-4, and BipA are intriguing examples of structural variations on a common theme that results in diverse behavior and function. Structural studies of translational GTPase factors have been greatly facilitated by the use of antibiotics, which have revealed their mechanism of action.

A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human.

PubMed

Vo, Tommy V; Das, Jishnu; Meyer, Michael J; Cordero, Nicolas A; Akturk, Nurten; Wei, Xiaomu; Fair, Benjamin J; Degatano, Andrew G; Fragoza, Robert; Liu, Lisa G; Matsuyama, Akihisa; Trickey, Michelle; Horibata, Sachi; Grimson, Andrew; Yamano, Hiroyuki; Yoshida, Minoru; Roth, Frederick P; Pleiss, Jeffrey A; Xia, Yu; Yu, Haiyuan

2016-01-14

Here, we present FissionNet, a proteome-wide binary protein interactome for S. pombe, comprising 2,278 high-quality interactions, of which ∼ 50% were previously not reported in any species. FissionNet unravels previously unreported interactions implicated in processes such as gene silencing and pre-mRNA splicing. We developed a rigorous network comparison framework that accounts for assay sensitivity and specificity, revealing extensive species-specific network rewiring between fission yeast, budding yeast, and human. Surprisingly, although genes are better conserved between the yeasts, S. pombe interactions are significantly better conserved in human than in S. cerevisiae. Our framework also reveals that different modes of gene duplication influence the extent to which paralogous proteins are functionally repurposed. Finally, cross-species interactome mapping demonstrates that coevolution of interacting proteins is remarkably prevalent, a result with important implications for studying human disease in model organisms. Overall, FissionNet is a valuable resource for understanding protein functions and their evolution. Copyright © 2016 Elsevier Inc. All rights reserved.

Defining functional groups based on running kinematics using Self-Organizing Maps and Support Vector Machines.

PubMed

Hoerzer, Stefan; von Tscharner, Vinzenz; Jacob, Christian; Nigg, Benno M

2015-07-16

A functional group is a collection of individuals who react in a similar way to a specific intervention/product such as a sport shoe. Matching footwear features to a functional group can possibly enhance footwear-related comfort, improve running performance, and decrease the risk of movement-related injuries. To match footwear features to a functional group, one has to first define the different groups using their distinctive movement patterns. Therefore, the main objective of this study was to propose and apply a methodological approach to define functional groups with different movement patterns using Self-Organizing Maps and Support Vector Machines. Further study objectives were to identify differences in age, gender and footwear-related comfort preferences between the functional groups. Kinematic data and subjective comfort preferences of 88 subjects (16-76 years; 45 m/43 f) were analysed. Eight functional groups with distinctive movement patterns were defined. The findings revealed that most of the groups differed in age or gender. Certain functional groups differed in their comfort preferences and, therefore, had group-specific footwear requirements to enhance footwear-related comfort. Some of the groups, which had group-specific footwear requirements, did not show any differences in age or gender. This is important because when defining functional groups simply using common grouping criteria like age or gender, certain functional groups with group-specific movement patterns and footwear requirements might not be detected. This emphasises the power of the proposed pattern recognition approach to automatically define groups by their distinctive movement patterns in order to be able to address their group-specific product requirements. Copyright © 2015 Elsevier Ltd. All rights reserved.

The crystal structures of EAP domains from Staphylococcus aureus reveal an unexpected homology to bacterial superantigens.

PubMed

Geisbrecht, Brian V; Hamaoka, Brent Y; Perman, Benjamin; Zemla, Adam; Leahy, Daniel J

2005-04-29

The Eap (extracellular adherence protein) of Staphylococcus aureus functions as a secreted virulence factor by mediating interactions between the bacterial cell surface and several extracellular host proteins. Eap proteins from different Staphylococcal strains consist of four to six tandem repeats of a structurally uncharacterized domain (EAP domain). We have determined the three-dimensional structures of three different EAP domains to 1.8, 2.2, and 1.35 A resolution, respectively. These structures reveal a core fold that is comprised of an alpha-helix lying diagonally across a five-stranded, mixed beta-sheet. Comparison of EAP domains with known structures reveals an unexpected homology with the C-terminal domain of bacterial superantigens. Examination of the structure of the superantigen SEC2 bound to the beta-chain of a T-cell receptor suggests a possible ligand-binding site within the EAP domain (Fields, B. A., Malchiodi, E. L., Li, H., Ysern, X., Stauffacher, C. V., Schlievert, P. M., Karjalainen, K., and Mariuzza, R. (1996) Nature 384, 188-192). These results provide the first structural characterization of EAP domains, relate EAP domains to a large class of bacterial toxins, and will guide the design of future experiments to analyze EAP domain structure/function relationships.

What Mutagenesis Can and Cannot Reveal About Allostery.

PubMed

Carlson, Gerald M; Fenton, Aron W

2016-05-10

Allosteric regulation of protein function is recognized to be widespread throughout biology; however, knowledge of allosteric mechanisms, the molecular changes within a protein that couple one binding site to another, is limited. Although mutagenesis is often used to probe allosteric mechanisms, we consider herein what the outcome of a mutagenesis study truly reveals about an allosteric mechanism. Arguably, the best way to evaluate the effects of a mutation on allostery is to monitor the allosteric coupling constant (Qax), a ratio of the substrate binding constants in the absence versus presence of an allosteric effector. A range of substitutions at a given residue position in a protein can reveal when a particular substitution causes gain-of-function, which addresses a key challenge in interpreting mutation-dependent changes in the magnitude of Qax. Thus, whole-protein mutagenesis studies offer an acceptable means of identifying residues that contribute to an allosteric mechanism. With this focus on monitoring Qax, and keeping in mind the equilibrium nature of allostery, we consider alternative possibilities for what an allosteric mechanism might be. We conclude that different possible mechanisms (rotation-of-solid-domains, movement of secondary structure, side-chain repacking, changes in dynamics, etc.) will result in different findings in whole-protein mutagenesis studies. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Caenorhabditis elegans ABCRNAi transporters interact genetically with rde-2 and mut-7.

PubMed

Sundaram, Prema; Han, Wang; Cohen, Nancy; Echalier, Benjamin; Albin, John; Timmons, Lisa

2008-02-01

RNA interference (RNAi) mechanisms are conserved and consist of an interrelated network of activities that not only respond to exogenous dsRNA, but also perform endogenous functions required in the fine tuning of gene expression and in maintaining genome integrity. Not surprisingly, RNAi functions have widespread influences on cellular function and organismal development. Previously, we observed a reduced capacity to mount an RNAi response in nine Caenorhabditis elegans mutants that are defective in ABC transporter genes (ABC(RNAi) mutants). Here, we report an exhaustive study of mutants, collectively defective in 49 different ABC transporter genes, that allowed for the categorization of one additional transporter into the ABC(RNAi) gene class. Genetic complementation tests reveal functions for ABC(RNAi) transporters in the mut-7/rde-2 branch of the RNAi pathway. These second-site noncomplementation interactions suggest that ABC(RNAi) proteins and MUT-7/RDE-2 function together in parallel pathways and/or as multiprotein complexes. Like mut-7 and rde-2, some ABC(RNAi) mutants display transposon silencing defects. Finally, our analyses reveal a genetic interaction network of ABC(RNAi) gene function with respect to this part of the RNAi pathway. From our results, we speculate that the coordinated activities of ABC(RNAi) transporters, through their effects on endogenous RNAi-related mechanisms, ultimately affect chromosome function and integrity.

Caenorhabditis elegans ABCRNAi Transporters Interact Genetically With rde-2 and mut-7

PubMed Central

Sundaram, Prema; Han, Wang; Cohen, Nancy; Echalier, Benjamin; Albin, John; Timmons, Lisa

2008-01-01

RNA interference (RNAi) mechanisms are conserved and consist of an interrelated network of activities that not only respond to exogenous dsRNA, but also perform endogenous functions required in the fine tuning of gene expression and in maintaining genome integrity. Not surprisingly, RNAi functions have widespread influences on cellular function and organismal development. Previously, we observed a reduced capacity to mount an RNAi response in nine Caenorhabditis elegans mutants that are defective in ABC transporter genes (ABCRNAi mutants). Here, we report an exhaustive study of mutants, collectively defective in 49 different ABC transporter genes, that allowed for the categorization of one additional transporter into the ABCRNAi gene class. Genetic complementation tests reveal functions for ABCRNAi transporters in the mut-7/rde-2 branch of the RNAi pathway. These second-site noncomplementation interactions suggest that ABCRNAi proteins and MUT-7/RDE-2 function together in parallel pathways and/or as multiprotein complexes. Like mut-7 and rde-2, some ABCRNAi mutants display transposon silencing defects. Finally, our analyses reveal a genetic interaction network of ABCRNAi gene function with respect to this part of the RNAi pathway. From our results, we speculate that the coordinated activities of ABCRNAi transporters, through their effects on endogenous RNAi-related mechanisms, ultimately affect chromosome function and integrity. PMID:18245353

Coupling functions: Universal insights into dynamical interaction mechanisms

NASA Astrophysics Data System (ADS)

Stankovski, Tomislav; Pereira, Tiago; McClintock, Peter V. E.; Stefanovska, Aneta

2017-10-01

The dynamical systems found in nature are rarely isolated. Instead they interact and influence each other. The coupling functions that connect them contain detailed information about the functional mechanisms underlying the interactions and prescribe the physical rule specifying how an interaction occurs. A coherent and comprehensive review is presented encompassing the rapid progress made recently in the analysis, understanding, and applications of coupling functions. The basic concepts and characteristics of coupling functions are presented through demonstrative examples of different domains, revealing the mechanisms and emphasizing their multivariate nature. The theory of coupling functions is discussed through gradually increasing complexity from strong and weak interactions to globally coupled systems and networks. A variety of methods that have been developed for the detection and reconstruction of coupling functions from measured data is described. These methods are based on different statistical techniques for dynamical inference. Stemming from physics, such methods are being applied in diverse areas of science and technology, including chemistry, biology, physiology, neuroscience, social sciences, mechanics, and secure communications. This breadth of application illustrates the universality of coupling functions for studying the interaction mechanisms of coupled dynamical systems.

The TiPS/TINS lecture: the molecular biology of mammalian glutamate receptor channels.

PubMed

Seeburg, P H

1993-08-01

In native brain membranes the principal excitatory neurotransmitter L-glutamate activates cation-conducting channels with distinct biophysical and pharmacological properties. Molecular cloning has revealed the existence of 16 channel subunits that can assemble in homomeric or heteromeric configurations in vitro to form receptor channels with disparate functional properties. This review describes the different channel types obtained by recombinant means and the genetic mechanisms controlling the expression of functionally important channel structures.

The TINS/TiPS Lecture. The molecular biology of mammalian glutamate receptor channels.

PubMed

Seeburg, P H

1993-09-01

In native brain membranes the principal excitatory neurotransmitter L-glutamate activates cation-conducting channels with distinct biophysical and pharmacological properties. Molecular cloning has revealed the existence of 16 channel subunits that can assemble in homomeric or heteromeric configurations in vitro to form receptor channels with disparate functional properties. This review describes the different channel types obtained by recombinant means and the genetic mechanisms controlling the expression of functionally important channel structures.

Electron doping effects on the electrical conductivity of zigzag carbon nanotubes and corresponding unzipped armchair graphene nanoribbons

NASA Astrophysics Data System (ADS)

Mousavi, Hamze; Jalilvand, Samira; Kurdestany, Jamshid Moradi; Grabowski, Marek

2017-10-01

The Kubo formula is used to extract the electrical conductivity (EC) of different diameters of doped zigzag carbon nanotubes and their corresponding unzipped armchair graphene nanoribbons, as a function of temperature and chemical potential, within the tight-binding Hamiltonian model and Green's functions approach. The results reveal more sensitivity to temperature for semiconducting systems in addition to a decrease in EC of all systems with increasing cross-sections.

Effect of different drying techniques on flowability characteristics and chemical properties of natural carbohydrate-protein Gum from durian fruit seed

PubMed Central

2013-01-01

Background A natural carbohydrate biopolymer was extracted from the agricultural biomass waste (durian seed). Subsequently, the crude biopolymer was purified by using the saturated barium hydroxide to minimize the impurities. Finally, the effect of different drying techniques on the flow characteristics and functional properties of the purified biopolymer was investigated. The present study elucidated the main functional characteristics such as flow characteristics, water- and oil-holding capacity, solubility, and foaming capacity. Results In most cases except for oven drying, the bulk density decreased, thus increasing the porosity. This might be attributed to the increase in the inter-particle voids of smaller sized particles with larger contact surface areas per unit volume. The current study revealed that oven-dried gum and freeze-dried gum had the highest and lowest compressibility index, thus indicating the weakest and strongest flowability among all samples. In the present work, the freeze-dried gum showed the lowest angle of repose, bulk, tapped and true density. This indicates the highest porosity degree of freeze dried gum among dried seed gums. It also exhibited the highest solubility, and foaming capacity thus providing the most desirable functional properties and flow characteristics among all drying techniques. Conclusion The present study revealed that freeze drying among all drying techniques provided the most desirable functional properties and flow characteristics for durian seed gum. PMID:23289739

Gene cooption and convergent evolution of oxygen transport hemoglobins in jawed and jawless vertebrates

PubMed Central

Hoffmann, Federico G.; Opazo, Juan C.; Storz, Jay F.

2010-01-01

Natural selection often promotes evolutionary innovation by coopting preexisting genes for new functions, and this process may be greatly facilitated by gene duplication. Here we report an example of cooptive convergence where paralogous members of the globin gene superfamily independently evolved a specialized O2 transport function in the two deepest branches of the vertebrate family tree. Specifically, phylogenetic evidence demonstrates that erythroid-specific O2 transport hemoglobins evolved independently from different ancestral precursor proteins in jawed vertebrates (gnathostomes) and jawless fish (cyclostomes, represented by lamprey and hagfish). A comprehensive phylogenetic analysis of the vertebrate globin gene superfamily revealed that the erythroid hemoglobins of cyclostomes are orthologous to the cytoglobin protein of gnathostome vertebrates, a hexacoordinate globin that has no O2 transport function and that is predominantly expressed in fibroblasts and related cell types. The phylogeny reconstruction also revealed that vertebrate-specific globins are grouped into four main clades: (i) cyclostome hemoglobin + cytoglobin, (ii) myoglobin + globin E, (iii) globin Y, and (iv) the α- and β-chain hemoglobins of gnathostomes. In the hemoglobins of gnathostomes and cyclostomes, multisubunit quaternary structures provide the basis for cooperative O2 binding and allosteric regulation by coupling the effects of ligand binding at individual subunits with interactions between subunits. However, differences in numerous structural details belie their independent origins. This example of convergent evolution of protein function provides an impressive demonstration of the ability of natural selection to cobble together complex design solutions by tinkering with different variations of the same basic protein scaffold. PMID:20660759

Insight into pattern of codon biasness and nucleotide base usage in serotonin receptor gene family from different mammalian species.

PubMed

Dass, J Febin Prabhu; Sudandiradoss, C

2012-07-15

5-HT (5-Hydroxy-tryptamine) or serotonin receptors are found both in central and peripheral nervous system as well as in non-neuronal tissues. In the animal and human nervous system, serotonin produces various functional effects through a variety of membrane bound receptors. In this study, we focus on 5-HT receptor family from different mammals and examined the factors that account for codon and nucleotide usage variation. A total of 110 homologous coding sequences from 11 different mammalian species were analyzed using relative synonymous codon usage (RSCU), correspondence analysis (COA) and hierarchical cluster analysis together with nucleotide base usage frequency of chemically similar amino acid codons. The mean effective number of codon (ENc) value of 37.06 for 5-HT(6) shows very high codon bias within the family and may be due to high selective translational efficiency. The COA and Spearman's rank correlation reveals that the nucleotide compositional mutation bias as the major factors influencing the codon usage in serotonin receptor genes. The hierarchical cluster analysis suggests that gene function is another dominant factor that affects the codon usage bias, while species is a minor factor. Nucleotide base usage was reported using Goldman, Engelman, Stietz (GES) scale reveals the presence of high uracil (>45%) content at functionally important hydrophobic regions. Our in silico approach will certainly help for further investigations on critical inference on evolution, structure, function and gene expression aspects of 5-HT receptors family which are potential antipsychotic drug targets. Copyright © 2012 Elsevier B.V. All rights reserved.

Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

PubMed

Ferreira, Ari J S; Siam, Rania; Setubal, João C; Moustafa, Ahmed; Sayed, Ahmed; Chambergo, Felipe S; Dawe, Adam S; Ghazy, Mohamed A; Sharaf, Hazem; Ouf, Amged; Alam, Intikhab; Abdel-Haleem, Alyaa M; Lehvaslaiho, Heikki; Ramadan, Eman; Antunes, André; Stingl, Ulrich; Archer, John A C; Jankovic, Boris R; Sogin, Mitchell; Bajic, Vladimir B; El-Dorry, Hamza

2014-01-01

Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.

Core Microbial Functional Activities in Ocean Environments Revealed by Global Metagenomic Profiling Analyses

PubMed Central

Ferreira, Ari J. S.; Siam, Rania; Setubal, João C.; Moustafa, Ahmed; Sayed, Ahmed; Chambergo, Felipe S.; Dawe, Adam S.; Ghazy, Mohamed A.; Sharaf, Hazem; Ouf, Amged; Alam, Intikhab; Abdel-Haleem, Alyaa M.; Lehvaslaiho, Heikki; Ramadan, Eman; Antunes, André; Stingl, Ulrich; Archer, John A. C.; Jankovic, Boris R.; Sogin, Mitchell; Bajic, Vladimir B.; El-Dorry, Hamza

2014-01-01

Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light. PMID:24921648

[Kennedy V Axis assessment in an Italian outpatient and inpatient population].

PubMed

Mundo, Emanuela; Bonalume, Laura; Del Corno, Franco; Madeddu, Fabio; Lang, Margherita

2010-01-01

Kennedy Axis V or K Axis acts is an alternative tool to the DSM-IVTR Global Assessment of Functioning (GAF) Scale, that many researchers describe as a scale with poor inter-rater reliability and clinical utility. Unlike the GAF scale, K Axis provides a multidimensional and multiaxial approach to measure personal, social and interpersonal functioning in psychiatric outpatients and inpatients. In this study, we examined K Axis's inter-raters reliability by using it with an Italian clinical population. Clinicians used Kennedy Axis V to assess global functioning among 180 inpatients, in 9 psychiatric services in Lombardia and Piemonte. Patients were divided into 4 different diagnostic groups, according to the DSM-IV-TR criteria. Intraclass correlations between two independent raters's scores reveal high level of interrater reliability for all K Axis scales (0,633 < ICC < 0,813). Highly significant results in the Kruskal-Wallis test demonstrate that the patient diagnosis influence all the scales scores. Significant differences in patients functioning profiles in all K Axis scales, apart from Violence one, were noted between different diagnosis groups. In this study high level of raters agreement was noted, even if K Axis scales were used in different mental health services from different clinicians. K Axis scales provide a useful profile of patient global functioning, in line with the specific pathology.

Unity and diversity of executive functions: Individual differences as a window on cognitive structure.

PubMed

Friedman, Naomi P; Miyake, Akira

2017-01-01

Executive functions (EFs) are high-level cognitive processes, often associated with the frontal lobes, that control lower level processes in the service of goal-directed behavior. They include abilities such as response inhibition, interference control, working memory updating, and set shifting. EFs show a general pattern of shared but distinct functions, a pattern described as "unity and diversity". We review studies of EF unity and diversity at the behavioral and genetic levels, focusing on studies of normal individual differences and what they reveal about the functional organization of these cognitive abilities. In particular, we review evidence that across multiple ages and populations, commonly studied EFs (a) are robustly correlated but separable when measured with latent variables; (b) are not the same as general intelligence or g; (c) are highly heritable at the latent level and seemingly also highly polygenic; and (d) activate both common and specific neural areas and can be linked to individual differences in neural activation, volume, and connectivity. We highlight how considering individual differences at the behavioral and neural levels can add considerable insight to the investigation of the functional organization of the brain, and conclude with some key points about individual differences to consider when interpreting neuropsychological patterns of dissociation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effects of different correlation metrics and preprocessing factors on small-world brain functional networks: a resting-state functional MRI study.

PubMed

Liang, Xia; Wang, Jinhui; Yan, Chaogan; Shu, Ni; Xu, Ke; Gong, Gaolang; He, Yong

2012-01-01

Graph theoretical analysis of brain networks based on resting-state functional MRI (R-fMRI) has attracted a great deal of attention in recent years. These analyses often involve the selection of correlation metrics and specific preprocessing steps. However, the influence of these factors on the topological properties of functional brain networks has not been systematically examined. Here, we investigated the influences of correlation metric choice (Pearson's correlation versus partial correlation), global signal presence (regressed or not) and frequency band selection [slow-5 (0.01-0.027 Hz) versus slow-4 (0.027-0.073 Hz)] on the topological properties of both binary and weighted brain networks derived from them, and we employed test-retest (TRT) analyses for further guidance on how to choose the "best" network modeling strategy from the reliability perspective. Our results show significant differences in global network metrics associated with both correlation metrics and global signals. Analysis of nodal degree revealed differing hub distributions for brain networks derived from Pearson's correlation versus partial correlation. TRT analysis revealed that the reliability of both global and local topological properties are modulated by correlation metrics and the global signal, with the highest reliability observed for Pearson's-correlation-based brain networks without global signal removal (WOGR-PEAR). The nodal reliability exhibited a spatially heterogeneous distribution wherein regions in association and limbic/paralimbic cortices showed moderate TRT reliability in Pearson's-correlation-based brain networks. Moreover, we found that there were significant frequency-related differences in topological properties of WOGR-PEAR networks, and brain networks derived in the 0.027-0.073 Hz band exhibited greater reliability than those in the 0.01-0.027 Hz band. Taken together, our results provide direct evidence regarding the influences of correlation metrics and specific preprocessing choices on both the global and nodal topological properties of functional brain networks. This study also has important implications for how to choose reliable analytical schemes in brain network studies.

Targeted Ablation of the Pde6h Gene in Mice Reveals Cross-species Differences in Cone and Rod Phototransduction Protein Isoform Inventory*

PubMed Central

Brennenstuhl, Christina; Tanimoto, Naoyuki; Burkard, Markus; Wagner, Rebecca; Bolz, Sylvia; Trifunovic, Dragana; Kabagema-Bilan, Clement; Paquet-Durand, Francois; Beck, Susanne C.; Huber, Gesine; Seeliger, Mathias W.; Ruth, Peter; Wissinger, Bernd; Lukowski, Robert

2015-01-01

Phosphodiesterase-6 (PDE6) is a multisubunit enzyme that plays a key role in the visual transduction cascade in rod and cone photoreceptors. Each type of photoreceptor utilizes discrete catalytic and inhibitory PDE6 subunits to fulfill its physiological tasks, i.e. the degradation of cyclic guanosine-3′,5′-monophosphate at specifically tuned rates and kinetics. Recently, the human PDE6H gene was identified as a novel locus for autosomal recessive (incomplete) color blindness. However, the three different classes of cones were not affected to the same extent. Short wave cone function was more preserved than middle and long wave cone function indicating that some basic regulation of the PDE6 multisubunit enzyme was maintained albeit by a unknown mechanism. To study normal and disease-related functions of cone Pde6h in vivo, we generated Pde6h knock-out (Pde6h−/−) mice. Expression of PDE6H in murine eyes was restricted to both outer segments and synaptic terminals of short and long/middle cone photoreceptors, whereas Pde6h−/− retinae remained PDE6H-negative. Combined in vivo assessment of retinal morphology with histomorphological analyses revealed a normal overall integrity of the retinal organization and an unaltered distribution of the different cone photoreceptor subtypes upon Pde6h ablation. In contrast to human patients, our electroretinographic examinations of Pde6h−/− mice suggest no defects in cone/rod-driven retinal signaling and therefore preserved visual functions. To this end, we were able to demonstrate the presence of rod PDE6G in cones indicating functional substitution of PDE6. The disparities between human and murine phenotypes caused by mutant Pde6h/PDE6H suggest species-to-species differences in the vulnerability of biochemical and neurosensory pathways of the visual signal transduction system. PMID:25739440

Functional diversification of taste cells in vertebrates

PubMed Central

Matsumoto, Ichiro; Ohmoto, Makoto; Abe, Keiko

2012-01-01

Tastes are senses resulting from the activation of taste cells distributed in oral epithelia. Sweet, umami, bitter, sour, and salty tastes are called the five “basic” tastes, but why five, and why these five? In this review, we dissect the peripheral gustatory system in vertebrates from molecular and cellular perspectives. Recent behavioral and molecular genetic studies have revealed the nature of functional taste receptors and cells and show that different taste qualities are accounted for by the activation of different subsets of taste cells. Based on this concept, the diversity of basic tastes should be defined by the diversity of taste cells in taste buds, which varies among species. PMID:23085625

Multimodal and Multi-tissue Measures of Connectivity Revealed by Joint Independent Component Analysis.

PubMed

Franco, Alexandre R; Ling, Josef; Caprihan, Arvind; Calhoun, Vince D; Jung, Rex E; Heileman, Gregory L; Mayer, Andrew R

2008-12-01

The human brain functions as an efficient system where signals arising from gray matter are transported via white matter tracts to other regions of the brain to facilitate human behavior. However, with a few exceptions, functional and structural neuroimaging data are typically optimized to maximize the quantification of signals arising from a single source. For example, functional magnetic resonance imaging (FMRI) is typically used as an index of gray matter functioning whereas diffusion tensor imaging (DTI) is typically used to determine white matter properties. While it is likely that these signals arising from different tissue sources contain complementary information, the signal processing algorithms necessary for the fusion of neuroimaging data across imaging modalities are still in a nascent stage. In the current paper we present a data-driven method for combining measures of functional connectivity arising from gray matter sources (FMRI resting state data) with different measures of white matter connectivity (DTI). Specifically, a joint independent component analysis (J-ICA) was used to combine these measures of functional connectivity following intensive signal processing and feature extraction within each of the individual modalities. Our results indicate that one of the most predominantly used measures of functional connectivity (activity in the default mode network) is highly dependent on the integrity of white matter connections between the two hemispheres (corpus callosum) and within the cingulate bundles. Importantly, the discovery of this complex relationship of connectivity was entirely facilitated by the signal processing and fusion techniques presented herein and could not have been revealed through separate analyses of both data types as is typically performed in the majority of neuroimaging experiments. We conclude by discussing future applications of this technique to other areas of neuroimaging and examining potential limitations of the methods.

Image Analysis of DNA Fiber and Nucleus in Plants.

PubMed

Ohmido, Nobuko; Wako, Toshiyuki; Kato, Seiji; Fukui, Kiichi

2016-01-01

Advances in cytology have led to the application of a wide range of visualization methods in plant genome studies. Image analysis methods are indispensable tools where morphology, density, and color play important roles in the biological systems. Visualization and image analysis methods are useful techniques in the analyses of the detailed structure and function of extended DNA fibers (EDFs) and interphase nuclei. The EDF is the highest in the spatial resolving power to reveal genome structure and it can be used for physical mapping, especially for closely located genes and tandemly repeated sequences. One the other hand, analyzing nuclear DNA and proteins would reveal nuclear structure and functions. In this chapter, we describe the image analysis protocol for quantitatively analyzing different types of plant genome, EDFs and interphase nuclei.

The effect of mirror therapy integrating functional electrical stimulation on the gait of stroke patients.

PubMed

Ji, Sang-Goo; Cha, Hyun-Gyu; Kim, Myoung-Kwon; Lee, Chang-Ryeol

2014-04-01

[Purpose] The aim of the present study was to examine whether mirror therapy in conjunction with FES in stroke patients can improve gait ability. [Subjects] This study was conducted with 30 subjects who were diagnosed with hemiparesis due to stroke. [Methods] Experimental group I contained 10 subjects who received mirror therapy in conjunction with functional electrical stimulation, experimental group II contained 10 subjects who received mirror therapy, and the control group contained 10 subjects who received a sham therapy. A gait analysis was performed using a three-dimensional motion capture system, which was a real-time tracking device that delivers data in an infrared mode via reflective markers using six cameras. [Results] The results showed a significant difference in gait velocity between groups after the experiment, and post hoc analysis revealed significant differences between experimental group I and the control group and between experimental group II and the control group, respectively. There were also significant differences in step length and stride length between the groups after the experiment, and post hoc analysis revealed significant differences between experimental group I and control group. [Conclusion] The present study showed that mirror therapy in conjunction with FES is more effective for improving gait ability than mirror therapy alone.

Applying an Integrative Framework of Executive Function to Preschoolers With Specific Language Impairment

PubMed Central

Plante, Elena; Doubleday, Kevin

2017-01-01

Purpose The first goal of this research was to compare verbal and nonverbal executive function abilities between preschoolers with and without specific language impairment (SLI). The second goal was to assess the group differences on 4 executive function components in order to determine if the components may be hierarchically related as suggested within a developmental integrative framework of executive function. Method This study included 26 4- and 5-year-olds diagnosed with SLI and 26 typically developing age- and sex-matched peers. Participants were tested on verbal and nonverbal measures of sustained selective attention, working memory, inhibition, and shifting. Results The SLI group performed worse compared with typically developing children on both verbal and nonverbal measures of sustained selective attention and working memory, the verbal inhibition task, and the nonverbal shifting task. Comparisons of standardized group differences between executive function measures revealed a linear increase with the following order: working memory, inhibition, shifting, and sustained selective attention. Conclusion The pattern of results suggests that preschoolers with SLI have deficits in executive functioning compared with typical peers, and deficits are not limited to verbal tasks. A significant linear relationship between group differences across executive function components supports the possibility of a hierarchical relationship between executive function skills. PMID:28724132

Behavioral Treatment and Normal Educational and Intellectual Functioning in Young Autistic Children.

ERIC Educational Resources Information Center

Lovaas, O. Ivar

1987-01-01

Reports the results of behavior modification treatment for two groups of similarly constituted, young autistic children. Pretreatment measures revealed no significant differences between the intensively treated experimental group and the minimally treated control groups. At follow-up, experimental group subjects (N=19) did significantly better…

If Some Doors Close, Others Will Open

ERIC Educational Resources Information Center

Stapel, C.; Lutman, Martha

1974-01-01

Two articles under one title reveal different aspects of folk high schools in the Netherlands. One discusses their primary objective, (the participation of people in social reform), and the diversity of course offerings. The other treats the schools' international functions: cultural exchange (sponsoring bi-national and multi-national seminars),…

Language-Switching Costs in Bilingual Mathematics Learning

ERIC Educational Resources Information Center

Grabner, Roland H.; Saalbach, Henrik; Eckstein, Doris

2012-01-01

Behavioral studies on bilingual learning have revealed cognitive costs (lower accuracy and/or higher processing time) when the language of application differs from the language of learning. The aim of this functional magnetic resonance imaging (fMRI) study was to provide insights into the cognitive underpinnings of these costs (so-called…

The Role of Competence in Children's Creation of Imaginary Friends.

ERIC Educational Resources Information Center

Harter, Susan; Chao, Christine

1992-01-01

The function of children's imaginary friends was investigated from the perspective of perceived competence. Teachers judged children with imaginary friends to be less competent and socially accepted by peers than other children. Children's descriptions of themselves and their imaginary friends revealed significant gender differences in the types…

Dissociated neural processing for decisions in managers and non-managers.

PubMed

Caspers, Svenja; Heim, Stefan; Lucas, Marc G; Stephan, Egon; Fischer, Lorenz; Amunts, Katrin; Zilles, Karl

2012-01-01

Functional neuroimaging studies of decision-making so far mainly focused on decisions under uncertainty or negotiation with other persons. Dual process theory assumes that, in such situations, decision making relies on either a rapid intuitive, automated or a slower rational processing system. However, it still remains elusive how personality factors or professional requirements might modulate the decision process and the underlying neural mechanisms. Since decision making is a key task of managers, we hypothesized that managers, facing higher pressure for frequent and rapid decisions than non-managers, prefer the heuristic, automated decision strategy in contrast to non-managers. Such different strategies may, in turn, rely on different neural systems. We tested managers and non-managers in a functional magnetic resonance imaging study using a forced-choice paradigm on word-pairs. Managers showed subcortical activation in the head of the caudate nucleus, and reduced hemodynamic response within the cortex. In contrast, non-managers revealed the opposite pattern. With the head of the caudate nucleus being an initiating component for process automation, these results supported the initial hypothesis, hinting at automation during decisions in managers. More generally, the findings reveal how different professional requirements might modulate cognitive decision processing.

Characterization of functional trait diversity among Indian cultivated and weedy rice populations

PubMed Central

Rathore, M.; Singh, Raghwendra; Kumar, B.; Chauhan, B. S.

2016-01-01

Weedy rice, a menace in rice growing areas globally, is biosimilar having attributes similar to cultivated and wild rice, and therefore is difficult to manage. A study was initiated to characterize the functional traits of 76 weedy rice populations and commonly grown rice cultivars from different agro-climatic zones for nine morphological, five physiological, and three phenological parameters in a field experiment under an augmented block design. Comparison between weedy and cultivated rice revealed a difference in duration (days) from panicle emergence to heading as the most variable trait and awn length as the least variable one, as evidenced from their coefficients of variation. The results of principal component analysis revealed the first three principal components to represent 47.3% of the total variation, which indicates an important role of transpiration, conductance, leaf-air temperature difference, days to panicle emergence, days to heading, flag leaf length, SPAD (soil-plant analysis development), grain weight, plant height, and panicle length to the diversity in weedy rice populations. The variations existing in weedy rice population are a major reason for its wider adaptability to varied environmental conditions and also a problem while trying to manage it. PMID:27072282

Blending Gelators to Tune Gel Structure and Probe Anion-Induced Disassembly

PubMed Central

Foster, Jonathan A; Edkins, Robert M; Cameron, Gary J; Colgin, Neil; Fucke, Katharina; Ridgeway, Sam; Crawford, Andrew G; Marder, Todd B; Beeby, Andrew; Cobb, Steven L; Steed, Jonathan W

2014-01-01

Blending different low molecular weight gelators (LMWGs) provides a convenient route to tune the properties of a gel and incorporate functionalities such as fluorescence. Blending a series of gelators having a common bis-urea motif, and functionalised with different amino acid-derived end-groups and differing length alkylene spacers is reported. Fluorescent gelators incorporating 1-and 2-pyrenyl moieties provide a probe of the mixed systems alongside structural and morphological data from powder diffraction and electron microscopy. Characterisation of the individual gelators reveals that although the expected α-urea tape motif is preserved, there is considerable variation in the gelation properties, molecular packing, fibre morphology and rheological behaviour. Mixing of the gelators revealed examples in which: 1) the gels formed separate, orthogonal networks maintaining their own packing and morphology, 2) the gels blended together into a single network, either adopting the packing and morphology of one gelator, or 3) a new structure not seen for either of the gelators individually was created. The strong binding of the urea functionalities to anions was exploited as a means of breaking down the gel structure, and the use of fluorescent gel blends provides new insights into anion-mediated gel dissolution. PMID:24302604

Dissociated Neural Processing for Decisions in Managers and Non-Managers

PubMed Central

Caspers, Svenja; Heim, Stefan; Lucas, Marc G.; Stephan, Egon; Fischer, Lorenz; Amunts, Katrin; Zilles, Karl

2012-01-01

Functional neuroimaging studies of decision-making so far mainly focused on decisions under uncertainty or negotiation with other persons. Dual process theory assumes that, in such situations, decision making relies on either a rapid intuitive, automated or a slower rational processing system. However, it still remains elusive how personality factors or professional requirements might modulate the decision process and the underlying neural mechanisms. Since decision making is a key task of managers, we hypothesized that managers, facing higher pressure for frequent and rapid decisions than non-managers, prefer the heuristic, automated decision strategy in contrast to non-managers. Such different strategies may, in turn, rely on different neural systems. We tested managers and non-managers in a functional magnetic resonance imaging study using a forced-choice paradigm on word-pairs. Managers showed subcortical activation in the head of the caudate nucleus, and reduced hemodynamic response within the cortex. In contrast, non-managers revealed the opposite pattern. With the head of the caudate nucleus being an initiating component for process automation, these results supported the initial hypothesis, hinting at automation during decisions in managers. More generally, the findings reveal how different professional requirements might modulate cognitive decision processing. PMID:22927984

Epitaxial growth of pentacene on alkali halide surfaces studied by Kelvin probe force microscopy.

PubMed

Neff, Julia L; Milde, Peter; León, Carmen Pérez; Kundrat, Matthew D; Eng, Lukas M; Jacob, Christoph R; Hoffmann-Vogel, Regina

2014-04-22

In the field of molecular electronics, thin films of molecules adsorbed on insulating surfaces are used as the functional building blocks of electronic devices. Control of the structural and electronic properties of the thin films is required for reliably operating devices. Here, noncontact atomic force and Kelvin probe force microscopies have been used to investigate the growth and electrostatic landscape of pentacene on KBr(001) and KCl(001) surfaces. We have found that, together with molecular islands of upright standing pentacene, a new phase of tilted molecules appears near step edges on KBr. Local contact potential differences (LCPD) have been studied with both Kelvin experiments and density functional theory calculations. Our images reveal that differently oriented molecules display different LCPD and that their value is independent of the number of molecular layers. These results point to the formation of an interface dipole, which may be explained by a partial charge transfer from the pentacene to the surface. Moreover, the monitoring of the evolution of the pentacene islands shows that they are strongly affected by dewetting: Multilayers build up at the expense of monolayers, and in the Kelvin images, previously unknown line defects appear, which reveal the epitaxial growth of pentacene crystals.

Structural genomics reveals EVE as a new ASCH/PUA-related domain

PubMed Central

Bertonati, Claudia; Punta, Marco; Fischer, Markus; Yachdav, Guy; Forouhar, Farhad; Zhou, Weihong; Kuzin, Alexander P.; Seetharaman, Jayaraman; Abashidze, Mariam; Ramelot, Theresa A.; Kennedy, Michael A.; Cort, John R.; Belachew, Adam; Hunt, John F.; Tong, Liang; Montelione, Gaetano T.; Rost, Burkhard

2014-01-01

Summary We report on several proteins recently solved by structural genomics consortia, in particular by the Northeast Structural Genomics consortium (NESG). The proteins considered in this study differ substantially in their sequences but they share a similar structural core, characterized by a pseudobarrel five-stranded beta sheet. This core corresponds to the PUA domain-like architecture in the SCOP database. By connecting sequence information with structural knowledge, we characterize a new subgroup of these proteins that we propose to be distinctly different from previously described PUA domain-like domains such as PUA proper or ASCH. We refer to these newly defined domains as EVE. Although EVE may have retained the ability of PUA domains to bind RNA, the available experimental and computational data suggests that both the details of its molecular function and its cellular function differ from those of other PUA domain-like domains. This study of EVE and its relatives illustrates how the combination of structure and genomics creates new insights by connecting a cornucopia of structures that map to the same evolutionary potential. Primary sequence information alone would have not been sufficient to reveal these evolutionary links. PMID:19191354

Structural Genomics Reveals EVE as a New ASCH/PUA-Related Domain

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

Bertonati, C.; Punta, M; Fischer, M

2008-01-01

We report on several proteins recently solved by structural genomics consortia, in particular by the Northeast Structural Genomics consortium (NESG). The proteins considered in this study differ substantially in their sequences but they share a similar structural core, characterized by a pseudobarrel five-stranded beta sheet. This core corresponds to the PUA domain-like architecture in the SCOP database. By connecting sequence information with structural knowledge, we characterize a new subgroup of these proteins that we propose to be distinctly different from previously described PUA domain-like domains such as PUA proper or ASCH. We refer to these newly defined domains as EVE.more » Although EVE may have retained the ability of PUA domains to bind RNA, the available experimental and computational data suggests that both the details of its molecular function and its cellular function differ from those of other PUA domain-like domains. This study of EVE and its relatives illustrates how the combination of structure and genomics creates new insights by connecting a cornucopia of structures that map to the same evolutionary potential. Primary sequence information alone would have not been sufficient to reveal these evolutionary links.« less

Calibration of Herschel SPIRE FTS observations at different spectral resolutions

NASA Astrophysics Data System (ADS)

Marchili, N.; Hopwood, R.; Fulton, T.; Polehampton, E. T.; Valtchanov, I.; Zaretski, J.; Naylor, D. A.; Griffin, M. J.; Imhof, P.; Lim, T.; Lu, N.; Makiwa, G.; Pearson, C.; Spencer, L.

2017-01-01

The SPIRE Fourier Transform Spectrometer on-board the Herschel Space Observatory had two standard spectral resolution modes for science observations: high resolution (HR) and low resolution (LR), which could also be performed in sequence (H+LR). A comparison of the HR and LR resolution spectra taken in this sequential mode revealed a systematic discrepancy in the continuum level. Analysing the data at different stages during standard pipeline processing demonstrates that the telescope and instrument emission affect HR and H+LR observations in a systematically different way. The origin of this difference is found to lie in the variation of both the telescope and instrument response functions, while it is triggered by fast variation of the instrument temperatures. As it is not possible to trace the evolution of the response functions using housekeeping data from the instrument subsystems, the calibration cannot be corrected analytically. Therefore, an empirical correction for LR spectra has been developed, which removes the systematic noise introduced by the variation of the response functions.

Two novel mutations in the POU1F1 gene generate null alleles through different mechanisms leading to combined pituitary hormone deficiency.

PubMed

Turton, J P; Strom, M; Langham, S; Dattani, M T; Le Tissier, P

2012-03-01

  Mutations in the POU1F1 gene severely affect the development and function of the anterior pituitary gland and lead to combined pituitary hormone deficiency (CPHD).   The clinical and genetic analysis of a patient presenting with CPHD and functional characterization of identified mutations.   We describe a male patient with extreme short stature, learning difficulties, anterior pituitary hypoplasia, secondary hypothyroidism and undetectable prolactin, growth hormone (GH) and insulin-like growth factor 1 (IGF1), with normal random cortisol.   The POU1F1 coding region was amplified by PCR and sequenced; the functional consequence of the mutations was analysed by cell transfection and in vitro assays.   Genetic analysis revealed compound heterozygosity for two novel putative loss of function mutations in POU1F1: a transition at position +3 of intron 1 [IVS1+3nt(A>G)] and a point mutation in exon 6 resulting in a substitution of arginine by tryptophan (R265W). Functional analysis revealed that IVS1+3nt(A>G) results in a reduction in the correctly spliced POU1F1 mRNA, which could be corrected by mutations of the +4, +5 and +6 nucleotides. Analysis of POU1F1(R265W) revealed complete loss of function resulting from severely reduced protein stability.   Combined pituitary hormone deficiency in this patient is caused by loss of POU1F1 function by two novel mechanisms, namely aberrant splicing (IVS1+3nt (A>G) and protein instability (R265W). Identification of the genetic basis of CPHD enabled the cessation of hydrocortisone therapy without the need for further assessment for evolving endocrinopathy. © 2012 Blackwell Publishing Ltd.

Exploring the Relationship of Organizational Culture and Implicit Leadership Theory to Performance Differences in the Nuclear and Fossil Energy Industry

NASA Astrophysics Data System (ADS)

Cravey, Kristopher J.

Notable performance differences exist between nuclear and fossil power generation plants in areas such as safety, outage duration efficiency, and capacity factor. This study explored the relationship of organizational culture and implicit leadership theory to these performance differences. A mixed methods approach consisting of quantitative instruments, namely the Organizational Culture Assessment Instrument and the GLOBE Leadership Scales, and qualitative interviews were used in this study. Subjects were operations middle managers in a U.S. energy company that serves nuclear or fossil power plants. Results from the quantitative instruments revealed no differences between nuclear and fossil groups in regards to organizational culture types and implicit leadership theories. However, the qualitative results did reveal divergence between the two groups in regards to what is valued in the organization and how that drives behaviors and decision making. These organizational phenomenological differences seem to explain why performance differences exist between nuclear and fossil plants because, ultimately, they affect how the organization functions.

Genome-wide investigation and expression profiling of APX gene family in Gossypium hirsutum provide new insights in redox homeostasis maintenance during different fiber development stages.

PubMed

Tao, Chengcheng; Jin, Xiang; Zhu, Liping; Xie, Quanliang; Wang, Xuchu; Li, Hongbin

2018-06-01

Ascorbate peroxidase (APX) is a member of heme-containing peroxidases which catalyze the H 2 O 2 -dependent oxidation of a wide range of substrates in plants and animals. As is known, H 2 O 2 acts as a signaling molecule in the regulation of fiber development. Our previous work reported that ascorbate peroxidase 1 (GhAPX1) was important for cotton fiber elongation. However, knowledge about APX gene family members and their evolutionary and functional characteristics in cotton is limited. Here, we report 26 GhAPX genes by genome-wide investigation of tetraploid cotton Gossypium hirsutum. Phylogenetic and gene structure analyses classified these APX members into five clades and syntenic analysis suggested two duplication events. Expression profiling of the 26 APXs revealed that ten members are expressed in cotton fibers. Notably, GhAPX10A, GhAPX10D, GhAPX12A, and GhAPX12D showed high expression levels in 30-day fiber, while GhAPX1A/D, GhAPX3A/D, and GhAPX6A/D showed very low expression levels. The enzyme activity and H 2 O 2 content assays revealed that cotton fiber kept high enzyme activity and the lowest H 2 O 2 level in 30-day fibers, indicating that other than GhAPX1, the newly reported APX members are responsible for the reactive oxygen species homeostasis in the cotton fiber maturation stages. Expression profiling of ten fiber-expressed APXs after phytohormone treatments revealed their regulation patterns by different stimuli, suggesting that GhAPX1, GhAPX12A, and GhAPX12D are responsible to most phytohormone treatments. Our data provided evolutionary and functional information of GhAPX gene family members and revealed that different members are responsible to redox homeostasis during different cotton fiber development stages.

Functional relevance of interindividual differences in temporal lobe callosal pathways: a DTI tractography study.

PubMed

Westerhausen, René; Grüner, Renate; Specht, Karsten; Hugdahl, Kenneth

2009-06-01

The midsagittal corpus callosum is topographically organized, that is, with regard to their cortical origin several subtracts can be distinguished within the corpus callosum that belong to specific functional brain networks. Recent diffusion tensor tractography studies have also revealed remarkable interindividual differences in the size and exact localization of these tracts. To examine the functional relevance of interindividual variability in callosal tracts, 17 right-handed male participants underwent structural and diffusion tensor magnetic resonance imaging. Probabilistic tractography was carried out to identify the callosal subregions that interconnect left and right temporal lobe auditory processing areas, and the midsagittal size of this tract was seen as indicator of the (anatomical) strength of this connection. Auditory information transfer was assessed applying an auditory speech perception task with dichotic presentations of consonant-vowel syllables (e.g., /ba-ga/). The frequency of correct left ear reports in this task served as a functional measure of interhemispheric transfer. Statistical analysis showed that a stronger anatomical connection between the superior temporal lobe areas supports a better information transfer. This specific structure-function association in the auditory modality supports the general notion that interindividual differences in callosal topography possess functional relevance.

Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease.

PubMed

Torres, Matthew P; Dewhurst, Henry; Sundararaman, Niveda

2016-11-01

Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable body of potential regulatory elements that impact hundreds of different biological processes important in eukaryotic biology and human health. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease*

PubMed Central

Dewhurst, Henry; Sundararaman, Niveda

2016-01-01

Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable body of potential regulatory elements that impact hundreds of different biological processes important in eukaryotic biology and human health. PMID:27697855

Interpreting and Utilising Intersubject Variability in Brain Function.

PubMed

Seghier, Mohamed L; Price, Cathy J

2018-06-01

We consider between-subject variance in brain function as data rather than noise. We describe variability as a natural output of a noisy plastic system (the brain) where each subject embodies a particular parameterisation of that system. In this context, variability becomes an opportunity to: (i) better characterise typical versus atypical brain functions; (ii) reveal the different cognitive strategies and processing networks that can sustain similar tasks; and (iii) predict recovery capacity after brain damage by taking into account both damaged and spared processing pathways. This has many ramifications for understanding individual learning preferences and explaining the wide differences in human abilities and disabilities. Understanding variability boosts the translational potential of neuroimaging findings, in particular in clinical and educational neuroscience. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Effectiveness of Social Behaviors for Autonomous Wheelchair Robot to Support Elderly People in Japan

PubMed Central

Shiomi, Masahiro; Iio, Takamasa; Kamei, Koji; Sharma, Chandraprakash; Hagita, Norihiro

2015-01-01

We developed a wheelchair robot to support the movement of elderly people and specifically implemented two functions to enhance their intention to use it: speaking behavior to convey place/location related information and speed adjustment based on individual preferences. Our study examines how the evaluations of our wheelchair robot differ when compared with human caregivers and a conventional autonomous wheelchair without the two proposed functions in a moving support context. 28 senior citizens participated in the experiment to evaluate three different conditions. Our measurements consisted of questionnaire items and the coding of free-style interview results. Our experimental results revealed that elderly people evaluated our wheelchair robot higher than the wheelchair without the two functions and the human caregivers for some items. PMID:25993038

Individual differences in children's innovative problem-solving are not predicted by divergent thinking or executive functions

PubMed Central

2016-01-01

Recent studies of children's tool innovation have revealed that there is variation in children's success in middle-childhood. In two individual differences studies, we sought to identify personal characteristics that might predict success on an innovation task. In Study 1, we found that although measures of divergent thinking were related to each other they did not predict innovation success. In Study 2, we measured executive functioning including: inhibition, working memory, attentional flexibility and ill-structured problem-solving. None of these measures predicted innovation, but, innovation was predicted by children's performance on a receptive vocabulary scale that may function as a proxy for general intelligence. We did not find evidence that children's innovation was predicted by specific personal characteristics. PMID:26926280

Extreme MHC class I diversity in the sedge warbler (Acrocephalus schoenobaenus); selection patterns and allelic divergence suggest that different genes have different functions.

PubMed

Biedrzycka, Aleksandra; O'Connor, Emily; Sebastian, Alvaro; Migalska, Magdalena; Radwan, Jacek; Zając, Tadeusz; Bielański, Wojciech; Solarz, Wojciech; Ćmiel, Adam; Westerdahl, Helena

2017-07-05

Recent work suggests that gene duplications may play an important role in the evolution of immunity genes. Passerine birds, and in particular Sylvioidea warblers, have highly duplicated major histocompatibility complex (MHC) genes, which are key in immunity, compared to other vertebrates. However, reasons for this high MHC gene copy number are yet unclear. High-throughput sequencing (HTS) allows MHC genotyping even in individuals with extremely duplicated genes. This HTS data can reveal evidence of selection, which may help to unravel the putative functions of different gene copies, i.e. neofunctionalization. We performed exhaustive genotyping of MHC class I in a Sylvioidea warbler, the sedge warbler, Acrocephalus schoenobaenus, using the Illumina MiSeq technique on individuals from a wild study population. The MHC diversity in 863 genotyped individuals by far exceeds that of any other bird species described to date. A single individual could carry up to 65 different alleles, a large proportion of which are expressed (transcribed). The MHC alleles were of three different lengths differing in evidence of selection, diversity and divergence within our study population. Alleles without any deletions and alleles containing a 6 bp deletion showed characteristics of classical MHC genes, with evidence of multiple sites subject to positive selection and high sequence divergence. In contrast, alleles containing a 3 bp deletion had no sites subject to positive selection and had low divergence. Our results suggest that sedge warbler MHC alleles that either have no deletion, or contain a 6 bp deletion, encode classical antigen presenting MHC molecules. In contrast, MHC alleles containing a 3 bp deletion may encode molecules with a different function. This study demonstrates that highly duplicated MHC genes can be characterised with HTS and that selection patterns can be useful for revealing neofunctionalization. Importantly, our results highlight the need to consider the putative function of different MHC genes in future studies of MHC in relation to disease resistance and fitness.

Revealing protein functions based on relationships of interacting proteins and GO terms.

PubMed

Teng, Zhixia; Guo, Maozu; Liu, Xiaoyan; Tian, Zhen; Che, Kai

2017-09-20

In recent years, numerous computational methods predicted protein function based on the protein-protein interaction (PPI) network. These methods supposed that two proteins share the same function if they interact with each other. However, it is reported by recent studies that the functions of two interacting proteins may be just related. It will mislead the prediction of protein function. Therefore, there is a need for investigating the functional relationship between interacting proteins. In this paper, the functional relationship between interacting proteins is studied and a novel method, called as GoDIN, is advanced to annotate functions of interacting proteins in Gene Ontology (GO) context. It is assumed that the functional difference between interacting proteins can be expressed by semantic difference between GO term and its relatives. Thus, the method uses GO term and its relatives to annotate the interacting proteins separately according to their functional roles in the PPI network. The method is validated by a series of experiments and compared with the concerned method. The experimental results confirm the assumption and suggest that GoDIN is effective on predicting functions of protein. This study demonstrates that: (1) interacting proteins are not equal in the PPI network, and their function may be same or similar, or just related; (2) functional difference between interacting proteins can be measured by their degrees in the PPI network; (3) functional relationship between interacting proteins can be expressed by relationship between GO term and its relatives.

Aging and strategic retrieval in a cued-recall test: the role of executive functions and fluid intelligence.

PubMed

Taconnat, Laurence; Clarys, David; Vanneste, Sandrine; Bouazzaoui, Badiâa; Isingrini, Michel

2007-06-01

Cued-recall in episodic memory was investigated in relation to low and high cognitive support at retrieval, executive function level and fluid intelligence level in 81 healthy adults divided first into two age groups (young and elderly adults). The first analyses showed that age-related differences were greater when a low cognitive support was provided to recall the words. An individual index of loss of performance when the number of cues was decreased was then calculated. Hierarchical regression analysis revealed that the executive functions measure (perseverative errors on the Wisconsin Card Sorting Test) was a better candidate than the fluid intelligence measure (Cattell's culture fair test) to account for the age-related variance of the size of performance loss. These findings suggest that age differences in implementing strategic retrieval may be mainly due to a decline in executive functions.

Functional Smiles: Tools for Love, Sympathy, and War.

PubMed

Rychlowska, Magdalena; Jack, Rachael E; Garrod, Oliver G B; Schyns, Philippe G; Martin, Jared D; Niedenthal, Paula M

2017-09-01

A smile is the most frequent facial expression, but not all smiles are equal. A social-functional account holds that smiles of reward, affiliation, and dominance serve basic social functions, including rewarding behavior, bonding socially, and negotiating hierarchy. Here, we characterize the facial-expression patterns associated with these three types of smiles. Specifically, we modeled the facial expressions using a data-driven approach and showed that reward smiles are symmetrical and accompanied by eyebrow raising, affiliative smiles involve lip pressing, and dominance smiles are asymmetrical and contain nose wrinkling and upper-lip raising. A Bayesian-classifier analysis and a detection task revealed that the three smile types are highly distinct. Finally, social judgments made by a separate participant group showed that the different smile types convey different social messages. Our results provide the first detailed description of the physical form and social messages conveyed by these three types of functional smiles and document the versatility of these facial expressions.

Combined Secretomics and Transcriptomics Revealed Cancer-Derived GDF15 is Involved in Diffuse-Type Gastric Cancer Progression and Fibroblast Activation.

PubMed

Ishige, Takayuki; Nishimura, Motoi; Satoh, Mamoru; Fujimoto, Mai; Fukuyo, Masaki; Semba, Toshihisa; Kado, Sayaka; Tsuchida, Sachio; Sawai, Setsu; Matsushita, Kazuyuki; Togawa, Akira; Matsubara, Hisahiro; Kaneda, Atsushi; Nomura, Fumio

2016-02-19

Gastric cancer is classified into two subtypes, diffuse and intestinal. The diffuse-type gastric cancer (DGC) has poorer prognosis, and the molecular pathology is not yet fully understood. The purpose of this study was to identify functional secreted molecules involved in DGC progression. We integrated the secretomics of six gastric cancer cell lines and gene expression analysis of gastric cancer tissues with publicly available microarray data. Hierarchical clustering revealed characteristic gene expression differences between diffuse- and intestinal-types. GDF15 was selected as a functional secreted molecule owing to high expression only in fetal tissues. Protein expression of GDF15 was higher in DGC cell lines and tissues. Serum levels of GDF15 were significant higher in DGC patients as compared with healthy individuals and chronic gastritis patients, and positively correlated with wall invasion and lymph node metastasis. In addition, the stimulation of GDF15 on NIH3T3 fibroblast enhanced proliferation and up-regulated expression of extracellular matrix genes, which were similar to TGF-β stimulation. These results indicate that GDF15 contributes to fibroblast activation. In conclusion, this study revealed that GDF15 may be a novel functional secreted molecule for DGC progression, possibly having important roles for cancer progression via the affecting fibroblast function, as well as TGF-β.

Ab initio study of gold-doped zigzag graphene nanoribbons

NASA Astrophysics Data System (ADS)

Srivastava, Pankaj; Dhar, Subhra; Jaiswal, Neeraj K.

2014-12-01

The electronic transport properties of zigzag graphene nanoribbons (ZGNRs) through covalent functionalization of gold (Au) atoms is investigated by using non-equilibrium Green's function combined with density functional theory. It is revealed that the electronic properties of Au-doped ZGNRs vary significantly due to spin and its non-inclusion. We find that the DOS profiles of Au-adsorbed ZGNR due to spin reveal very less number of states available for conduction, whereas non-inclusion of spin results in higher DOS across the Fermi level. Edge Au-doped ribbons exhibit stable structure and are energetically more favorable than the center Au-doped ZGNRs. Though the chemical interaction at the ZGNR-Au interface modifies the Fermi level, Au-adsorbed ZGNR reveals semimetallic properties. A prominent qualitative change of the I-V curve from linear to nonlinear is observed as the Au atom shifts from center toward the edges of the ribbon. Number of peaks present near the Fermi level ensures conductance channels available for charge transport in case of Au-center-substituted ZGNR. We predict semimetallic nature of the Au-adsorbed ZGNR with a high DOS peak distributed over a narrow energy region at the Fermi level and fewer conductance channels. Our calculations for the magnetic properties predict that Au functionalization leads to semiconducting nature with different band gaps for spin up and spin down. The outcomes are compared with the experimental and theoretical results available for other materials.

Functional ("psychogenic") amnesia.

PubMed

Brandt, Jason; Van Gorp, Wilfred G

2006-07-01

Patients who present with severely impaired memory functioning without a discernable neurological cause typically have experienced one or more severely stressful life events. These patients, who are described as having "psychogenic" or "dissociative" amnesia, typically differ from patients with the neurologic amnestic syndrome in that memory for their personal life histories is much more severely affected than is their ability to learn and retain new information; that is, they have isolated retrograde amnesia. Recent cognitive and brain imaging research has begun to reveal some of the cerebral mechanisms underlying functional amnesia, but this disorder remains best conceptualized as a relatively rare form of illness-simulating behavior rather than a disease. Neuropsychological assessment is often useful in revealing the circumscribed nature of the patient's performance deficits, the spared functions that can be brought to bear in rehabilitation, and the emotional disorders requiring psychiatric treatment. Controlled treatment trials are nonexistent, but case reports suggest that supportive psychotherapy, systematic relaxation training, hypnosis, and sedative/anxiolytic medications are useful in facilitating recovery. These treatments are often combined with a psychoeducational approach that essentially reteaches the patient his or her life story.

A poly(acrylonitrile)-functionalized porous aromatic framework synthesized by atom-transfer radical polymerization for the extraction of uranium from seawater

DOE PAGES

Yue, Yanfeng; Zhang, Chenxi; Tang, Qing; ...

2015-10-30

In order to ensure a sustainable reserve of fuel for nuclear power generation, tremendous research efforts have been devoted to developing advanced sorbent materials for extracting uranium from seawater. In this work, a porous aromatic framework (PAF) was surface-functionalized with poly(acrylonitrile) through atom-transfer radical polymerization (ATRP). Batches of this adsorbent were conditioned with potassium hydroxide (KOH) at room temperature or 80 °C prior to contact with a uranium-spiked seawater simulant, with minimal differences in uptake observed as a function of conditioning temperature. A maximum capacity of 4.81 g-U/kg-ads was obtained following 42 days contact with uranium-spiked filtered environmental seawater, whichmore » demonstrates a comparable adsorption rate. A kinetic investigation revealed extremely rapid uranyl uptake, with more than 80% saturation reached within 14 days. Furthermore, relying on the semiordered structure of the PAF adsorbent, density functional theory (DFT) calculations reveal cooperative interactions between multiple adsorbent groups yield a strong driving force for uranium binding.« less

Structural And Functional Studies of ALIX Interactions With YPXnL Late Domains of HIV-1 And EIAV

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

Zhai, Q.; Fisher, R.D.; Chung, H.-Y.

2009-05-28

Retrovirus budding requires short peptide motifs (late domains) located within the viral Gag protein that function by recruiting cellular factors. The YPX{sub n}L late domains of HIV and other lentiviruses recruit the protein ALIX (also known as AIP1), which also functions in vesicle formation at the multivesicular body and in the abscission stage of cytokinesis. Here, we report the crystal structures of ALIX in complex with the YPX{sub n}L late domains from HIV-1 and EIAV. The two distinct late domains bind at the same site on the ALIX V domain but adopt different conformations that allow them to make equivalentmore » contacts. Binding studies and functional assays verified the importance of key interface residues and revealed that binding affinities are tuned by context-dependent effects. These results reveal how YPX{sub n}L late domains recruit ALIX to facilitate virus budding and how ALIX can bind YPX{sub n}L sequences with both n = 1 and n = 3.« less

Using Ecological Momentary Assessment to Investigate Short-Term Variations in Sexual Functioning in a Sample of Peri-Menopausal Women from Iran

PubMed Central

Pakpour, Amir H.; Yekaninejad, Mir Saeed; Pallich, Gianandrea; Burri, Andrea

2015-01-01

The investigation of short-term changes in female sexual functioning has received little attention so far. The aims of the study were to gain empirical knowledge on within-subject and within- and across-variable fluctuations in women’s sexual functioning over time. More specifically, to investigate the stability of women´s self-reported sexual functioning and the moderating effects of contextual and interpersonal factors. A convenience sample of 206 women, recruited across eight Health care Clinics in Rasht, Iran. Ecological momentary assessment was used to examine fluctuations of sexual functioning over a six week period. A shortened version of the Female Sexual Function Index (FSFI) was applied to assess sexual functioning. Self-constructed questions were included to assess relationship satisfaction, partner’s sexual performance and stress levels. Mixed linear two-level model analyses revealed a link between orgasm and relationship satisfaction (Beta = 0.125, P = 0.074) with this link varying significantly between women. Analyses further revealed a significant negative association between stress and all six domains of women’s sexual functioning. Women not only reported differing levels of stress over the course of the assessment period, but further differed from each other in how much stress they experienced and how much this influenced their sexual response. Orgasm and sexual satisfaction were both significantly associated with all other domains of sexual function (P<0.001). And finally, a link between partner performance and all domains of women`s sexual functioning (P<0.001) could be detected. Except for lubrication (P = 0.717), relationship satisfaction had a significant effect on all domains of the sexual response (P<0.001). Overall, our findings support the new group of criteria introduced in the DSM-5, called “associated features” such as partner factors and relationship factors. Consideration of these criteria is important and necessary for clinicians when diagnosing FSD. PMID:25692787

Increased sensitivity to age-related differences in brain functional connectivity during continuous multiple object tracking compared to resting-state.

PubMed

Dørum, Erlend S; Kaufmann, Tobias; Alnæs, Dag; Andreassen, Ole A; Richard, Geneviève; Kolskår, Knut K; Nordvik, Jan Egil; Westlye, Lars T

2017-03-01

Age-related differences in cognitive agility vary greatly between individuals and cognitive functions. This heterogeneity is partly mirrored in individual differences in brain network connectivity as revealed using resting-state functional magnetic resonance imaging (fMRI), suggesting potential imaging biomarkers for age-related cognitive decline. However, although convenient in its simplicity, the resting state is essentially an unconstrained paradigm with minimal experimental control. Here, based on the conception that the magnitude and characteristics of age-related differences in brain connectivity is dependent on cognitive context and effort, we tested the hypothesis that experimentally increasing cognitive load boosts the sensitivity to age and changes the discriminative network configurations. To this end, we obtained fMRI data from younger (n=25, mean age 24.16±5.11) and older (n=22, mean age 65.09±7.53) healthy adults during rest and two load levels of continuous multiple object tracking (MOT). Brain network nodes and their time-series were estimated using independent component analysis (ICA) and dual regression, and the edges in the brain networks were defined as the regularized partial temporal correlations between each of the node pairs at the individual level. Using machine learning based on a cross-validated regularized linear discriminant analysis (rLDA) we attempted to classify groups and cognitive load from the full set of edge-wise functional connectivity indices. While group classification using resting-state data was highly above chance (approx. 70% accuracy), functional connectivity (FC) obtained during MOT strongly increased classification performance, with 82% accuracy for the young and 95% accuracy for the old group at the highest load level. Further, machine learning revealed stronger differentiation between rest and task in young compared to older individuals, supporting the notion of network dedifferentiation in cognitive aging. Task-modulation in edgewise FC was primarily observed between attention- and sensorimotor networks; with decreased negative correlations between attention- and default mode networks in older adults. These results demonstrate that the magnitude and configuration of age-related differences in brain functional connectivity are partly dependent on cognitive context and load, which emphasizes the importance of assessing brain connectivity differences across a range of cognitive contexts beyond the resting-state. Copyright © 2017 Elsevier Inc. All rights reserved.

Combined Metabolomic and Genetic Approaches Reveal a Link between the Polyamine Pathway and Albumin 2 in Developing Pea Seeds1[W][OA

PubMed Central

Vigeolas, Helene; Chinoy, Catherine; Zuther, Ellen; Blessington, Bernard; Geigenberger, Peter; Domoney, Claire

2008-01-01

Several legume seed proteins that are potentially allergenic, poorly digested by farm animals, and/or have undesirable functional properties, have been described. One of these is the albumin protein in pea (Pisum sativum) called PA2. A naturally occurring mutant line that lacks PA2 has been exploited in studies to determine the biological function of this nonstorage protein in seed development. The mutant, which has a small seed, a tall plant phenotype, and lacks most of the PA2-encoding genes, has been crossed with a standard cultivar, ‘Birte,’ which contains PA2 to give rise to a recombinant inbred (RI) population. An F3 line carrying the mutation and having a short plant phenotype has been used to generate backcross (BC) lines with ‘Birte.’ Despite having a lower albumin content, seeds from the mutant parent and RI lines lacking PA2 have an equivalent or higher seed nitrogen content. Metabolite profiling of seeds revealed major differences in amino acid composition and polyamine content in the two parent lines. This was investigated further in BC lines, where the effects of differences in seed size and plant height between the two parents were eliminated. Here, differences in polyamine synthesis were maintained as was a difference in total seed protein between the BC line lacking PA2 and ‘Birte.’ Analysis of enzyme activities in the pathways of polyamine synthesis revealed that the differences in spermidine content were attributable to changes in the overall activities of spermidine synthase and arginine decarboxylase. Although the genes encoding spermidine synthase and PA2 both localized to the pea linkage group I, the two loci were shown not to be closely linked and to have recombined in the BC lines. A distinct locus on linkage group III contains a gene that is related to PA2 but expressed predominantly in flowers. The results provide evidence for a role of PA2 in regulating polyamine metabolism, which has important functions in development, metabolism, and stress responses in plants. PMID:18024559

Health-related quality of life results from the PRODIGE 5/ACCORD 17 randomised trial of FOLFOX versus fluorouracil-cisplatin regimen in oesophageal cancer.

PubMed

Bascoul-Mollevi, C; Gourgou, S; Galais, M-P; Raoul, J-L; Bouché, O; Douillard, J-Y; Adenis, A; Etienne, P-L; Juzyna, B; Bedenne, L; Conroy, T

2017-10-01

A recent prospective randomised trial did not reveal significant differences in median progression-free survival between two chemoradiotherapy (CRT) regimens for inoperable non-metastatic oesophageal cancer patients. This secondary analysis aimed to describe the impact of CRT on health-related quality of life (HRQOL), physical functioning, dysphagia, fatigue and pain and to evaluate whether baseline HRQOL domains can predict overall survival. A total of 267 patients were randomly assigned to receive with 50 Gy of radiotherapy in 25 fractions six cycles of FOLFOX or four cycles of fluorouracil and cisplatin on day 1. HRQOL was prospectively assessed using the European Organization for Research and Treatment of Cancer Core Quality of Life Questionnaire version 3.0 with the oesophageal cancer module (QLQ-OES18). Both groups showed high baseline compliance. Subsequently, compliance reduced to 41% at the 6-month follow-up. Baseline HRQOL scores showed no statistical differences between treatment arms. During treatment, both groups exhibited lower physical and social functioning and increased fatigue and dyspnoea, although dysphagia moderately improved in the fluorouracil-cisplatin arm only (p = 0.047). During follow-up, HRQOL scores revealed no significant differences between chemotherapy regimens. Linear mixed model exhibited a treatment-by-time interaction effect for dysphagia (p = 0.017) with a greater decrease in dysphagia in the fluorouracil-cisplatin group. Time until definitive deterioration analysis showed no significant differences in global HRQOL, functional or main symptom domains. However, time until definitive deterioration was significantly longer for the fluorouracil and cisplatin arm compared with FOLFOX for appetite loss (p = 0.002), QLQ-OES-18 pain (p = 0.008), trouble swallowing saliva (p = 0.011) and trouble talking (p = 0.020). Analyses of HRQOL scores revealed no statistically significant differences between patients with inoperable non-metastatic oesophageal cancer treated by FOLFOX versus those treated with a fluorouracil-cisplatin regimen as part of definitive CRT. Copyright © 2017 Elsevier Ltd. All rights reserved.

Expression atlas and comparative coexpression network analyses reveal important genes involved in the formation of lignified cell wall in Brachypodium distachyon.

PubMed

Sibout, Richard; Proost, Sebastian; Hansen, Bjoern Oest; Vaid, Neha; Giorgi, Federico M; Ho-Yue-Kuang, Severine; Legée, Frédéric; Cézart, Laurent; Bouchabké-Coussa, Oumaya; Soulhat, Camille; Provart, Nicholas; Pasha, Asher; Le Bris, Philippe; Roujol, David; Hofte, Herman; Jamet, Elisabeth; Lapierre, Catherine; Persson, Staffan; Mutwil, Marek

2017-08-01

While Brachypodium distachyon (Brachypodium) is an emerging model for grasses, no expression atlas or gene coexpression network is available. Such tools are of high importance to provide insights into the function of Brachypodium genes. We present a detailed Brachypodium expression atlas, capturing gene expression in its major organs at different developmental stages. The data were integrated into a large-scale coexpression database ( www.gene2function.de), enabling identification of duplicated pathways and conserved processes across 10 plant species, thus allowing genome-wide inference of gene function. We highlight the importance of the atlas and the platform through the identification of duplicated cell wall modules, and show that a lignin biosynthesis module is conserved across angiosperms. We identified and functionally characterised a putative ferulate 5-hydroxylase gene through overexpression of it in Brachypodium, which resulted in an increase in lignin syringyl units and reduced lignin content of mature stems, and led to improved saccharification of the stem biomass. Our Brachypodium expression atlas thus provides a powerful resource to reveal functionally related genes, which may advance our understanding of important biological processes in grasses. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Identifying enhanced cortico-basal ganglia loops associated with prolonged dance training

PubMed Central

Li, Gujing; He, Hui; Huang, Mengting; Zhang, Xingxing; Lu, Jing; Lai, Yongxiu; Luo, Cheng; Yao, Dezhong

2015-01-01

Studies have revealed that prolonged, specialized training combined with higher cognitive conditioning induces enhanced brain alternation. In particular, dancers with long-term dance experience exhibit superior motor control and integration with their sensorimotor networks. However, little is known about the functional connectivity patterns of spontaneous intrinsic activities in the sensorimotor network of dancers. Our study examined the functional connectivity density (FCD) of dancers with a mean period of over 10 years of dance training in contrast with a matched non-dancer group without formal dance training using resting-state fMRI scans. FCD was mapped and analyzed, and the functional connectivity (FC) analyses were then performed based on the difference of FCD. Compared to the non-dancers, the dancers exhibited significantly increased FCD in the precentral gyri, postcentral gyri and bilateral putamen. Furthermore, the results of the FC analysis revealed enhanced connections between the middle cingulate cortex and the bilateral putamen and between the precentral and the postcentral gyri. All findings indicated an enhanced functional integration in the cortico-basal ganglia loops that govern motor control and integration in dancers. These findings might reflect improved sensorimotor function for the dancers consequent to long-term dance training. PMID:26035693

Individual Differences Reveal Correlates of Hidden Hearing Deficits

PubMed Central

Masud, Salwa; Mehraei, Golbarg; Verhulst, Sarah; Shinn-Cunningham, Barbara G.

2015-01-01

Clinical audiometry has long focused on determining the detection thresholds for pure tones, which depend on intact cochlear mechanics and hair cell function. Yet many listeners with normal hearing thresholds complain of communication difficulties, and the causes for such problems are not well understood. Here, we explore whether normal-hearing listeners exhibit such suprathreshold deficits, affecting the fidelity with which subcortical areas encode the temporal structure of clearly audible sound. Using an array of measures, we evaluated a cohort of young adults with thresholds in the normal range to assess both cochlear mechanical function and temporal coding of suprathreshold sounds. Listeners differed widely in both electrophysiological and behavioral measures of temporal coding fidelity. These measures correlated significantly with each other. Conversely, these differences were unrelated to the modest variation in otoacoustic emissions, cochlear tuning, or the residual differences in hearing threshold present in our cohort. Electroencephalography revealed that listeners with poor subcortical encoding had poor cortical sensitivity to changes in interaural time differences, which are critical for localizing sound sources and analyzing complex scenes. These listeners also performed poorly when asked to direct selective attention to one of two competing speech streams, a task that mimics the challenges of many everyday listening environments. Together with previous animal and computational models, our results suggest that hidden hearing deficits, likely originating at the level of the cochlear nerve, are part of “normal hearing.” PMID:25653371

Mapping causal functional contributions derived from the clinical assessment of brain damage after stroke

PubMed Central

Zavaglia, Melissa; Forkert, Nils D.; Cheng, Bastian; Gerloff, Christian; Thomalla, Götz; Hilgetag, Claus C.

2015-01-01

Lesion analysis reveals causal contributions of brain regions to mental functions, aiding the understanding of normal brain function as well as rehabilitation of brain-damaged patients. We applied a novel lesion inference technique based on game theory, Multi-perturbation Shapley value Analysis (MSA), to a large clinical lesion dataset. We used MSA to analyze the lesion patterns of 148 acute stroke patients together with their neurological deficits, as assessed by the National Institutes of Health Stroke Scale (NIHSS). The results revealed regional functional contributions to essential behavioral and cognitive functions as reflected in the NIHSS, particularly by subcortical structures. There were also side specific differences of functional contributions between the right and left hemispheric brain regions which may reflect the dominance of the left hemispheric syndrome aphasia in the NIHSS. Comparison of MSA to established lesion inference methods demonstrated the feasibility of the approach for analyzing clinical data and indicated its capability for objectively inferring functional contributions from multiple injured, potentially interacting sites, at the cost of having to predict the outcome of unknown lesion configurations. The analysis of regional functional contributions to neurological symptoms measured by the NIHSS contributes to the interpretation of this widely used standardized stroke scale in clinical practice as well as clinical trials and provides a first approximation of a ‘map of stroke’. PMID:26448908

Mapping causal functional contributions derived from the clinical assessment of brain damage after stroke.

PubMed

Zavaglia, Melissa; Forkert, Nils D; Cheng, Bastian; Gerloff, Christian; Thomalla, Götz; Hilgetag, Claus C

2015-01-01

Lesion analysis reveals causal contributions of brain regions to mental functions, aiding the understanding of normal brain function as well as rehabilitation of brain-damaged patients. We applied a novel lesion inference technique based on game theory, Multi-perturbation Shapley value Analysis (MSA), to a large clinical lesion dataset. We used MSA to analyze the lesion patterns of 148 acute stroke patients together with their neurological deficits, as assessed by the National Institutes of Health Stroke Scale (NIHSS). The results revealed regional functional contributions to essential behavioral and cognitive functions as reflected in the NIHSS, particularly by subcortical structures. There were also side specific differences of functional contributions between the right and left hemispheric brain regions which may reflect the dominance of the left hemispheric syndrome aphasia in the NIHSS. Comparison of MSA to established lesion inference methods demonstrated the feasibility of the approach for analyzing clinical data and indicated its capability for objectively inferring functional contributions from multiple injured, potentially interacting sites, at the cost of having to predict the outcome of unknown lesion configurations. The analysis of regional functional contributions to neurological symptoms measured by the NIHSS contributes to the interpretation of this widely used standardized stroke scale in clinical practice as well as clinical trials and provides a first approximation of a 'map of stroke'.

Functional connectivity pattern during rest within the episodic memory network in association with episodic memory performance in bipolar disorder.

PubMed

Oertel-Knöchel, Viola; Reinke, Britta; Matura, Silke; Prvulovic, David; Linden, David E J; van de Ven, Vincent

2015-02-28

In this study, we sought to examine the intrinsic functional organization of the episodic memory network during rest in bipolar disorder (BD). The previous work suggests that deficits in intrinsic functional connectivity may account for impaired memory performance. We hypothesized that regions involved in episodic memory processing would reveal aberrant functional connectivity in patients with bipolar disorder. We examined 21 patients with BD and 21 healthy matched controls who underwent functional magnetic resonance imaging (fMRI) during a resting condition. We did a seed-based functional connectivity analysis (SBA), using the regions of the episodic memory network that showed a significantly different activation pattern during task-related fMRI as seeds. The functional connectivity scores (FC) were further correlated with episodic memory task performance. Our results revealed decreased FC scores within frontal areas and between frontal and temporal/hippocampal/limbic regions in BD patients in comparison with controls. We observed higher FC in BD patients compared with controls between frontal and limbic regions. The decrease in fronto-frontal functional connectivity in BD patients showed a significant positive association with episodic memory performance. The association between task-independent dysfunctional frontal-limbic FC and episodic memory performance may be relevant for current pathophysiological models of the disease. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Symptomatology of recurrent low back pain in nursing and administrative professions

PubMed Central

Läubli, Thomas; Hodler, Juerg; Klipstein, Andreas

2007-01-01

The aim of the present study was to explore if (a) recurrent low back pain (LBP) has different symptomatologies in cases from occupations with predominantly sitting postures compared to cases from occupations involving dynamic postures and frequent lifting and (b) if in the two occupational groups, different factors were associated with the presence of recurrent LBP. Hundred and eleven female subjects aged between 45 and 62 years with a long-standing occupation either in administrative or nursing professions, with and without recurrent LBP were examined. An extensive evaluation of six areas of interest (pain and disability, clinical examination, functional tests, MR examination, physical and psychosocial workplace factors) was performed. The variables from the six areas of interest were analyzed for their potential to discriminate between the four groups of subjects (administrative worker and nurses with and without recurrent LBP) by canonical discriminant analysis. As expected, the self-evaluation of physical and psychosocial workplace factors showed significant differences between the two occupational groups, which holds true for cases as well as for controls (P < 0.01). The functional tests revealed a tendency for rather good capacity in nurses with LBP and a decreased capacity in administrative personnel with LBP (P = 0.049). Neither self completed pain and disability questionnaires nor clinical examination or MR imaging revealed any significant difference between LBP cases from sedentary and non-sedentary occupations. When comparing LBP cases and controls within the two occupational groups, the functional tests revealed significant differences (P = 0.0001) yet only in administrative personnel. The clinical examination on the other hand only discriminated between LBP cases and controls in the nurses group (P < 0.0001). Neither MRI imaging nor self reported physical and psychosocial workplace factors discriminated between LBP cases and controls from both occupational groups. Although we used a battery of tests that have broad application in clinical and epidemiological studies of LBP, a clear difference in the pattern of symptoms between LBP cases from nursing and hospital administration personnel could not be ascertained. We conclude that there is no evidence for different mechanisms leading to non-specific, recurrent LBP in the two occupations, and thus no generalizable recommendations for the prevention and therapy of non-specific LBP in the two professions can be given. PMID:17611784

Investigating functional redundancy versus complementarity in Hawaiian herbivorous coral reef fishes.

PubMed

Kelly, Emily L A; Eynaud, Yoan; Clements, Samantha M; Gleason, Molly; Sparks, Russell T; Williams, Ivor D; Smith, Jennifer E

2016-12-01

Patterns of species resource use provide insight into the functional roles of species and thus their ecological significance within a community. The functional role of herbivorous fishes on coral reefs has been defined through a variety of methods, but from a grazing perspective, less is known about the species-specific preferences of herbivores on different groups of reef algae and the extent of dietary overlap across an herbivore community. Here, we quantified patterns of redundancy and complementarity in a highly diverse community of herbivores at a reef on Maui, Hawaii, USA. First, we tracked fish foraging behavior in situ to record bite rate and type of substrate bitten. Second, we examined gut contents of select herbivorous fishes to determine consumption at a finer scale. Finally, we placed foraging behavior in the context of resource availability to determine how fish selected substrate type. All species predominantly (73-100 %) foraged on turf algae, though there were differences among the types of macroalgae and other substrates bitten. Increased resolution via gut content analysis showed the composition of turf algae consumed by fishes differed across herbivore species. Consideration of foraging behavior by substrate availability revealed 50 % of herbivores selected for turf as opposed to other substrate types, but overall, there were variable foraging portfolios across all species. Through these three methods of investigation, we found higher complementarity among herbivorous fishes than would be revealed using a single metric. These results suggest differences across species in the herbivore "rain of bites" that graze and shape benthic community composition.

miRNA profiling of high, low and non-producing CHO cells during biphasic fed-batch cultivation reveals process relevant targets for host cell engineering.

PubMed

Stiefel, Fabian; Fischer, Simon; Sczyrba, Alexander; Otte, Kerstin; Hesse, Friedemann

2016-05-10

Fed-batch cultivation of recombinant Chinese hamster ovary (CHO) cell lines is one of the most widely used production modes for commercial manufacturing of recombinant protein therapeutics. Furthermore, fed-batch cultivations are often conducted as biphasic processes where the culture temperature is decreased to maximize volumetric product yields. However, it remains to be elucidated which intracellular regulatory elements actually control the observed pro-productive phenotypes. Recently, several studies have revealed microRNAs (miRNAs) to be important molecular switches of cell phenotypes. In this study, we analyzed miRNA profiles of two different recombinant CHO cell lines (high and low producer), and compared them to a non-producing CHO DG44 host cell line during fed-batch cultivation at 37°C versus a temperature shift to 30°C. Taking advantage of next-generation sequencing combined with cluster, correlation and differential expression analyses, we could identify 89 different miRNAs, which were differentially expressed in the different cell lines and cultivation phases. Functional validation experiments using 19 validated target miRNAs confirmed that these miRNAs indeed induced changes in process relevant phenotypes. Furthermore, computational miRNA target prediction combined with functional clustering identified putative target genes and cellular pathways, which might be regulated by these miRNAs. This study systematically identified novel target miRNAs during different phases and conditions of a biphasic fed-batch production process and functionally evaluated their potential for host cell engineering. Copyright © 2016. Published by Elsevier B.V.

Effect of allo- and xenotransplantation of embryonic nervous tissue and umbilical cord blood-derived stem cells on structural and functional state of cerebral cortex of albino rats in posttraumatic period.

PubMed

Ereniev, S I; Semchenko, V V; Sysheva, E V; Bogdashin, I V; Shapovalova, V V; Khizhnyak, A S; Gasanenko, L N

2005-11-01

Comparative study of the structural and functional state of cerebral cortex of adult albino rats after intracerebral allo- and xenotransplantation of embryonic nervous tissue and intravenous injection of umbilical cord blood-derived stem cells at different terms after diffuse-focal cerebral trauma revealed the best cerebroprotective effect on day 7 of posttraumatic period in animals receiving embryonic nervous tissue.

Downregulation of a mitochondria associated protein SLP-2 inhibits tumor cell motility, proliferation and enhances cell sensitivity to chemotherapeutic reagents.

PubMed

Wang, Yueqi; Cao, Wenfeng; Yu, Zaicheng; Liu, Zhihua

2009-09-01

Results from tissue microarray in this study and our previous reports revealed that stomatin-like protein 2 (SLP-2) is notably associated with tumorigenesis and metastasis. Many members of stomatin family are involved in tumor as mitochondrial component, and recent study has revealed that SLP-2 may also function in mitochondria. To further investigate the function of SLP-2, we used siRNA target SLP-2. Data showed that knock-down of SLP-2 potently inhibited cell motility, proliferation and slightly altered cell cycle without any significant change of apoptosis. Moreover, by combined application with different chemotherapeutic reagents, we observed the enhancement of cell chemosensitivity by SLP-2 depletion. We also confirmed that, SLP-2 localizes in mitochondria, affects mitochondrial membrane potential (MMP) and ATP production. We conclude that, SLP-2 is a mitochondrial protein and therefore, functions in energy process by MMP maintenance, and subsequently affecting cell motility, proliferation and chemosensitivity.

Monosynaptic rabies virus reveals premotor network organization and synaptic specificity of cholinergic partition cells.

PubMed

Stepien, Anna E; Tripodi, Marco; Arber, Silvia

2010-11-04

Movement is the behavioral output of neuronal activity in the spinal cord. Motor neurons are grouped into motor neuron pools, the functional units innervating individual muscles. Here we establish an anatomical rabies virus-based connectivity assay in early postnatal mice. We employ it to study the connectivity scheme of premotor neurons, the neuronal cohorts monosynaptically connected to motor neurons, unveiling three aspects of organization. First, motor neuron pools are connected to segmentally widely distributed yet stereotypic interneuron populations, differing for pools innervating functionally distinct muscles. Second, depending on subpopulation identity, interneurons take on local or segmentally distributed positions. Third, cholinergic partition cells involved in the regulation of motor neuron excitability segregate into ipsilaterally and bilaterally projecting populations, the latter exhibiting preferential connections to functionally equivalent motor neuron pools bilaterally. Our study visualizes the widespread yet precise nature of the connectivity matrix for premotor interneurons and reveals exquisite synaptic specificity for bilaterally projecting cholinergic partition cells. Copyright © 2010 Elsevier Inc. All rights reserved.

Molecular and cellular organization of taste neurons in adult Drosophila pharynx

PubMed Central

Chen, Yu-Chieh (David); Dahanukar, Anupama

2017-01-01

SUMMARY The Drosophila pharyngeal taste organs are poorly characterized despite their location at important sites for monitoring food quality. Functional analysis of pharyngeal neurons has been hindered by the paucity of molecular tools to manipulate them, as well as their relative inaccessibility for neurophysiological investigations. Here, we generate receptor-to-neuron maps of all three pharyngeal taste organs by performing a comprehensive chemoreceptor-GAL4/LexA expression analysis. The organization of pharyngeal neurons reveals similarities and distinctions in receptor repertoires and neuronal groupings compared to external taste neurons. We validate the mapping results by pinpointing a single pharyngeal neuron required for feeding avoidance of L-canavanine. Inducible activation of pharyngeal taste neurons reveals functional differences between external and internal taste neurons and functional subdivision within pharyngeal sweet neurons. Our results provide road maps of pharyngeal taste organs in an insect model system for probing the role of these understudied neurons in controlling feeding behaviors. PMID:29212040

Genes versus environment: geography and phylogenetic relationships shape the chemical profiles of stingless bees on a global scale

PubMed Central

Leonhardt, Sara D.; Rasmussen, Claus; Schmitt, Thomas

2013-01-01

Chemical compounds are highly important in the ecology of animals. In social insects, compounds on the body surface represent a particularly interesting trait, because they comprise different compound classes that are involved in different functions, such as communication, recognition and protection, all of which can be differentially affected by evolutionary processes. Here, we investigate the widely unknown and possibly antagonistic influence of phylogenetic and environmental factors on the composition of the cuticular chemistry of tropical stingless bees. We chose stingless bees because some species are unique in expressing not only self-produced compounds, but also compounds that are taken up from the environment. By relating the cuticular chemistry of 40 bee species from all over the world to their molecular phylogeny and geographical occurrence, we found that distribution patterns of different groups of compounds were differentially affected by genetic relatedness and biogeography. The ability to acquire environmental compounds was, for example, highly correlated with the bees' phylogeny and predominated in evolutionarily derived species. Owing to the presence of environmentally derived compounds, those species further expressed a higher chemical and thus functional diversity. In Old World species, chemical similarity of both environmentally derived and self-produced compounds was particularly high among sympatric species, even when they were less related to each other than to allopatric species, revealing a strong environmental effect even on largely genetically determined compounds. Thus, our findings do not only reveal an unexpectedly strong influence of the environment on the cuticular chemistry of stingless bees, but also demonstrate that even within one morphological trait (an insect's cuticular profile), different components (compound classes) can be differentially affected by different drivers (relatedness and biogeography), depending on the functional context. PMID:23658202

Functional rotation induced by alternating protonation states in the multidrug transporter AcrB: all-atom molecular dynamics simulations.

PubMed

Yamane, Tsutomu; Murakami, Satoshi; Ikeguchi, Mitsunori

2013-10-29

The multidrug transporter AcrB actively exports a wide variety of noxious compounds using proton-motive force as an energy source in Gram-negative bacteria. AcrB adopts an asymmetric structure comprising three protomers with different conformations that are sequentially converted during drug export; these cyclic conformational changes during drug export are referred to as functional rotation. To investigate functional rotation driven by proton-motive force, all-atom molecular dynamics simulations were performed. Using different protonation states for the titratable residues in the middle of the transmembrane domain, our simulations revealed the correlation between the specific protonation states and the side-chain configurations. Changing the protonation state for Asp408 induced a spontaneous structural transition, which suggests that the proton translocation stoichiometry may be one proton per functional rotation cycle. Furthermore, our simulations demonstrate that alternating the protonation states in the transmembrane domain induces functional rotation in the porter domain, which is primarily responsible for drug transport.

Gender differences in functional connectivities between insular subdivisions and selective pain-related brain structures.

PubMed

Dai, Yu-Jie; Zhang, Xin; Yang, Yang; Nan, Hai-Yan; Yu, Ying; Sun, Qian; Yan, Lin-Feng; Hu, Bo; Zhang, Jin; Qiu, Zi-Yu; Gao, Yi; Cui, Guang-Bin; Chen, Bi-Liang; Wang, Wen

2018-03-14

The incidence of pain disorders in women is higher than in men, making gender differences in pain a research focus. The human insular cortex is an important brain hub structure for pain processing and is divided into several subdivisions, serving different functions in pain perception. Here we aimed to examine the gender differences of the functional connectivities (FCs) between the twelve insular subdivisions and selected pain-related brain structures in healthy adults. Twenty-six healthy males and 11 age-matched healthy females were recruited in this cross-sectional study. FCs between the 12 insular subdivisions (as 12 regions of interest (ROIs)) and the whole brain (ROI-whole brain level) or 64 selected pain-related brain regions (64 ROIs, ROI-ROI level) were measured between the males and females. Significant gender differences in the FCs of the insular subdivisions were revealed: (1) The FCs between the dorsal dysgranular insula (dId) and other brain regions were significantly increased in males using two different techniques (ROI-whole brain and ROI-ROI analyses); (2) Based on the ROI-whole brain analysis, the FC increases in 4 FC-pairs were observed in males, including the left dId - the right median cingulate and paracingulate/ right posterior cingulate gyrus/ right precuneus, the left dId - the right median cingulate and paracingulate, the left dId - the left angular as well as the left dId - the left middle frontal gyrus; (3) According to the ROI-ROI analysis, increased FC between the left dId and the right rostral anterior cingulate cortex was investigated in males. In summary, the gender differences in the FCs of the insular subdivisions with pain-related brain regions were revealed in the current study, offering neuroimaging evidence for gender differences in pain processing. ClinicalTrials.gov, NCT02820974 . Registered 28 June 2016.

Chemical functionalization of graphene to augment stem cell osteogenesis and inhibit biofilm formation on polymer composites for orthopedic applications.

PubMed

Kumar, Sachin; Raj, Shammy; Kolanthai, Elayaraja; Sood, A K; Sampath, S; Chatterjee, Kaushik

2015-02-11

Toward designing the next generation of resorbable biomaterials for orthopedic applications, we studied poly(ε-caprolactone) (PCL) composites containing graphene. The role, if any, of the functionalization of graphene on mechanical properties, stem cell response, and biofilm formation was systematically evaluated. PCL composites of graphene oxide (GO), reduced GO (RGO), and amine-functionalized GO (AGO) were prepared at different filler contents (1%, 3%, and 5%). Although the addition of the nanoparticles to PCL markedly increased the storage modulus, this increase was largest for GO followed by AGO and RGO. In vitro cell studies revealed that the AGO and GO particles significantly increased human mesenchymal stem cell proliferation. AGO was most effective in augmenting stem cell osteogenesis leading to mineralization. Bacterial studies revealed that interaction with functionalized GO induced bacterial cell death because of membrane damage, which was further accentuated by amine groups in AGO. As a result, AGO composites were best at inhibiting biofilm formation. The synergistic effect of oxygen containing functional groups and amine groups on AGO imparts the optimal combination of improved modulus, favorable stem cell response, and biofilm inhibition in AGO-reinforced composites desired for orthopedic applications. This work elucidates the importance of chemical functionalization of graphene in polymer composites for biomedical applications.

Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology.

PubMed

Gibson, Molly K; Forsberg, Kevin J; Dantas, Gautam

2015-01-01

Antibiotic resistance is a dire clinical problem with important ecological dimensions. While antibiotic resistance in human pathogens continues to rise at alarming rates, the impact of environmental resistance on human health is still unclear. To investigate the relationship between human-associated and environmental resistomes, we analyzed functional metagenomic selections for resistance against 18 clinically relevant antibiotics from soil and human gut microbiota as well as a set of multidrug-resistant cultured soil isolates. These analyses were enabled by Resfams, a new curated database of protein families and associated highly precise and accurate profile hidden Markov models, confirmed for antibiotic resistance function and organized by ontology. We demonstrate that the antibiotic resistance functions that give rise to the resistance profiles observed in environmental and human-associated microbial communities significantly differ between ecologies. Antibiotic resistance functions that most discriminate between ecologies provide resistance to β-lactams and tetracyclines, two of the most widely used classes of antibiotics in the clinic and agriculture. We also analyzed the antibiotic resistance gene composition of over 6000 sequenced microbial genomes, revealing significant enrichment of resistance functions by both ecology and phylogeny. Together, our results indicate that environmental and human-associated microbial communities harbor distinct resistance genes, suggesting that antibiotic resistance functions are largely constrained by ecology.

A multifunctional chemical sensor based on a three-dimensional lanthanide metal-organic framework

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

Du, Pei-Yao; Liao, Sheng-Yun; Gu, Wen, E-mail: guwen68@nankai.edu.cn

2016-12-15

A 3D lanthanide MOF with formula [Sm{sub 2}(abtc){sub 1.5}(H{sub 2}O){sub 3}(DMA)]·H{sub 2}O·DMA (1) has been successfully synthesized via solvothermal method. Luminescence studies reveal that 1 exhibits dual functional detection benzyl alcohol and benzaldehyde among different aromatic molecules. In addition, 1 displays a turn-on luminescence sensing with respect to ethanol among different alcohol molecules, which suggests that 1 is also a promising luminescent probe for high selective sensing of ethanol. - Highlights: • A three-dimensional lanthanide metal-organic framework has been synthesized. • Complex 1 exhibits dual functional detection benzyl alcohol and benzaldehyde among different aromatic molecules. • Complex 1 displays amore » turn-on luminescence sensing with respect to ethanol among different alcohol molecules.« less

Effects of temperature and pressure on the nucleation and growth of silver clusters from supersaturated vapor: A molecular dynamics analysis

NASA Astrophysics Data System (ADS)

Wang, Qin; Xie, Hui; Chen, Yongshi; Liu, Chao

2017-04-01

The nucleation and growth of silver nanoparticles in the supersaturated system are investigated by molecular dynamics simulation at different temperatures and pressures. The variety of the atoms in the biggest cluster and the size of average clusters in the system versus the time are estimated to reveal the relationship between the nucleation as well as cluster growth. The nucleation rates in different situations are calculated with the threshold method. The effect of temperature and pressure on the nucleation rate is identified as obeying a linear function. Finally, the development of basal elements, such as monomers, dimers and trimmers, is revealed how the temperature and pressure affect the nucleation and growth of the silver cluster.

A widespread plant-fungal-bacterial symbiosis promotes plant biodiversity, plant nutrition and seedling recruitment.

PubMed

van der Heijden, Marcel G A; de Bruin, Susanne; Luckerhoff, Ludo; van Logtestijn, Richard S P; Schlaeppi, Klaus

2016-02-01

Highly diverse microbial assemblages colonize plant roots. It is still poorly understood whether different members of this root microbiome act synergistically by supplying different services (for example, different limiting nutrients) to plants and plant communities. In order to test this, we manipulated the presence of two widespread plant root symbionts, arbuscular mycorrhizal fungi and nitrogen-fixing rhizobia bacteria in model grassland communities established in axenic microcosms. Here, we demonstrate that both symbionts complement each other resulting in increased plant diversity, enhanced seedling recruitment and improved nutrient acquisition compared with a single symbiont situation. Legume seedlings obtained up to 15-fold higher productivity if they formed an association with both symbionts, opposed to productivity they reached with only one symbiont. Our results reveal the importance of functional diversity of symbionts and demonstrate that different members of the root microbiome can complement each other in acquiring different limiting nutrients and in driving important ecosystem functions.

Tissue-specific autophagy responses to aging and stress in C. elegans.

PubMed

Chapin, Hannah C; Okada, Megan; Merz, Alexey J; Miller, Dana L

2015-06-01

Cellular function relies on a balance between protein synthesis and breakdown. Macromolecular breakdown through autophagy is broadly required for cellular and tissue development, function, and recovery from stress. While Caenorhabditis elegans is frequently used to explore cellular responses to development and stress, the most common assays for autophagy in this system lack tissue-level resolution. Different tissues within an organism have unique functional characteristics and likely vary in their reliance on autophagy under different conditions. To generate a tissue-specific map of autophagy in C. elegans we used a dual fluorescent protein (dFP) tag that releases monomeric fluorescent protein (mFP) upon arrival at the lysosome. Tissue-specific expression of dFP::LGG-1 revealed autophagic flux in all tissues, but mFP accumulation was most dramatic in the intestine. We also observed variable responses to stress: starvation increased autophagic mFP release in all tissues, whereas anoxia primarily increased intestinal autophagic flux. We observed autophagic flux with tagged LGG-1, LGG-2, and two autophagic cargo reporters: a soluble cytoplasmic protein, and mitochondrial TOMM-7. Finally, an increase in mFP in older worms was consistent with an age-dependent shift in proteostasis. These novel measures of autophagic flux in C. elegans reveal heterogeneity in autophagic response across tissues during stress and aging.

Design of robust flow processing networks with time-programmed responses

NASA Astrophysics Data System (ADS)

Kaluza, P.; Mikhailov, A. S.

2012-04-01

Can artificially designed networks reach the levels of robustness against local damage which are comparable with those of the biochemical networks of a living cell? We consider a simple model where the flow applied to an input node propagates through the network and arrives at different times to the output nodes, thus generating a pattern of coordinated responses. By using evolutionary optimization algorithms, functional networks - with required time-programmed responses - were constructed. Then, continuing the evolution, such networks were additionally optimized for robustness against deletion of individual nodes or links. In this manner, large ensembles of functional networks with different kinds of robustness were obtained, making statistical investigations and comparison of their structural properties possible. We have found that, generally, different architectures are needed for various kinds of robustness. The differences are statistically revealed, for example, in the Laplacian spectra of the respective graphs. On the other hand, motif distributions of robust networks do not differ from those of the merely functional networks; they are found to belong to the first Alon superfamily, the same as that of the gene transcription networks of single-cell organisms.

Functional proteomic analyses of Bothrops atrox venom reveals phenotypes associated with habitat variation in the Amazon.

PubMed

Sousa, Leijiane F; Portes-Junior, José A; Nicolau, Carolina A; Bernardoni, Juliana L; Nishiyama, Milton Y; Amazonas, Diana R; Freitas-de-Sousa, Luciana A; Mourão, Rosa Hv; Chalkidis, Hipócrates M; Valente, Richard H; Moura-da-Silva, Ana M

2017-04-21

Venom variability is commonly reported for venomous snakes including Bothrops atrox. Here, we compared the composition of venoms from B. atrox snakes collected at Amazonian conserved habitats (terra-firme upland forest and várzea) and human modified areas (pasture and degraded areas). Venom samples were submitted to shotgun proteomic analysis as a whole or compared after fractionation by reversed-phase chromatography. Whole venom proteomes revealed a similar composition among the venoms with predominance of SVMPs, CTLs, and SVSPs and intermediate amounts of PLA 2 s and LAAOs. However, when distribution of particular isoforms was analyzed by either method, the venom from várzea snakes showed a decrease in hemorrhagic SVMPs and an increase in SVSPs, and procoagulant SVMPs and PLA 2 s. These differences were validated by experimental approaches including both enzymatic and in vivo assays, and indicated restrictions in respect to antivenom efficacy to variable components. Thus, proteomic analysis at the isoform level combined to in silico prediction of functional properties may indicate venom biological activity. These results also suggest that the prevalence of functionally distinct isoforms contributes to the variability of the venoms and could reflect the adaptation of B. atrox to distinct prey communities in different Amazon habitats. In this report, we compared isoforms present in venoms from snakes collected at different Amazonian habitats. By means of a species venom gland transcriptome and the in silico functional prediction of each isoform, we were able to predict the principal venom activities in vitro and in animal models. We also showed remarkable differences in the venom pools from snakes collected at the floodplain (várzea habitat) compared to other habitats. Not only was this venom less hemorrhagic and more procoagulant, when compared to the venom pools from the other three habitats studied, but also this enhanced procoagulant activity was not efficiently neutralized by Bothrops antivenom. Thus, using a functional proteomic approach, we highlighted intraspecific differences in B. atrox venom that could impact both in the ecology of snakes but also in the treatment of snake bite patients in the region. Copyright © 2017 Elsevier B.V. All rights reserved.

Ligation site in proteins recognized in silico

PubMed Central

Brylinski, Michal; Konieczny, Leszek; Roterman, Irena

2006-01-01

Recognition of a ligation site in a protein molecule is important for identifying its biological activity. The model for in silico recognition of ligation sites in proteins is presented. The idealized hydrophobic core stabilizing protein structure is represented by a three-dimensional Gaussian function. The experimentally observed distribution of hydrophobicity compared with the theoretical distribution reveals differences. The area of high differences indicates the ligation site. Availability http://bioinformatics.cm-uj.krakow.pl/activesite PMID:17597871

The picosecond structure of ultra-fast rogue waves

NASA Astrophysics Data System (ADS)

Klein, Avi; Shahal, Shir; Masri, Gilad; Duadi, Hamootal; Sulimani, Kfir; Lib, Ohad; Steinberg, Hadar; Kolpakov, Stanislav A.; Fridman, Moti

2018-02-01

We investigated ultrafast rogue waves in fiber lasers and found three different patterns of rogue waves: single- peaks, twin-peaks, and triple-peaks. The statistics of the different patterns as a function of the pump power of the laser reveals that the probability for all rogue waves patterns increase close to the laser threshold. We developed a numerical model which prove that the ultrafast rogue waves patterns result from both the polarization mode dispersion in the fiber and the non-instantaneous nature of the saturable absorber. This discovery reveals that there are three different types of rogue waves in fiber lasers: slow, fast, and ultrafast, which relate to three different time-scales and are governed by three different sets of equations: the laser rate equations, the nonlinear Schrodinger equation, and the saturable absorber equations, accordingly. This discovery is highly important for analyzing rogue waves and other extreme events in fiber lasers and can lead to realizing types of rogue waves which were not possible so far such as triangular rogue waves.

Method for revealing biases in precision mass measurements

NASA Astrophysics Data System (ADS)

Vabson, V.; Vendt, R.; Kübarsepp, T.; Noorma, M.

2013-02-01

A practical method for the quantification of systematic errors of large-scale automatic comparators is presented. This method is based on a comparison of the performance of two different comparators. First, the differences of 16 equal partial loads of 1 kg are measured with a high-resolution mass comparator featuring insignificant bias and 1 kg maximum load. At the second stage, a large-scale comparator is tested by using combined loads with known mass differences. Comparing the different results, the biases of any comparator can be easily revealed. These large-scale comparator biases are determined over a 16-month period, and for the 1 kg loads, a typical pattern of biases in the range of ±0.4 mg is observed. The temperature differences recorded inside the comparator concurrently with mass measurements are found to remain within a range of ±30 mK, which obviously has a minor effect on the detected biases. Seasonal variations imply that the biases likely arise mainly due to the functioning of the environmental control at the measurement location.

Functional diversity patterns of abyssal nematodes in the Eastern Mediterranean: A comparison between cold seeps and typical deep sea sediments

NASA Astrophysics Data System (ADS)

Kalogeropoulou, V.; Keklikoglou, K.; Lampadariou, N.

2015-04-01

Spatial patterns in deep sea nematode biological trait composition and functional diversity were investigated between chemosynthetic and typical deep sea ecosystems as well as between different microhabitats within the chemosynthetic ecosystems, in the Eastern Mediterranean. The chemosynthetic ecosystems chosen were two mud volcanoes, Napoli at 1950 m depth and Amsterdam at 2040 m depth which are cold seeps characterized by high chemosynthetic activity and spatial heterogeneity. Typical deep sea ecosystems consisted of fine-grained silt-clay sediments which were collected from three areas located in the south Ionian Sea at 2765 to 2840 m depth, the southern Cretan margin at 1089 to 1998 m depth and the Levantine Sea at 3055 to 3870 m depth. A range of biological traits (9 traits; 31 categories) related to buccal morphology, tail shape, body size, body shape, life history strategy, sediment position, cuticle morphology, amphid shape and presence of somatic setae were combined to identify patterns in the functional composition of nematode assemblages between the two habitats, the two mud volcanoes (macroscale) and between the microhabitats within the mud volcanoes (microscale). Data on trait correspondence was provided by biological information on species and genera. A total of 170 nematode species were allocated in 67 different trait combinations, i.e. functional groups, based on taxonomic, morphological and behavioral characteristics. The Biological Trait Analysis (BTA) revealed significant differences between the mud volcanoes and the typical deep sea sediments indicating the presence of different biological functions in ecologically very different environments. Moreover, chemosynthetic activity and habitat heterogeneity within mud volcanoes enhance the presence of different biological and ecological functions in nematode assemblages of different microhabitats. Functional diversity and species richness patterns varied significantly across the different environmental gradients prevailing in the study areas. Biological trait analysis, with the addition of newly introduced trait categories, and functional diversity outcomes provided greater explanatory power of ecosystem functioning than species richness and taxonomic diversity.

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

Hartmann, A.; Frenkel, J.; Hopf, R.

Amyloidosis is a systemic disease frequently involving the myocardium and leading to functional disturbances of the heart. Amyloidosis can mimic other cardiac diseases. A conclusive clinical diagnosis of cardiac involvement can only be made by a combination of different diagnostic methods. In 7 patients with myocardial amyloidosis we used a combined first-pass and static scintigraphy with technetium-99 m-pyrophosphate. There was only insignificant myocardial uptake of the tracer. The first-pass studies however revealed reduced systolic function in 4/7 patients and impaired diastolic function in 6/7 patients. Therefore, although cardiac amyloid could not be demonstrated in the static scintigraphy due to amyloidmore » fibril amount and composition, myocardial functional abnormalities were seen in the first-pass study.« less

Intraspecific Polymorphism, Interspecific Divergence, and the Origins of Function-Altering Mutations in Deer Mouse Hemoglobin

PubMed Central

Natarajan, Chandrasekhar; Hoffmann, Federico G.; Lanier, Hayley C.; Wolf, Cole J.; Cheviron, Zachary A.; Spangler, Matthew L.; Weber, Roy E.; Fago, Angela; Storz, Jay F.

2015-01-01

Major challenges for illuminating the genetic basis of phenotypic evolution are to identify causative mutations, to quantify their functional effects, to trace their origins as new or preexisting variants, and to assess the manner in which segregating variation is transduced into species differences. Here, we report an experimental analysis of genetic variation in hemoglobin (Hb) function within and among species of Peromyscus mice that are native to different elevations. A multilocus survey of sequence variation in the duplicated HBA and HBB genes in Peromyscus maniculatus revealed that function-altering amino acid variants are widely shared among geographically disparate populations from different elevations, and numerous amino acid polymorphisms are also shared with closely related species. Variation in Hb-O2 affinity within and among populations of P. maniculatus is attributable to numerous amino acid mutations that have individually small effects. One especially surprising feature of the Hb polymorphism in P. maniculatus is that an appreciable fraction of functional standing variation in the two transcriptionally active HBA paralogs is attributable to recurrent gene conversion from a tandemly linked HBA pseudogene. Moreover, transpecific polymorphism in the duplicated HBA genes is not solely attributable to incomplete lineage sorting or introgressive hybridization; instead, it is mainly attributable to recurrent interparalog gene conversion that has occurred independently in different species. Partly as a result of concerted evolution between tandemly duplicated globin genes, the same amino acid changes that contribute to variation in Hb function within P. maniculatus also contribute to divergence in Hb function among different species of Peromyscus. In the case of function-altering Hb mutations in Peromyscus, there is no qualitative or quantitative distinction between segregating variants within species and fixed differences between species. PMID:25556236

Metagenomics Reveals Microbial Community Composition And Function With Depth In Arctic Permafrost Cores

NASA Astrophysics Data System (ADS)

Jansson, J.; Tas, N.; Wu, Y.; Ulrich, C.; Kneafsey, T. J.; Torn, M. S.; Hubbard, S. S.; Chakraborty, R.; Graham, D. E.; Wullschleger, S. D.

2013-12-01

The Arctic is one of the most climatically sensitive regions on Earth and current surveys show that permafrost degradation is widespread in arctic soils. Biogeochemical feedbacks of permafrost thaw are expected to be dominated by the release of currently stored carbon back into the atmosphere as CO2 and CH4. Understanding the dynamics of C release from permafrost requires assessment of microbial functions from different soil compartments. To this end, as part of the Next Generation Ecosystem Experiment in the Arctic, we collected two replicate permafrost cores (1m and 3m deep) from a transitional polygon near Barrow, AK. At this location, permafrost starts from 0.5m in depth and is characterized by variable ice content and higher pH than surface soils. Prior to sectioning, the cores were CT-scanned to determine the physical heterogeneity throughout the cores. In addition to detailed geochemical characterization, we used Illumina MiSeq technology to sequence 16SrRNA genes throughout the depths of the cores at 1 cm intervals. Selected depths were also chosen for metagenome sequencing of total DNA (including phylogenetic and functional genes) using the Illumina HiSeq platform. The 16S rRNA gene sequence data revealed that the microbial community composition and diversity changed dramatically with depth. The microbial diversity decreased sharply below the first few centimeters of the permafrost and then gradually increased in deeper layers. Based on the metagenome sequence data, the permafrost microbial communities were found to contain members with a large metabolic potential for carbon processing, including pathways for fermentation and methanogenesis. The surface active layers had more representatives of Verrucomicrobia (potential methane oxidizers) whereas the deep permafrost layers were dominated by several different species of Actinobacteria. The latter are known to have a diverse metabolic capability and are able to adapt to stress by entering a dormant yet viable state. In addition, several isolates were obtained from different depths throughout the cores, including methanogens from some of the deeper layers. Together these data present a new view of potential geochemical cycles carried out by microorganisms in permafrost and reveal how community members and functions are distributed with depth.

IQ, Fetal Testosterone and Individual Variability in Children's Functional Lateralization

ERIC Educational Resources Information Center

Mercure, Evelyne; Ashwin, Emma; Dick, Frederic; Halit, Hanife; Auyeung, Bonnie; Baron-Cohen, Simon; Johnson, Mark H.

2009-01-01

Previous event-related potential (ERP) studies have revealed that faces and words show a robust difference in the lateralization of their N170. The present study investigated the development of this differential lateralization in school-age boys. We assessed the potential role of fetal testosterone (FT) level as a factor biasing the prenatal…

NEO-P1 Profiles in PTSD as a Function of Trauma Level.

ERIC Educational Resources Information Center

Talbert, F. Suzanne; And Others

1993-01-01

Administered NEO Personality Inventory (NEO-PI) and Combat Exposure Scale to 100 Vietnam veterans with combat-related Posttraumatic Stress Disorder (PTSD) and sorted subjects into three groups based on trauma exposure level. Found no significant differences among personality profiles of three trauma-exposed groups. Revealed normative NEO-PI…

Statistical process control for residential treated wood

Treesearch

Patricia K. Lebow; Timothy M. Young; Stan Lebow

2017-01-01

This paper is the first stage of a study that attempts to improve the process of manufacturing treated lumber through the use of statistical process control (SPC). Analysis of industrial and auditing agency data sets revealed there are differences between the industry and agency probability density functions (pdf) for normalized retention data. Resampling of batches of...

Implicit and Explicit Olfactory Memory in People with and without Down Syndrome

ERIC Educational Resources Information Center

Johns, Adam; Homewood, Judi; Stevenson, Richard; Taylor, Alan

2012-01-01

This study examined differences in implicit and explicit memory performance between people with Down syndrome (DS), their siblings, children matched on mental age, and university undergraduates, using olfactory stimuli. The DS and mental-age matched participants were also compared on two tasks of executive function. The data revealed implicit…

The Acquisition of Lexical Meaning in a Study Abroad Context: The Spanish Prepositions "por" and "para."

ERIC Educational Resources Information Center

Lafford, Barbara A.; Ryan, John M.

1995-01-01

Examination of the development of form/function relations of the prepositions "por" and "para" at different levels of proficiency in the interlanguage of study-abroad students in Granada, Spain, revealed "noncanonical" as well as "canonical" uses of these prepositions. The most common noncanonical uses were…

Do the Brain Networks of Scientists Account for Their Superiority in Hypothesis-Generating?

ERIC Educational Resources Information Center

Lee, Jun-Ki

2012-01-01

Where do scientists' superior abilities originate from when generating a creative idea? What different brain functions are activated between scientists and i) general academic high school students and ii) science high school students when generating a biological hypothesis? To reveal brain level explanations for these questions, this paper…

Social Processes Affecting the Mnemonic Consequences of Rumors on Children's Memory

ERIC Educational Resources Information Center

Principe, Gabrielle F.; Daley, Lauren; Kauth, Kyli

2010-01-01

This research examined whether the impact of overheard rumors on children's memory for their experiences varies as a function of social processes. The results of two experiments revealed that the very same errant rumor had different consequences for children's recollections depending on the degree and type of social interactions they had with…

Intellectual Characteristics of Diabetic Children at Diagnosis and One Year Later.

ERIC Educational Resources Information Center

Rovet, Joanne F.; And Others

A longitudinal investigation of neurocognitive function was conducted on 63 newly diagnosed pediatric patients with insulin-dependent diabetes mellitus (IDDM) at onset of illness and 1-year post diagnosis. The results at diagnosis, when the children were ages 4 months to 12 years, revealed no differences compared to sibling controls, nor any…

Form and Functions: Publishing the Canadian Government "Weekly Checklist" on the Internet.

ERIC Educational Resources Information Center

Davies, Ron; Chalk, Tanis

1996-01-01

When a Canadian government documents listing was distributed over the Internet, differences were revealed in the design and implementation of print, FTP, Gopher and World Wide Web versions. Publishing form was found to affect: ability to provide specific editions for target audiences, amount of information delivered at one time, presentation…

Patterns of Children's Adrenocortical Reactivity to Interparental Conflict and Associations with Child Adjustment: A Growth Mixture Modeling Approach

ERIC Educational Resources Information Center

Koss, Kalsea J.; George, Melissa R. W.; Davies, Patrick T.; Cicchetti, Dante; Cummings, E. Mark; Sturge-Apple, Melissa L.

2013-01-01

Examining children's physiological functioning is an important direction for understanding the links between interparental conflict and child adjustment. Utilizing growth mixture modeling, the present study examined children's cortisol reactivity patterns in response to a marital dispute. Analyses revealed three different patterns of cortisol…

Circadian Rhythms, Sleep Deprivation, and Human Performance

PubMed Central

Goel, Namni; Basner, Mathias; Rao, Hengyi; Dinges, David F.

2014-01-01

Much of the current science on, and mathematical modeling of, dynamic changes in human performance within and between days is dominated by the two-process model of sleep–wake regulation, which posits a neurobiological drive for sleep that varies homeostatically (increasing as a saturating exponential during wakefulness and decreasing in a like manner during sleep), and a circadian process that neurobiologically modulates both the homeostatic drive for sleep and waking alertness and performance. Endogenous circadian rhythms in neurobehavioral functions, including physiological alertness and cognitive performance, have been demonstrated using special laboratory protocols that reveal the interaction of the biological clock with the sleep homeostatic drive. Individual differences in circadian rhythms and genetic and other components underlying such differences also influence waking neurobehavioral functions. Both acute total sleep deprivation and chronic sleep restriction increase homeostatic sleep drive and degrade waking neurobehavioral functions as reflected in sleepiness, attention, cognitive speed, and memory. Recent evidence indicating a high degree of stability in neurobehavioral responses to sleep loss suggests that these trait-like individual differences are phenotypic and likely involve genetic components, including circadian genes. Recent experiments have revealed both sleep homeostatic and circadian effects on brain metabolism and neural activation. Investigation of the neural and genetic mechanisms underlying the dynamically complex interaction between sleep homeostasis and circadian systems is beginning. A key goal of this work is to identify biomarkers that accurately predict human performance in situations in which the circadian and sleep homeostatic systems are perturbed. PMID:23899598

Quantifying athlete self-talk.

PubMed

Hardy, James; Hall, Craig R; Hardy, Lew

2005-09-01

Two studies were conducted. The aims of Study 1 were (a) to generate quantitative data on the content of athletes' self-talk and (b) to examine differences in the use of self-talk in general as well as the functions of self-talk in practice and competition settings. Differences in self-talk between the sexes, sport types and skill levels were also assessed. Athletes (n = 295, mean age = 21.9 years) from a variety of sports and competitive levels completed the Self-Talk Use Questionnaire (STUQ), which was developed specifically for the study. In Study 1, single-factor between-group multivariate analyses of variance revealed significant differences across sex and sport type for the content of self-talk. Mixed-model multivariate analyses of variance revealed overall greater use of self-talk, as well as increased use of the functions of self-talk, in competition compared with practice. Moreover, individual sport athletes reported greater use of self-talk, as well as the functions of self-talk, than their team sport counterparts. In Study 2, recreational volleyball players (n = 164, mean age = 21.5 years) completed a situationally modified STUQ. The results were very similar to those of Study 1. That the content of athlete self-talk was generally positive, covert and abbreviated lends support to the application of Vygotsky's (1986) verbal self-regulation theory to the study of self-talk in sport. Researchers are encouraged to examine the effectiveness of self-talk in future studies.

The structure of bradyzoite-specific enolase from Toxoplasma gondii reveals insights into its dual cytoplasmic and nuclear functions

DOE PAGES

Ruan, Jiapeng; Mouveaux, Thomas; Light, Samuel H.; ...

2015-03-01

In addition to catalyzing a central step in glycolysis, enolase assumes a remarkably diverse set of secondary functions in different organisms, including transcription regulation as documented for the oncogene c-Myc promoter-binding protein 1. The apicomplexan parasite Toxoplasma gondii differentially expresses two nuclear-localized, plant-like enolases: enolase 1 (TgENO1) in the latent bradyzoite cyst stage and enolase 2 (TgENO2) in the rapidly replicative tachyzoite stage. A 2.75 Å resolution crystal structure of bradyzoite enolase 1, the second structure to be reported of a bradyzoite-specific protein inToxoplasma, captures an open conformational state and reveals that distinctive plant-like insertions are located on surface loops.more » The enolase 1 structure reveals that a unique residue, Glu164, in catalytic loop 2 may account for the lower activity of this cyst-stage isozyme. Recombinant TgENO1 specifically binds to a TTTTCT DNA motif present in the cyst matrix antigen 1 (TgMAG1) gene promoter as demonstrated by gel retardation. Furthermore, direct physical interactions of both nuclear TgENO1 and TgENO2 with the TgMAG1 gene promoter are demonstrated n vivo using chromatin immunoprecipitation (ChIP) assays. Structural and biochemical studies reveal that T. gondii enolase functions are multifaceted, including the coordination of gene regulation in parasitic stage development. Lastly, enolase 1 provides a potential lead in the design of drugs against Toxoplasma brain cysts.« less

Correlation between urodynamic function and 3D cat scan anatomy in neobladders: does it exist?

PubMed

Crivellaro, S; Mami, E; Wald, C; Smith, J J; Kocjancic, E; Stoffel, J; Bresette, J; Libertino, J A

2009-01-01

We compared the functional and anatomical differences among three different orthotopic neobladders, utilizing video urodynamics and 3D CT to determine what parameters, if any, correlate to function. Thirty-four patients were able to participate in the evaluation of their neobladder by 3D CT and video urodynamics. Three different orthotopic neobladders were identified (12 ileal, 7 ileocecal, 15 sigmoid). Multiple measurements, observations and functional data have been obtained. Statistical analysis for this study employed a linear regression test and an odds ratio calculation (using StatSoft V. 5.1). In comparing three different neobladders, no significant differences were noted. Looking at the entire population, the following association was statistically significant in linear correlation: the maximal capacity and the neobladder volume; the pressure at the maximal capacity and the distance from the symphysis, the pressure at maximal flow and both the distance from the symphysis and the thickness of the neobladder. The distance from the left femoral head was directly correlated with the post void residual and inversely correlated with the maximal flow. The Odds ratio calculation revealed (with significant P < 0.05) that the further the center of the neobladder is from the right femoral head, the higher risk of incontinence. The study seems to show no significant anatomical or functional difference among the three different types of neobladders. A possible correlation between the position of the neobladder and urinary incontinence is suggested, recognizing further study in a larger population is required.

Flow sensing by pinniped whiskers

PubMed Central

Miersch, L.; Hanke, W.; Wieskotten, S.; Hanke, F. D.; Oeffner, J.; Leder, A.; Brede, M.; Witte, M.; Dehnhardt, G.

2011-01-01

Beside their haptic function, vibrissae of harbour seals (Phocidae) and California sea lions (Otariidae) both represent highly sensitive hydrodynamic receptor systems, although their vibrissal hair shafts differ considerably in structure. To quantify the sensory performance of both hair types, isolated single whiskers were used to measure vortex shedding frequencies produced in the wake of a cylinder immersed in a rotational flow tank. These measurements revealed that both whisker types were able to detect the vortex shedding frequency but differed considerably with respect to the signal-to-noise ratio (SNR). While the signal detected by sea lion whiskers was substantially corrupted by noise, harbour seal whiskers showed a higher SNR with largely reduced noise. However, further analysis revealed that in sea lion whiskers, each noise signal contained a dominant frequency suggested to function as a characteristic carrier signal. While in harbour seal whiskers the unique surface structure explains its high sensitivity, this more or less steady fundamental frequency might represent the mechanism underlying hydrodynamic reception in the fast swimming sea lion by being modulated in response to hydrodynamic stimuli impinging on the hair. PMID:21969689

Carbon utilization profile of the filamentous fungal species Fusarium fujikuroi, Penicillium decumbens, and Sarocladium strictum isolated from marine coastal environments.

PubMed

Fuentes, Marcelo E; Quiñones, Renato A

Facultative marine filamentous fungi have recently emerged as a functional component in coastal marine systems. However, little is known about their ecological role and functions in biogeochemical cycles. Penicillium decumbens, S. strictum, and F. fujikuroi were isolated from the coastal upwelling zone off south-central Chile. Their carbon profiles were characterized using Biolog FF MicroPlates. These species used a wide range of carbon sources, mainly carbohydrates, but also amino acids, suggesting the use of metabolic routes that include glycolysis/gluconeogenesis. Substrate richness revealed a great capacity for the utilization of nutritional sources, reflected by the following Shannon Indices of utilization of specific substrates: 4.02 for S. strictum, 4.01 for P. decumbes, and 3.91 for F. fujikuroi, which reveals a high physiological capacity for oxidizing different substrates. Significant differences were found between 18 substrates utilized by all three species. Results suggest that filamentous fungi should be considered an integral part of the marine microbial community and included in biogeochemical cycling models of upwelling ecosystems.

Tweeting Supertyphoon Haiyan: Evolving Functions of Twitter during and after a Disaster Event.

PubMed

David, Clarissa C; Ong, Jonathan Corpus; Legara, Erika Fille T

2016-01-01

When disaster events capture global attention users of Twitter form transient interest communities that disseminate information and other messages online. This paper examines content related to Typhoon Haiyan (locally known as Yolanda) as it hit the Philippines and triggered international humanitarian response and media attention. It reveals how Twitter conversations about disasters evolve over time, showing an issue attention cycle on a social media platform. The paper examines different functions of Twitter and the information hubs that drive and sustain conversation about the event. Content analysis shows that the majority of tweets contain information about the typhoon or its damage, and disaster relief activities. There are differences in types of content between the most retweeted messages and posts that are original tweets. Original tweets are more likely to come from ordinary users, who are more likely to tweet emotions, messages of support, and political content compared with official sources and key information hubs that include news organizations, aid organization, and celebrities. Original tweets reveal use of the site beyond information to relief coordination and response.

Structure-guided mutational analysis reveals the functional requirements for product specificity of DOT1 enzymes.

PubMed

Dindar, Gülcin; Anger, Andreas M; Mehlhorn, Christine; Hake, Sandra B; Janzen, Christian J

2014-11-12

DOT1 enzymes are conserved methyltransferases that catalyse the methylation of lysine 79 on histone H3 (H3K79). Most eukaryotes contain one DOT1 enzyme, whereas African trypanosomes have two homologues, DOT1A and DOT1B, with different enzymatic activities. DOT1A mediates mono- and dimethylation of H3K76, the homologue of H3K79 in other organisms, whereas DOT1B additionally catalyses H3K76 trimethylation. However, it is unclear how these different enzymatic activities are achieved. Here we employ a trypanosomal nucleosome reconstitution system and structure-guided homology modelling to identify critical residues within and outside the catalytic centre that modulate product specificity. Exchange of these residues transfers the product specificity from one enzyme to the other, and reveals the existence of distinct regulatory domains adjacent to the catalytic centre. Our study provides the first evidence that a few crucial residues in DOT1 enzymes are sufficient to catalyse methyl-state-specific reactions. These results might also have far-reaching consequences for the functional understanding of homologous enzymes in higher eukaryotes.

High Mobility Group N Proteins Modulate the Fidelity of the Cellular Transcriptional Profile in a Tissue- and Variant-specific Manner*

PubMed Central

Kugler, Jamie E.; Horsch, Marion; Huang, Di; Furusawa, Takashi; Rochman, Mark; Garrett, Lillian; Becker, Lore; Bohla, Alexander; Hölter, Sabine M.; Prehn, Cornelia; Rathkolb, Birgit; Racz, Ildikó; Aguilar-Pimentel, Juan Antonio; Adler, Thure; Adamski, Jerzy; Beckers, Johannes; Busch, Dirk H.; Eickelberg, Oliver; Klopstock, Thomas; Ollert, Markus; Stöger, Tobias; Wolf, Eckhard; Wurst, Wolfgang; Yildirim, Ali Önder; Zimmer, Andreas; Gailus-Durner, Valérie; Fuchs, Helmut; Hrabě de Angelis, Martin; Garfinkel, Benny; Orly, Joseph; Ovcharenko, Ivan; Bustin, Michael

2013-01-01

The nuclei of most vertebrate cells contain members of the high mobility group N (HMGN) protein family, which bind specifically to nucleosome core particles and affect chromatin structure and function, including transcription. Here, we study the biological role of this protein family by systematic analysis of phenotypes and tissue transcription profiles in mice lacking functional HMGN variants. Phenotypic analysis of Hmgn1tm1/tm1, Hmgn3tm1/tm1, and Hmgn5tm1/tm1 mice and their wild type littermates with a battery of standardized tests uncovered variant-specific abnormalities. Gene expression analysis of four different tissues in each of the Hmgntm1/tm1 lines reveals very little overlap between genes affected by specific variants in different tissues. Pathway analysis reveals that loss of an HMGN variant subtly affects expression of numerous genes in specific biological processes. We conclude that within the biological framework of an entire organism, HMGNs modulate the fidelity of the cellular transcriptional profile in a tissue- and HMGN variant-specific manner. PMID:23620591

Tweeting Supertyphoon Haiyan: Evolving Functions of Twitter during and after a Disaster Event

PubMed Central

David, Clarissa C.; Ong, Jonathan Corpus; Legara, Erika Fille T.

2016-01-01

When disaster events capture global attention users of Twitter form transient interest communities that disseminate information and other messages online. This paper examines content related to Typhoon Haiyan (locally known as Yolanda) as it hit the Philippines and triggered international humanitarian response and media attention. It reveals how Twitter conversations about disasters evolve over time, showing an issue attention cycle on a social media platform. The paper examines different functions of Twitter and the information hubs that drive and sustain conversation about the event. Content analysis shows that the majority of tweets contain information about the typhoon or its damage, and disaster relief activities. There are differences in types of content between the most retweeted messages and posts that are original tweets. Original tweets are more likely to come from ordinary users, who are more likely to tweet emotions, messages of support, and political content compared with official sources and key information hubs that include news organizations, aid organization, and celebrities. Original tweets reveal use of the site beyond information to relief coordination and response. PMID:27019425

Functional abnormalities in normally appearing athletes following mild traumatic brain injury: a functional MRI study

PubMed Central

Slobounov, Semyon M.; Zhang, K.; Pennell, D.; Ray, W.; Johnson, B.; Sebastianelli, W.

2010-01-01

Memory problems are one of the most common symptoms of sport-related mild traumatic brain injury (MTBI), known as concussion. Surprisingly, little research has examined spatial memory in concussed athletes given its importance in athletic environments. Here, we combine functional magnetic resonance imaging (fMRI) with a virtual reality (VR) paradigm designed to investigate the possibility of residual functional deficits in recently concussed but asymptomatic individuals. Specifically, we report performance of spatial memory navigation tasks in a VR environment and fMRI data in 15 athletes suffering from MTBI and 15 neurologically normal, athletically active age matched controls. No differences in performance were observed between these two groups of subjects in terms of success rate (94 and 92%) and time to complete the spatial memory navigation tasks (mean = 19.5 and 19.7 s). Whole brain analysis revealed that similar brain activation patterns were observed during both encoding and retrieval among the groups. However, concussed athletes showed larger cortical networks with additional increases in activity outside of the shared region of interest (ROI) during encoding. Quantitative analysis of blood oxygen level dependent (BOLD) signal revealed that concussed individuals had a significantly larger cluster size during encoding at parietal cortex, right dorsolateral prefrontal cortex, and right hippocampus. In addition, there was a significantly larger BOLD signal percent change at the right hippocampus. Neither cluster size nor BOLD signal percent change at shared ROIs was different between groups during retrieval. These major findings are discussed with respect to current hypotheses regarding the neural mechanism responsible for alteration of brain functions in a clinical setting. PMID:20039023

From Hippocampus to Whole-Brain: The Role of Integrative Processing in Episodic Memory Retrieval

PubMed Central

Geib, Benjamin R.; Stanley, Matthew L.; Dennis, Nancy A.; Woldorff, Marty G.; Cabeza, Roberto

2017-01-01

Multivariate functional connectivity analyses of neuroimaging data have revealed the importance of complex, distributed interactions between disparate yet interdependent brain regions. Recent work has shown that topological properties of functional brain networks are associated with individual and group differences in cognitive performance, including in episodic memory. After constructing functional whole-brain networks derived from an event-related fMRI study of memory retrieval, we examined differences in functional brain network architecture between forgotten and remembered words. This study yielded three main findings. First, graph theory analyses showed that successfully remembering compared to forgetting was associated with significant changes in the connectivity profile of the left hippocampus and a corresponding increase in efficient communication with the rest of the brain. Second, bivariate functional connectivity analyses indicated stronger interactions between the left hippocampus and a retrieval assembly for remembered versus forgotten items. This assembly included the left precuneus, left caudate, bilateral supramarginal gyrus, and the bilateral dorsolateral superior frontal gyrus. Integrative properties of the retrieval assembly were greater for remembered than forgotten items. Third, whole-brain modularity analyses revealed that successful memory retrieval was marginally significantly associated with a less segregated modular architecture in the network. The magnitude of the decreases in modularity between remembered and forgotten conditions was related to memory performance. These findings indicate that increases in integrative properties at the nodal, retrieval assembly, and whole-brain topological levels facilitate memory retrieval, while also underscoring the potential of multivariate brain connectivity approaches for providing valuable new insights into the neural bases of memory processes. PMID:28112460

Dynamic succession of substrate-associated bacterial composition and function during Ganoderma lucidum growth

PubMed Central

Li, Qiang; Zou, Jie; Tan, Hao; Tan, Wei; Peng, Weihong

2018-01-01

Background Ganoderma lucidum, a valuable medicinal fungus, is widely distributed in China. It grows alongside with a complex microbial ecosystem in the substrate. As sequencing technology advances, it is possible to reveal the composition and functions of substrate-associated bacterial communities. Methods We analyzed the bacterial community dynamics in the substrate during the four typical growth stages of G. lucidum using next-generation sequencing. Results The physicochemical properties of the substrate (e.g. acidity, moisture, total nitrogen, total phosphorus and total potassium) changed between different growth stages. A total of 598,771 sequences from 12 samples were obtained and assigned to 22 bacterial phyla. Proteobacteria and Firmicutes were the dominant phyla. Bacterial community composition and diversity significantly differed between the elongation stage and the other three growth stages. LEfSe analysis revealed a large number of bacterial taxa (e.g. Bacteroidetes, Acidobacteria and Nitrospirae) with significantly higher abundance at the elongation stage. Functional pathway prediction uncovered significant abundance changes of a number of bacterial functional pathways between the elongation stage and other growth stages. At the elongation stage, the abundance of the environmental information processing pathway (mainly membrane transport) decreased, whereas that of the metabolism-related pathways increased. Discussion The changes in bacterial community composition, diversity and predicted functions were most likely related to the changes in the moisture and nutrient conditions in the substrate with the growth of G. lucidum, particularly at the elongation stage. Our findings shed light on the G. lucidum-bacteria-substrate relationships, which should facilitate the industrial cultivation of G. lucidum. PMID:29915697

Multi-voxel Patterns Reveal Functionally Differentiated Networks Underlying Auditory Feedback Processing of Speech

PubMed Central

Zheng, Zane Z.; Vicente-Grabovetsky, Alejandro; MacDonald, Ewen N.; Munhall, Kevin G.; Cusack, Rhodri; Johnsrude, Ingrid S.

2013-01-01

The everyday act of speaking involves the complex processes of speech motor control. An important component of control is monitoring, detection and processing of errors when auditory feedback does not correspond to the intended motor gesture. Here we show, using fMRI and converging operations within a multi-voxel pattern analysis framework, that this sensorimotor process is supported by functionally differentiated brain networks. During scanning, a real-time speech-tracking system was employed to deliver two acoustically different types of distorted auditory feedback or unaltered feedback while human participants were vocalizing monosyllabic words, and to present the same auditory stimuli while participants were passively listening. Whole-brain analysis of neural-pattern similarity revealed three functional networks that were differentially sensitive to distorted auditory feedback during vocalization, compared to during passive listening. One network of regions appears to encode an ‘error signal’ irrespective of acoustic features of the error: this network, including right angular gyrus, right supplementary motor area, and bilateral cerebellum, yielded consistent neural patterns across acoustically different, distorted feedback types, only during articulation (not during passive listening). In contrast, a fronto-temporal network appears sensitive to the speech features of auditory stimuli during passive listening; this preference for speech features was diminished when the same stimuli were presented as auditory concomitants of vocalization. A third network, showing a distinct functional pattern from the other two, appears to capture aspects of both neural response profiles. Taken together, our findings suggest that auditory feedback processing during speech motor control may rely on multiple, interactive, functionally differentiated neural systems. PMID:23467350

NFAT5-Regulated Macrophage Polarization Supports the Proinflammatory Function of Macrophages and T Lymphocytes.

PubMed

Tellechea, Mónica; Buxadé, Maria; Tejedor, Sonia; Aramburu, Jose; López-Rodríguez, Cristina

2018-01-01

Macrophages are exquisite sensors of tissue homeostasis that can rapidly switch between pro- and anti-inflammatory or regulatory modes to respond to perturbations in their microenvironment. This functional plasticity involves a precise orchestration of gene expression patterns whose transcriptional regulators have not been fully characterized. We had previously identified the transcription factor NFAT5 as an activator of TLR-induced responses, and in this study we explore its contribution to macrophage functions in different polarization settings. We found that both in classically and alternatively polarized macrophages, NFAT5 enhanced functions associated with a proinflammatory profile such as bactericidal capacity and the ability to promote Th1 polarization over Th2 responses. In this regard, NFAT5 upregulated the Th1-stimulatory cytokine IL-12 in classically activated macrophages, whereas in alternatively polarized ones it enhanced the expression of the pro-Th1 mediators Fizz-1 and arginase 1, indicating that it could promote proinflammatory readiness by regulating independent genes in differently polarized macrophages. Finally, adoptive transfer assays in vivo revealed a reduced antitumor capacity in NFAT5-deficient macrophages against syngeneic Lewis lung carcinoma and ID8 ovarian carcinoma cells, a defect that in the ID8 model was associated with a reduced accumulation of effector CD8 T cells at the tumor site. Altogether, detailed analysis of the effect of NFAT5 in pro- and anti-inflammatory macrophages uncovered its ability to regulate distinct genes under both polarization modes and revealed its predominant role in promoting proinflammatory macrophage functions. Copyright © 2017 by The American Association of Immunologists, Inc.

Magnetic exchange in {Gd(III)-radical} complexes: method assessment, mechanism of coupling and magneto-structural correlations.

PubMed

Gupta, Tulika; Rajeshkumar, Thayalan; Rajaraman, Gopalan

2014-07-28

Density functional studies have been performed on ten different {Gd(III)-radical} complexes exhibiting both ferro and antiferromagnetic exchange interaction with an aim to assess a suitable exchange-correlation functional within DFT formalism. This study has also been extended to probe the mechanism of magnetic coupling and to develop suitable magneto-structural correlations for this pair. Our method assessments reveal the following order of increasing accuracy for the evaluation of J values compared to experimental coupling constants: B(40HF)LYP < BHandHLYP < TPSSH < PW91 < PBE < BP86 < OLYP < BLYP < PBE0 < X3LYP < B3LYP < B2PLYP. Grimme's double-hybrid functional is found to be superior compared to other functionals tested and this is followed very closely by the conventional hybrid B3LYP functional. At the basis set front, our calculations reveal that the incorporation of relativistic effect is important in these calculations and the relativistically corrected effective core potential (ECP) basis set is found to yield better Js compared to other methods. The supposedly empty 5d/6s/6p orbitals of Gd(III) are found to play an important role in the mechanism of magnetic coupling and different contributions to the exchange terms are probed using Molecular Orbital (MO) and Natural Bond Orbital (NBO) analysis. Magneto-structural correlations for Gd-O distances, Gd-O-N angles and Gd-O-N-C dihedral angles are developed where the bond angles as well as dihedral angle parameters are found to dictate the sign and strength of the magnetic coupling in this series.

Algebraic Topology of Multi-Brain Connectivity Networks Reveals Dissimilarity in Functional Patterns during Spoken Communications

PubMed Central

Tadić, Bosiljka; Andjelković, Miroslav; Boshkoska, Biljana Mileva; Levnajić, Zoran

2016-01-01

Human behaviour in various circumstances mirrors the corresponding brain connectivity patterns, which are suitably represented by functional brain networks. While the objective analysis of these networks by graph theory tools deepened our understanding of brain functions, the multi-brain structures and connections underlying human social behaviour remain largely unexplored. In this study, we analyse the aggregate graph that maps coordination of EEG signals previously recorded during spoken communications in two groups of six listeners and two speakers. Applying an innovative approach based on the algebraic topology of graphs, we analyse higher-order topological complexes consisting of mutually interwoven cliques of a high order to which the identified functional connections organise. Our results reveal that the topological quantifiers provide new suitable measures for differences in the brain activity patterns and inter-brain synchronisation between speakers and listeners. Moreover, the higher topological complexity correlates with the listener’s concentration to the story, confirmed by self-rating, and closeness to the speaker’s brain activity pattern, which is measured by network-to-network distance. The connectivity structures of the frontal and parietal lobe consistently constitute distinct clusters, which extend across the listener’s group. Formally, the topology quantifiers of the multi-brain communities exceed the sum of those of the participating individuals and also reflect the listener’s rated attributes of the speaker and the narrated subject. In the broader context, the presented study exposes the relevance of higher topological structures (besides standard graph measures) for characterising functional brain networks under different stimuli. PMID:27880802

The structure of bradyzoite-specific enolase from Toxoplasma gondii reveals insights into its dual cytoplasmic and nuclear functions

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

Ruan, Jiapeng; Mouveaux, Thomas; Light, Samuel H.

2015-03-01

The second crystal structure of a parasite protein preferentially enriched in the brain cyst of T. gondii has been solved at 2.75 Å resolution. Bradyzoite enolase 1 is reported to have differential functions as a glycolytic enzyme and a transcriptional regulator in bradyzoites. In addition to catalyzing a central step in glycolysis, enolase assumes a remarkably diverse set of secondary functions in different organisms, including transcription regulation as documented for the oncogene c-Myc promoter-binding protein 1. The apicomplexan parasite Toxoplasma gondii differentially expresses two nuclear-localized, plant-like enolases: enolase 1 (TgENO1) in the latent bradyzoite cyst stage and enolase 2 (TgENO2)more » in the rapidly replicative tachyzoite stage. A 2.75 Å resolution crystal structure of bradyzoite enolase 1, the second structure to be reported of a bradyzoite-specific protein in Toxoplasma, captures an open conformational state and reveals that distinctive plant-like insertions are located on surface loops. The enolase 1 structure reveals that a unique residue, Glu164, in catalytic loop 2 may account for the lower activity of this cyst-stage isozyme. Recombinant TgENO1 specifically binds to a TTTTCT DNA motif present in the cyst matrix antigen 1 (TgMAG1) gene promoter as demonstrated by gel retardation. Furthermore, direct physical interactions of both nuclear TgENO1 and TgENO2 with the TgMAG1 gene promoter are demonstrated in vivo using chromatin immunoprecipitation (ChIP) assays. Structural and biochemical studies reveal that T. gondii enolase functions are multifaceted, including the coordination of gene regulation in parasitic stage development. Enolase 1 provides a potential lead in the design of drugs against Toxoplasma brain cysts.« less

The neural markers of MRI to differentiate depression and panic disorder.

PubMed

Lai, Chien-Han

2018-04-27

Depression and panic disorder (PD) share the common pathophysiology from the perspectives of neurotransmitters. The relatively high comorbidity between depression and PD contributes to the substantial obstacles to differentiate from depression and PD, especially for the brain pathophysiology. There are significant differences in the diagnostic criteria between depression and PD. However, the paradox of similar pathophysiology and different diagnostic criteria in these two disorders were still the issues needing to be addressed. Therefore the clarification of potential difference in the field of neuroscience and pathophysiology between depression and PD can help the clinicians and scientists to understand more comprehensively about significant differences between depression and PD. The researchers should be curious about the underlying difference of pathophysiology beneath the significant distinction of clinical symptoms. In this review article, I tried to find some evidences for the differences between depression and PD, especially for neural markers revealed by magnetic resonance imaging (MRI). The distinctions of structural and functional alterations in depression and PD are reviewed. From the structural perspectives, PD seems to have less severe gray matter alterations in frontal and temporal lobes than depression. The study of white matter microintegrity reveals more widespread alterations in fronto-limbic circuit of depression patients than PD patients, such as the uncinate fasciculus and anterior thalamic radiation. PD might have a more restrictive pattern of structural alterations when compared to depression. For the functional perspectives, the core site of depression pathophysiology is the anterior subnetwork of resting-state network, such as anterior cingulate cortex, which is not significantly altered in PD. A possibly emerging pattern of fronto-limbic distinction between depression and PD has been revealed by these explorative reports. The future trend for machine learning and pattern recognition might confirm the differentiation pattern between depression and PD based on the explorative results. Copyright © 2018 Elsevier Inc. All rights reserved.

Engineering and functional properties of biodegradable pellets developed from various agro-industrial wastes using extrusion technology.

PubMed

Jan, Kulsum; Riar, C S; Saxena, D C

2015-12-01

Different agro-industrial wastes were mixed with different plasticizers and extruded to form the pellets to be used further for development of biodegradable molded pots. Bulk density and macro-porosity are the important engineering properties used to determine the functional characteristics of the biodegradable pellets viz., expansion volume, water solubility, product colour, flowability and compactness. Significant differences in the functional properties of pellets with varying bulk densities (loose and tapped) and macro-porosities (loose, tapped) were observed. The observed mean bulk density of biodegradable pellets made from different formulations ranged between 0.213 and 0.560 g/ml for loose fill conditions and 0.248 to 0.604 g/ml for tapped fill conditions. Biodegradable pellets bear a good compaction for both loose and tapped fill methods. The mean macro-porosity of biodegradable pellets ranged between 1.19 and 54.48 % for loose fill condition and 0.29 to 53.35 % for tapped fill condition. Hausner ratio (HR) for biodegradable pellets varied from 1.026 to 1.328, indicating a good flowability of biodegradable pellets. Pearson's correlation between engineering properties and functional properties of biodegradable pellets revealed that from engineering properties functional properties can be predicted.

A guide to large-scale RNA sample preparation.

PubMed

Baronti, Lorenzo; Karlsson, Hampus; Marušič, Maja; Petzold, Katja

2018-05-01

RNA is becoming more important as an increasing number of functions, both regulatory and enzymatic, are being discovered on a daily basis. As the RNA boom has just begun, most techniques are still in development and changes occur frequently. To understand RNA functions, revealing the structure of RNA is of utmost importance, which requires sample preparation. We review the latest methods to produce and purify a variation of RNA molecules for different purposes with the main focus on structural biology and biophysics. We present a guide aimed at identifying the most suitable method for your RNA and your biological question and highlighting the advantages of different methods. Graphical abstract In this review we present different methods for large-scale production and purification of RNAs for structural and biophysical studies.

Inhibition of RAS activation due to a homozygous ezrin variant in patients with profound intellectual disability.

PubMed

Riecken, Lars Björn; Tawamie, Hasan; Dornblut, Carsten; Buchert, Rebecca; Ismayel, Amina; Schulz, Alexander; Schumacher, Johannes; Sticht, Heinrich; Pohl, Katja J; Cui, Yan; Reis, André; Morrison, Helen; Abou Jamra, Rami

2015-02-01

Gain-of-function alterations in several components and modulators of the Ras-MAPK pathway lead to dysregulation of the pathway and cause a broad spectrum of autosomal dominant developmental disorders, collectively known as RASopathies. These findings demonstrate the importance of tight multilevel Ras regulation to safeguard signaling output and prevent aberrant activity. We have recently identified ezrin as a novel regulatory element required for Ras activation. Homozygosity mapping and exome sequencing have now revealed the first presumably disease-causing variant in the coding gene EZR in two siblings with a profound intellectual disability. Localization and membrane targeting of the altered ezrin protein appeared normal but molecular modeling suggested protein interaction surfaces to be disturbed. Functional analysis revealed that the altered ezrin protein is no longer able to bind Ras and facilitate its activation. Furthermore, expression of the altered ezrin protein in different cell lines resulted in abnormal cellular processes, including reduced proliferation and neuritogenesis, thus revealing a possible mechanism for its phenotype in humans. To our knowledge, this is the first report of an autosomal recessively inherited loss-of-function mutation causing reduced Ras activity and thus extends and complements the pathogenicity spectrum of known Ras-MAPK pathway disturbances. © 2014 WILEY PERIODICALS, INC.

Cdx ParaHox genes acquired distinct developmental roles after gene duplication in vertebrate evolution.

PubMed

Marlétaz, Ferdinand; Maeso, Ignacio; Faas, Laura; Isaacs, Harry V; Holland, Peter W H

2015-08-01

The functional consequences of whole genome duplications in vertebrate evolution are not fully understood. It remains unclear, for instance, why paralogues were retained in some gene families but extensively lost in others. Cdx homeobox genes encode conserved transcription factors controlling posterior development across diverse bilaterians. These genes are part of the ParaHox gene cluster. Multiple Cdx copies were retained after genome duplication, raising questions about how functional divergence, overlap, and redundancy respectively contributed to their retention and evolutionary fate. We examined the degree of regulatory and functional overlap between the three vertebrate Cdx genes using single and triple morpholino knock-down in Xenopus tropicalis followed by RNA-seq. We found that one paralogue, Cdx4, has a much stronger effect on gene expression than the others, including a strong regulatory effect on FGF and Wnt genes. Functional annotation revealed distinct and overlapping roles and subtly different temporal windows of action for each gene. The data also reveal a colinear-like effect of Cdx genes on Hox genes, with repression of Hox paralogy groups 1 and 2, and activation increasing from Hox group 5 to 11. We also highlight cases in which duplicated genes regulate distinct paralogous targets revealing pathway elaboration after whole genome duplication. Despite shared core pathways, Cdx paralogues have acquired distinct regulatory roles during development. This implies that the degree of functional overlap between paralogues is relatively low and that gene expression pattern alone should be used with caution when investigating the functional evolution of duplicated genes. We therefore suggest that developmental programmes were extensively rewired after whole genome duplication in the early evolution of vertebrates.

Effects of sex and proficiency in second language processing as revealed by a large-scale fNIRS study of school-aged children.

PubMed

Sugiura, Lisa; Ojima, Shiro; Matsuba-Kurita, Hiroko; Dan, Ippeita; Tsuzuki, Daisuke; Katura, Takusige; Hagiwara, Hiroko

2015-10-01

Previous neuroimaging studies in adults have revealed that first and second languages (L1/L2) share similar neural substrates, and that proficiency is a major determinant of the neural organization of L2 in the lexical-semantic and syntactic domains. However, little is known about neural substrates of children in the phonological domain, or about sex differences. Here, we conducted a large-scale study (n = 484) of school-aged children using functional near-infrared spectroscopy and a word repetition task, which requires a great extent of phonological processing. We investigated cortical activation during word processing, emphasizing sex differences, to clarify similarities and differences between L1 and L2, and proficiency-related differences during early L2 learning. L1 and L2 shared similar neural substrates with decreased activation in L2 compared to L1 in the posterior superior/middle temporal and angular/supramarginal gyri for both sexes. Significant sex differences were found in cortical activation within language areas during high-frequency word but not during low-frequency word processing. During high-frequency word processing, widely distributed areas including the angular/supramarginal gyri were activated in boys, while more restricted areas, excluding the angular/supramarginal gyri were activated in girls. Significant sex differences were also found in L2 proficiency-related activation: activation significantly increased with proficiency in boys, whereas no proficiency-related differences were found in girls. Importantly, cortical sex differences emerged with proficiency. Based on previous research, the present results indicate that sex differences are acquired or enlarged during language development through different cognitive strategies between sexes, possibly reflecting their different memory functions. © 2015 Wiley Periodicals, Inc.

Molecular characterization of DnaJ 5 homologs in silkworm Bombyx mori and its expression during egg diapause.

PubMed

Sirigineedi, Sasibhushan; Vijayagowri, Esvaran; Murthy, Geetha N; Rao, Guruprasada; Ponnuvel, Kangayam M

2014-12-01

A comparison of the cDNA sequences (1 056 bp) of Bombyx mori DnaJ 5 homolog with B. mori genome revealed that unlike in other Hsps, it has an intron of 234 bp. The DnaJ 5 homolog contains 351 amino acids, of which 70 contain the conserved DnaJ domain at the N-terminal end. This homolog of B. mori has all desirable functional domains similar to other insects, and the 13 different DnaJ homologs identified in B. mori genome were distributed on different chromosomes. The expressed sequence tag database analysis of Hsp40 gene expression revealed higher expression in wing disc followed by diapause-induced eggs. Microarray analysis revealed higher expression of DnaJ 5 homolog at 18th h after oviposition in diapause-induced eggs. Further validation of DnaJ 5 expression through qPCR in diapause-induced and nondiapause eggs at different time intervals revealed higher expression in diapause eggs at 18 and 24 h after oviposition, which coincided with the expression of Hsp70 as the Hsp 40 is its co-chaperone. This study thus provides an outline of the genome organization of Hsp40 gene, and its role in egg diapause induction in B. mori. © 2013 Institute of Zoology, Chinese Academy of Sciences.

Modular biological function is most effectively captured by combining molecular interaction data types.

PubMed

Ames, Ryan M; Macpherson, Jamie I; Pinney, John W; Lovell, Simon C; Robertson, David L

2013-01-01

Large-scale molecular interaction data sets have the potential to provide a comprehensive, system-wide understanding of biological function. Although individual molecules can be promiscuous in terms of their contribution to function, molecular functions emerge from the specific interactions of molecules giving rise to modular organisation. As functions often derive from a range of mechanisms, we demonstrate that they are best studied using networks derived from different sources. Implementing a graph partitioning algorithm we identify subnetworks in yeast protein-protein interaction (PPI), genetic interaction and gene co-regulation networks. Among these subnetworks we identify cohesive subgraphs that we expect to represent functional modules in the different data types. We demonstrate significant overlap between the subgraphs generated from the different data types and show these overlaps can represent related functions as represented by the Gene Ontology (GO). Next, we investigate the correspondence between our subgraphs and the Gene Ontology. This revealed varying degrees of coverage of the biological process, molecular function and cellular component ontologies, dependent on the data type. For example, subgraphs from the PPI show enrichment for 84%, 58% and 93% of annotated GO terms, respectively. Integrating the interaction data into a combined network increases the coverage of GO. Furthermore, the different annotation types of GO are not predominantly associated with one of the interaction data types. Collectively our results demonstrate that successful capture of functional relationships by network data depends on both the specific biological function being characterised and the type of network data being used. We identify functions that require integrated information to be accurately represented, demonstrating the limitations of individual data types. Combining interaction subnetworks across data types is therefore essential for fully understanding the complex and emergent nature of biological function.

Characterizing the binaural contribution to speech-in-noise reception in elderly hearing-impaired listeners.

PubMed

Neher, Tobias

2017-02-01

To scrutinize the binaural contribution to speech-in-noise reception, four groups of elderly participants with or without audiometric asymmetry <2 kHz and with or without near-normal binaural intelligibility level difference (BILD) completed tests of monaural and binaural phase sensitivity as well as cognitive function. Groups did not differ in age, overall degree of hearing loss, or cognitive function. Analyses revealed an influence of BILD status but not audiometric asymmetry on monaural phase sensitivity, strong correlations between monaural and binaural detection thresholds, and monaural and binaural but not cognitive BILD contributions. Furthermore, the N 0 S π threshold at 500 Hz predicted BILD performance effectively.

Identification of three duplicated Spin genes in medaka (Oryzias latipes).

PubMed

Wang, Xiao-Lei; Mei, Jie; Sun, Min; Hong, Yun-Han; Gui, Jian-Fang

2005-05-09

Gene and genomic duplications are very important and frequent events in fish evolution, and the divergence of duplicated genes in sequences and functions is a focus of research on gene evolution. Here, we report the identification and characterization of three duplicated Spindlin (Spin) genes from medaka (Oryzias latipes): OlSpinA, OlSpinB, and OlSpinC. Molecular cloning, genomic DNA Blast analysis and phylogenetic relationship analysis demonstrated that the three duplicated OlSpin genes should belong to gene duplication. Furthermore, Western blot analysis revealed significant expression differences of the three OlSpins among different tissues and during embryogenesis in medaka, and suggested that sequence and functional divergence might have occurred in evolution among them.

Differential structural and resting state connectivity between insular subdivisions and other pain-related brain regions.

PubMed

Wiech, K; Jbabdi, S; Lin, C S; Andersson, J; Tracey, I

2014-10-01

Functional neuroimaging studies suggest that the anterior, mid, and posterior division of the insula subserve different functions in the perception of pain. The anterior insula (AI) has predominantly been associated with cognitive-affective aspects of pain, while the mid and posterior divisions have been implicated in sensory-discriminative processing. We examined whether this functional segregation is paralleled by differences in (1) structural and (2) resting state connectivity and (3) in correlations with pain-relevant psychological traits. Analyses were restricted to the 3 insular subdivisions and other pain-related brain regions. Both type of analyses revealed largely overlapping results. The AI division was predominantly connected to the ventrolateral prefrontal cortex (structural and resting state connectivity) and orbitofrontal cortex (structural connectivity). In contrast, the posterior insula showed strong connections to the primary somatosensory cortex (SI; structural connectivity) and secondary somatosensory cortex (SII; structural and resting state connectivity). The mid insula displayed a hybrid connectivity pattern with strong connections with the ventrolateral prefrontal cortex, SII (structural and resting state connectivity) and SI (structural connectivity). Moreover, resting state connectivity revealed strong connectivity of all 3 subdivisions with the thalamus. On the behavioural level, AI structural connectivity was related to the individual degree of pain vigilance and awareness that showed a positive correlation with AI-amygdala connectivity and a negative correlation with AI-rostral anterior cingulate cortex connectivity. In sum, our findings show a differential structural and resting state connectivity for the anterior, mid, and posterior insula with other pain-relevant brain regions, which might at least partly explain their different functional profiles in pain processing. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

A new multi-scale method to reveal hierarchical modular structures in biological networks.

PubMed

Jiao, Qing-Ju; Huang, Yan; Shen, Hong-Bin

2016-11-15

Biological networks are effective tools for studying molecular interactions. Modular structure, in which genes or proteins may tend to be associated with functional modules or protein complexes, is a remarkable feature of biological networks. Mining modular structure from biological networks enables us to focus on a set of potentially important nodes, which provides a reliable guide to future biological experiments. The first fundamental challenge in mining modular structure from biological networks is that the quality of the observed network data is usually low owing to noise and incompleteness in the obtained networks. The second problem that poses a challenge to existing approaches to the mining of modular structure is that the organization of both functional modules and protein complexes in networks is far more complicated than was ever thought. For instance, the sizes of different modules vary considerably from each other and they often form multi-scale hierarchical structures. To solve these problems, we propose a new multi-scale protocol for mining modular structure (named ISIMB) driven by a node similarity metric, which works in an iteratively converged space to reduce the effects of the low data quality of the observed network data. The multi-scale node similarity metric couples both the local and the global topology of the network with a resolution regulator. By varying this resolution regulator to give different weightings to the local and global terms in the metric, the ISIMB method is able to fit the shape of modules and to detect them on different scales. Experiments on protein-protein interaction and genetic interaction networks show that our method can not only mine functional modules and protein complexes successfully, but can also predict functional modules from specific to general and reveal the hierarchical organization of protein complexes.

Abnormalities in fronto-striatal connectivity within language networks relate to differences in grey-matter heterogeneity in Asperger syndrome☆

PubMed Central

Radulescu, Eugenia; Minati, Ludovico; Ganeshan, Balaji; Harrison, Neil A.; Gray, Marcus A.; Beacher, Felix D.C.C.; Chatwin, Chris; Young, Rupert C.D.; Critchley, Hugo D.

2013-01-01

Asperger syndrome (AS) is an Autism Spectrum Disorder (ASD) characterised by qualitative impairment in the development of emotional and social skills with relative preservation of general intellectual abilities, including verbal language. People with AS may nevertheless show atypical language, including rate and frequency of speech production. We previously observed that abnormalities in grey matter homogeneity (measured with texture analysis of structural MR images) in AS individuals when compared with controls are also correlated with the volume of caudate nucleus. Here, we tested a prediction that these distributed abnormalities in grey matter compromise the functional integrity of brain networks supporting verbal communication skills. We therefore measured the functional connectivity between caudate nucleus and cortex during a functional neuroimaging study of language generation (verbal fluency), applying psycho-physiological interaction (PPI) methods to test specifically for differences attributable to grey matter heterogeneity in AS participants. Furthermore, we used dynamic causal modelling (DCM) to characterise the causal directionality of these differences in interregional connectivity during word production. Our results revealed a diagnosis-dependent influence of grey matter heterogeneity on the functional connectivity of the caudate nuclei with right insula/inferior frontal gyrus and anterior cingulate, respectively with the left superior frontal gyrus and right precuneus. Moreover, causal modelling of interactions between inferior frontal gyri, caudate and precuneus, revealed a reliance on bottom-up (stimulus-driven) connections in AS participants that contrasted with a dominance of top-down (cognitive control) connections from prefrontal cortex observed in control participants. These results provide detailed support for previously hypothesised central disconnectivity in ASD and specify discrete brain network targets for diagnosis and therapy in ASD. PMID:24179823

Proteomic Profiling in the Brain of CLN1 Disease Model Reveals Affected Functional Modules.

PubMed

Tikka, Saara; Monogioudi, Evanthia; Gotsopoulos, Athanasios; Soliymani, Rabah; Pezzini, Francesco; Scifo, Enzo; Uusi-Rauva, Kristiina; Tyynelä, Jaana; Baumann, Marc; Jalanko, Anu; Simonati, Alessandro; Lalowski, Maciej

2016-03-01

Neuronal ceroid lipofuscinoses (NCL) are the most commonly inherited progressive encephalopathies of childhood. Pathologically, they are characterized by endolysosomal storage with different ultrastructural features and biochemical compositions. The molecular mechanisms causing progressive neurodegeneration and common molecular pathways linking expression of different NCL genes are largely unknown. We analyzed proteome alterations in the brains of a mouse model of human infantile CLN1 disease-palmitoyl-protein thioesterase 1 (Ppt1) gene knockout and its wild-type age-matched counterpart at different stages: pre-symptomatic, symptomatic and advanced. For this purpose, we utilized a combination of laser capture microdissection-based quantitative liquid chromatography tandem mass spectrometry (MS) and matrix-assisted laser desorption/ionization time-of-flight MS imaging to quantify/visualize the changes in protein expression in disease-affected brain thalamus and cerebral cortex tissue slices, respectively. Proteomic profiling of the pre-symptomatic stage thalamus revealed alterations mostly in metabolic processes and inhibition of various neuronal functions, i.e., neuritogenesis. Down-regulation in dynamics associated with growth of plasma projections and cellular protrusions was further corroborated by findings from RNA sequencing of CLN1 patients' fibroblasts. Changes detected at the symptomatic stage included: mitochondrial functions, synaptic vesicle transport, myelin proteome and signaling cascades, such as RhoA signaling. Considerable dysregulation of processes related to mitochondrial cell death, RhoA/Huntington's disease signaling and myelin sheath breakdown were observed at the advanced stage of the disease. The identified changes in protein levels were further substantiated by bioinformatics and network approaches, immunohistochemistry on brain tissues and literature knowledge, thus identifying various functional modules affected in the CLN1 childhood encephalopathy.

Identification of Loci and Functional Characterization of Trichothecene Biosynthesis Genes in Filamentous Fungi of the Genus Trichoderma▿†

PubMed Central

Cardoza, R. E.; Malmierca, M. G.; Hermosa, M. R.; Alexander, N. J.; McCormick, S. P.; Proctor, R. H.; Tijerino, A. M.; Rumbero, A.; Monte, E.; Gutiérrez, S.

2011-01-01

Trichothecenes are mycotoxins produced by Trichoderma, Fusarium, and at least four other genera in the fungal order Hypocreales. Fusarium has a trichothecene biosynthetic gene (TRI) cluster that encodes transport and regulatory proteins as well as most enzymes required for the formation of the mycotoxins. However, little is known about trichothecene biosynthesis in the other genera. Here, we identify and characterize TRI gene orthologues (tri) in Trichoderma arundinaceum and Trichoderma brevicompactum. Our results indicate that both Trichoderma species have a tri cluster that consists of orthologues of seven genes present in the Fusarium TRI cluster. Organization of genes in the cluster is the same in the two Trichoderma species but differs from the organization in Fusarium. Sequence and functional analysis revealed that the gene (tri5) responsible for the first committed step in trichothecene biosynthesis is located outside the cluster in both Trichoderma species rather than inside the cluster as it is in Fusarium. Heterologous expression analysis revealed that two T. arundinaceum cluster genes (tri4 and tri11) differ in function from their Fusarium orthologues. The Tatri4-encoded enzyme catalyzes only three of the four oxygenation reactions catalyzed by the orthologous enzyme in Fusarium. The Tatri11-encoded enzyme catalyzes a completely different reaction (trichothecene C-4 hydroxylation) than the Fusarium orthologue (trichothecene C-15 hydroxylation). The results of this study indicate that although some characteristics of the tri/TRI cluster have been conserved during evolution of Trichoderma and Fusarium, the cluster has undergone marked changes, including gene loss and/or gain, gene rearrangement, and divergence of gene function. PMID:21642405

COPT6 Is a Plasma Membrane Transporter That Functions in Copper Homeostasis in Arabidopsis and Is a Novel Target of SQUAMOSA Promoter-binding Protein-like 7*

PubMed Central

Jung, Ha-il; Gayomba, Sheena R.; Rutzke, Michael A.; Craft, Eric; Kochian, Leon V.; Vatamaniuk, Olena K.

2012-01-01

Among the mechanisms controlling copper homeostasis in plants is the regulation of its uptake and tissue partitioning. Here we characterized a newly identified member of the conserved CTR/COPT family of copper transporters in Arabidopsis thaliana, COPT6. We showed that COPT6 resides at the plasma membrane and mediates copper accumulation when expressed in the Saccharomyces cerevisiae copper uptake mutant. Although the primary sequence of COPT6 contains the family conserved domains, including methionine-rich motifs in the extracellular N-terminal domain and a second transmembrane helix (TM2), it is different from the founding family member, S. cerevisiae Ctr1p. This conclusion was based on the finding that although the positionally conserved Met106 residue in the TM2 of COPT6 is functionally essential, the conserved Met27 in the N-terminal domain is not. Structure-function studies revealed that the N-terminal domain is dispensable for COPT6 function in copper-replete conditions but is important under copper-limiting conditions. In addition, COPT6 interacts with itself and with its homolog, COPT1, unlike Ctr1p, which interacts only with itself. Analyses of the expression pattern showed that although COPT6 is expressed in different cell types of different plant organs, the bulk of its expression is located in the vasculature. We also show that COPT6 expression is regulated by copper availability that, in part, is controlled by a master regulator of copper homeostasis, SPL7. Finally, studies using the A. thaliana copt6-1 mutant and plants overexpressing COPT6 revealed its essential role during copper limitation and excess. PMID:22865877

Statistical characterization of Earth’s heterogeneities from seismic scattering

NASA Astrophysics Data System (ADS)

Zheng, Y.; Wu, R.

2009-12-01

The distortion of a teleseismic wavefront carries information about the heterogeneities through which the wave propagates and it is manifestited as logarithmic amplitude (logA) and phase fluctuations of the direct P wave recorded by a seismic network. By cross correlating the fluctuations (e.g., logA-logA or phase-phase), we obtain coherence functions, which depend on spatial lags between stations and incident angles between the incident waves. We have mathematically related the depth-dependent heterogeneity spectrum to the observable coherence functions using seismic scattering theory. We will show that our method has sharp depth resolution. Using the HiNet seismic network data in Japan, we have inverted power spectra for two depth ranges, ~0-120km and below ~120km depth. The coherence functions formed by different groups of stations or by different groups of earthquakes at different back azimuths are similar. This demonstrates that the method is statistically stable and the inhomogeneities are statistically stationary. In both depth intervals, the trend of the spectral amplitude decays from large scale to small scale in a power-law fashion with exceptions at ~50km for the logA data. Due to the spatial spacing of the seismometers, only information from length scale 15km to 200km is inverted. However our scattering method provides new information on small to intermediate scales that are comparable to scales of the recycled materials and thus is complimentary to the global seismic tomography which reveals mainly large-scale heterogeneities on the order of ~1000km. The small-scale heterogeneities revealed here are not likely of pure thermal origin. Therefore, the length scale and strength of heterogeneities as a function of depth may provide important constraints in mechanical mixing of various components in the mantle convection.

Development of large-scale functional brain networks in children.

PubMed

Supekar, Kaustubh; Musen, Mark; Menon, Vinod

2009-07-01

The ontogeny of large-scale functional organization of the human brain is not well understood. Here we use network analysis of intrinsic functional connectivity to characterize the organization of brain networks in 23 children (ages 7-9 y) and 22 young-adults (ages 19-22 y). Comparison of network properties, including path-length, clustering-coefficient, hierarchy, and regional connectivity, revealed that although children and young-adults' brains have similar "small-world" organization at the global level, they differ significantly in hierarchical organization and interregional connectivity. We found that subcortical areas were more strongly connected with primary sensory, association, and paralimbic areas in children, whereas young-adults showed stronger cortico-cortical connectivity between paralimbic, limbic, and association areas. Further, combined analysis of functional connectivity with wiring distance measures derived from white-matter fiber tracking revealed that the development of large-scale brain networks is characterized by weakening of short-range functional connectivity and strengthening of long-range functional connectivity. Importantly, our findings show that the dynamic process of over-connectivity followed by pruning, which rewires connectivity at the neuronal level, also operates at the systems level, helping to reconfigure and rebalance subcortical and paralimbic connectivity in the developing brain. Our study demonstrates the usefulness of network analysis of brain connectivity to elucidate key principles underlying functional brain maturation, paving the way for novel studies of disrupted brain connectivity in neurodevelopmental disorders such as autism.

Development of Large-Scale Functional Brain Networks in Children

PubMed Central

Supekar, Kaustubh; Musen, Mark; Menon, Vinod

2009-01-01

The ontogeny of large-scale functional organization of the human brain is not well understood. Here we use network analysis of intrinsic functional connectivity to characterize the organization of brain networks in 23 children (ages 7–9 y) and 22 young-adults (ages 19–22 y). Comparison of network properties, including path-length, clustering-coefficient, hierarchy, and regional connectivity, revealed that although children and young-adults' brains have similar “small-world” organization at the global level, they differ significantly in hierarchical organization and interregional connectivity. We found that subcortical areas were more strongly connected with primary sensory, association, and paralimbic areas in children, whereas young-adults showed stronger cortico-cortical connectivity between paralimbic, limbic, and association areas. Further, combined analysis of functional connectivity with wiring distance measures derived from white-matter fiber tracking revealed that the development of large-scale brain networks is characterized by weakening of short-range functional connectivity and strengthening of long-range functional connectivity. Importantly, our findings show that the dynamic process of over-connectivity followed by pruning, which rewires connectivity at the neuronal level, also operates at the systems level, helping to reconfigure and rebalance subcortical and paralimbic connectivity in the developing brain. Our study demonstrates the usefulness of network analysis of brain connectivity to elucidate key principles underlying functional brain maturation, paving the way for novel studies of disrupted brain connectivity in neurodevelopmental disorders such as autism. PMID:19621066

Do obesity and weight loss affect vocal function?

PubMed

Solomon, Nancy Pearl; Helou, Leah B; Dietrich-Burns, Katie; Stojadinovic, Alexander

2011-02-01

Obesity may be associated with increased tissue bulk in the laryngeal airway, neck, and chest wall, and as such may affect vocal function. Eight obese and eight nonobese adults participated in this study; the obese participants underwent bariatric surgical procedures. This mixed-design study included cross-sectional analysis for group differences and longitudinal analysis for multidimensional changes in vocal function from four assessments collected over 6 months. No significant differences were detected between groups from the preoperative assessment. Further, no changes were detected over time for acoustic parameters, maximum phonation time, laryngeal airway resistance, and airflow during a sustained vowel for either group. Only minor differences were detected for strain, pitch, and loudness perceptions of voice over time, but not between groups. Phonation threshold pressure (PTP), at comfortable and high pitches (30% and 80% of the F0 range) changed significantly over time, but not between groups. Examination of individual data revealed a trend for PTP at 30% F0 to decrease as body mass index decreased. PTP may be informative for assessing vocal function in clients who present with obesity and voice symptoms. © Thieme Medical Publishers.

Kinematic and kinetic synergies of the lower extremities during the pull in olympic weightlifting.

PubMed

Kipp, Kristof; Redden, Josh; Sabick, Michelle; Harris, Chad

2012-07-01

The purpose of this study was to identify multijoint lower extremity kinematic and kinetic synergies in weightlifting and compare these synergies between joints and across different external loads. Subjects completed sets of the clean exercise at loads equal to 65, 75, and 85% of their estimated 1-RM. Functional data analysis was used to extract principal component functions (PCF's) for hip, knee, and ankle joint angles and moments of force during the pull phase of the clean at all loads. The PCF scores were then compared between joints and across loads to determine how much of each PCF was present at each joint and how it differed across loads. The analyses extracted two kinematic and four kinetic PCF's. The statistical comparisons indicated that all kinematic and two of the four kinetic PCF's did not differ across load, but scaled according to joint function. The PCF's captured a set of joint- and load-specific synergies that quantified biomechanical function of the lower extremity during Olympic weightlifting and revealed important technical characteristics that should be considered in sports training and future research.

Human chimera-type galectin-3: defining the critical tail length for high-affinity glycoprotein/cell surface binding and functional competition with galectin-1 in neuroblastoma cell growth regulation.

PubMed

Kopitz, Jürgen; Vértesy, Sabine; André, Sabine; Fiedler, Sabine; Schnölzer, Martina; Gabius, Hans-Joachim

2014-09-01

Many human proteins have a modular design with receptor and structural domains. Using adhesion/growth-regulatory galectin-3 as model, we describe an interdisciplinary strategy to define the functional significance of its tail established by nine non-triple helical collagen-like repeats (I-IX) and the N-terminal peptide. Genetic engineering with sophisticated mass spectrometric product analysis provided the tools for biotesting, i.e. eight protein variants with different degrees of tail truncation. Evidently,various aspects of galectin-3 activity (cis binding and cell bridging) are affected by tail shortening in a different manner. Thus, this combined approach reveals an unsuspected complexity of structure-function relationship, encouraging further application beyond this chimera-type galectin. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Metaproteogenomics Reveals Taxonomic and Functional Changes between Cecal and Fecal Microbiota in Mouse

PubMed Central

Tanca, Alessandro; Manghina, Valeria; Fraumene, Cristina; Palomba, Antonio; Abbondio, Marcello; Deligios, Massimo; Silverman, Michael; Uzzau, Sergio

2017-01-01

Previous studies on mouse models report that cecal and fecal microbial communities may differ in the taxonomic structure, but little is known about their respective functional activities. Here, we employed a metaproteogenomic approach, including 16S rRNA gene sequencing, shotgun metagenomics and shotgun metaproteomics, to analyze the microbiota of paired mouse cecal contents (CCs) and feces, with the aim of identifying changes in taxon-specific functions. As a result, Gram-positive anaerobes were observed as considerably higher in CCs, while several key enzymes, involved in oxalate degradation, glutamate/glutamine metabolism, and redox homeostasis, and most actively expressed by Bacteroidetes, were clearly more represented in feces. On the whole, taxon and function abundance appeared to vary consistently with environmental changes expected to occur throughout the transit from the cecum to outside the intestine, especially when considering metaproteomic data. The results of this study indicate that functional and metabolic differences exist between CC and stool samples, paving the way to further metaproteogenomic investigations aimed at elucidating the functional dynamics of the intestinal microbiota. PMID:28352255

Separate effects of sex hormones and sex chromosomes on brain structure and function revealed by high-resolution magnetic resonance imaging and spatial navigation assessment of the Four Core Genotype mouse model.

PubMed

Corre, Christina; Friedel, Miriam; Vousden, Dulcie A; Metcalf, Ariane; Spring, Shoshana; Qiu, Lily R; Lerch, Jason P; Palmert, Mark R

2016-03-01

Males and females exhibit several differences in brain structure and function. To examine the basis for these sex differences, we investigated the influences of sex hormones and sex chromosomes on brain structure and function in mice. We used the Four Core Genotype (4CG) mice, which can generate both male and female mice with XX or XY sex chromosome complement, allowing the decoupling of sex chromosomes from hormonal milieu. To examine whole brain structure, high-resolution ex vivo MRI was performed, and to assess differences in cognitive function, mice were trained on a radial arm maze. Voxel-wise and volumetric analyses of MRI data uncovered a striking independence of hormonal versus chromosomal influences in 30 sexually dimorphic brain regions. For example, the bed nucleus of the stria terminalis and the parieto-temporal lobe of the cerebral cortex displayed steroid-dependence while the cerebellar cortex, corpus callosum, and olfactory bulbs were influenced by sex chromosomes. Spatial learning and memory demonstrated strict hormone-dependency with no apparent influence of sex chromosomes. Understanding the influences of chromosomes and hormones on brain structure and function is important for understanding sex differences in brain structure and function, an endeavor that has eventual implications for understanding sex biases observed in the prevalence of psychiatric disorders.

Combination of volume and perfusion parameters reveals different types of grey matter changes in schizophrenia.

PubMed

Xu, Lixue; Qin, Wen; Zhuo, Chuanjun; Liu, Huaigui; Zhu, Jiajia; Yu, Chunshui

2017-03-27

Diverse brain structural and functional changes have been reported in schizophrenia. Identifying different types of brain changes may help to understand the neural mechanisms and to develop reliable biomarkers in schizophrenia. We aimed to categorize different grey matter changes in schizophrenia based on grey matter volume (GMV) and cerebral blood flow (CBF). Structural and perfusion magnetic resonance imaging data were acquired in 100 schizophrenia patients and 95 healthy comparison subjects. Voxel-based GMV comparison was used to show structural changes, CBF analysis was used to demonstrate functional changes. We identified three types of grey matter changes in schizophrenia: structural and functional impairments in the anterior cingulate cortex and insular cortex, displaying reduction in both GMV and CBF; structural impairment with preserved function in the frontal and temporal cortices, demonstrating decreased GMV with normal CBF; pure functional abnormality in the anterior cingulate cortex and lateral prefrontal cortex and putamen, showing altered CBF with normal GMV. By combination of GMV and CBF, we identified three types of grey matter changes in schizophrenia. These findings may help to understand the complex manifestations and to develop reliable biomarkers in schizophrenia.

Relating children's attentional capabilities to intelligence, memory, and academic achievement: a test of construct specificity in children with asthma.

PubMed

Annett, Robert D; Bender, Bruce G; Gordon, Michael

2007-01-01

The relationship between attention, intelligence, memory, achievement, and behavior in a large population (N = 939) of children without neuropsychologic problems was investigated in children with mild and moderate asthma. It was hypothesized that different levels of children's attentional capabilities would be associated with different levels of intellectual, memory, and academic abilities. Children ages 6-12 at the eight clinical centers of the Childhood Asthma Management Program (CAMP) were enrolled in this study. Standardized measures of child neuropsychological and behavioral performance were administered to all participants, with analyses examining both the developmental trajectory of child attentional capabilities and the associations between Continuous Performance Test (CPT) scores and intellectual functioning, and measures of memory, academic achievement, and behavioral functioning. Findings demonstrated that correct responses on the CPT increase significantly with age, while commission errors decrease significantly with age. Performance levels on the CPT were associated with differences in child intellectual function, memory, and academic achievement. Overall these findings reveal how impairments in child attention skills were associated with normal levels of performance on measures of children's intelligence, memory, academic achievement, and behavioral functioning, suggesting that CPT performance is a salient marker of brain function.

Be together, not the same: Spatiotemporal organization of different cilia types generates distinct transport functions

NASA Astrophysics Data System (ADS)

Nawroth, Janna; Guo, Hanliang; Ruby, Edward; Dabiri, John; McFall-Ngai, Margaret; Kanso, Eva

2016-11-01

Motile cilia are microscopic, hair-like structures on the cell surface that can sense and propel the extracellular fluid environment. Cilia are often thought to be limited to stereotypic morphologies, beat kinematics and non-discriminatory clearance functions, but we find that the spatiotemporal organization of different cilia types and beat behaviors can generate complex flow patterns and transport functions. Here, we present a case study in the Hawaiian bobtail squid where collective ciliary activity and resulting flow fields help recruit symbiont bacteria to the animal host. In particular, we demonstrate empirically and computationally how the squid's internal cilia act like a microfluidic device that actively filters the water for potential bacterial candidates and also provides a sheltered zone allowing for accumulation of mucus and bacteria into a biofilm. Moreover, in this sheltered zone, different cilia-driven flows enhance diffusion of biochemical signals, which could accelerate specific bacteria-host recognition. These results suggest that studying cilia activity on the population level might reveal a diverse range of biological transport and sensing functions. Moreover, understanding cilia as functional building blocks could inspire the design of ciliated robots and devices.

Phylogenetic and Functional Substrate Specificity for Endolithic Microbial Communities in Hyper-Arid Environments

PubMed Central

Crits-Christoph, Alexander; Robinson, Courtney K.; Ma, Bing; Ravel, Jacques; Wierzchos, Jacek; Ascaso, Carmen; Artieda, Octavio; Souza-Egipsy, Virginia; Casero, M. Cristina; DiRuggiero, Jocelyne

2016-01-01

Under extreme water deficit, endolithic (inside rock) microbial ecosystems are considered environmental refuges for life in cold and hot deserts, yet their diversity and functional adaptations remain vastly unexplored. The metagenomic analyses of the communities from two rock substrates, calcite and ignimbrite, revealed that they were dominated by Cyanobacteria, Actinobacteria, and Chloroflexi. The relative distribution of major phyla was significantly different between the two substrates and biodiversity estimates, from 16S rRNA gene sequences and from the metagenomic data, all pointed to a higher taxonomic diversity in the calcite community. While both endolithic communities showed adaptations to extreme aridity and to the rock habitat, their functional capabilities revealed significant differences. ABC transporters and pathways for osmoregulation were more diverse in the calcite chasmoendolithic community. In contrast, the ignimbrite cryptoendolithic community was enriched in pathways for secondary metabolites, such as non-ribosomal peptides (NRP) and polyketides (PK). Assemblies of the metagenome data produced population genomes for the major phyla found in both communities and revealed a greater diversity of Cyanobacteria population genomes for the calcite substrate. Draft genomes of the dominant Cyanobacteria in each community were constructed with more than 93% estimated completeness. The two annotated proteomes shared 64% amino acid identity and a significantly higher number of genes involved in iron update, and NRPS gene clusters, were found in the draft genomes from the ignimbrite. Both the community-wide and genome-specific differences may be related to higher water availability and the colonization of large fissures and cracks in the calcite in contrast to a harsh competition for colonization space and nutrient resources in the narrow pores of the ignimbrite. Together, these results indicated that the habitable architecture of both lithic substrates- chasmoendolithic versus cryptoendolithic – might be an essential element in determining the colonization and the diversity of the microbial communities in endolithic substrates at the dry limit for life. PMID:27014224

Comparative and Evolutionary Analysis of the HES/HEY Gene Family Reveal Exon/Intron Loss and Teleost Specific Duplication Events

PubMed Central

Ma, Zhaowu; Zhou, Yang; Abbood, Nibras Najm; Liu, Jianfeng; Su, Li; Jia, Haibo; Guo, An-Yuan

2012-01-01

Background HES/HEY genes encode a family of basic helix-loop-helix (bHLH) transcription factors with both bHLH and Orange domain. HES/HEY proteins are direct targets of the Notch signaling pathway and play an essential role in developmental decisions, such as the developments of nervous system, somitogenesis, blood vessel and heart. Despite their important functions, the origin and evolution of this HES/HEY gene family has yet to be elucidated. Methods and Findings In this study, we identified genes of the HES/HEY family in representative species and performed evolutionary analysis to elucidate their origin and evolutionary process. Our results showed that the HES/HEY genes only existed in metazoans and may originate from the common ancestor of metazoans. We identified HES/HEY genes in more than 10 species representing the main lineages. Combining the bHLH and Orange domain sequences, we constructed the phylogenetic trees by different methods (Bayesian, ML, NJ and ME) and classified the HES/HEY gene family into four groups. Our results indicated that this gene family had undergone three expansions, which were along with the origins of Eumetazoa, vertebrate, and teleost. Gene structure analysis revealed that the HES/HEY genes were involved in exon and/or intron loss in different species lineages. Genes of this family were duplicated in bony fishes and doubled than other vertebrates. Furthermore, we studied the teleost-specific duplications in zebrafish and investigated the expression pattern of duplicated genes in different tissues by RT-PCR. Finally, we proposed a model to show the evolution of this gene family with processes of expansion, exon/intron loss, and motif loss. Conclusions Our study revealed the evolution of HES/HEY gene family, the expression and function divergence of duplicated genes, which also provide clues for the research of Notch function in development. This study shows a model of gene family analysis with gene structure evolution and duplication. PMID:22808219

Comparative and evolutionary analysis of the HES/HEY gene family reveal exon/intron loss and teleost specific duplication events.

PubMed

Zhou, Mi; Yan, Jun; Ma, Zhaowu; Zhou, Yang; Abbood, Nibras Najm; Liu, Jianfeng; Su, Li; Jia, Haibo; Guo, An-Yuan

2012-01-01

HES/HEY genes encode a family of basic helix-loop-helix (bHLH) transcription factors with both bHLH and Orange domain. HES/HEY proteins are direct targets of the Notch signaling pathway and play an essential role in developmental decisions, such as the developments of nervous system, somitogenesis, blood vessel and heart. Despite their important functions, the origin and evolution of this HES/HEY gene family has yet to be elucidated. In this study, we identified genes of the HES/HEY family in representative species and performed evolutionary analysis to elucidate their origin and evolutionary process. Our results showed that the HES/HEY genes only existed in metazoans and may originate from the common ancestor of metazoans. We identified HES/HEY genes in more than 10 species representing the main lineages. Combining the bHLH and Orange domain sequences, we constructed the phylogenetic trees by different methods (Bayesian, ML, NJ and ME) and classified the HES/HEY gene family into four groups. Our results indicated that this gene family had undergone three expansions, which were along with the origins of Eumetazoa, vertebrate, and teleost. Gene structure analysis revealed that the HES/HEY genes were involved in exon and/or intron loss in different species lineages. Genes of this family were duplicated in bony fishes and doubled than other vertebrates. Furthermore, we studied the teleost-specific duplications in zebrafish and investigated the expression pattern of duplicated genes in different tissues by RT-PCR. Finally, we proposed a model to show the evolution of this gene family with processes of expansion, exon/intron loss, and motif loss. Our study revealed the evolution of HES/HEY gene family, the expression and function divergence of duplicated genes, which also provide clues for the research of Notch function in development. This study shows a model of gene family analysis with gene structure evolution and duplication.

Cytotoxicity of cadmium-free quantum dots and their use in cell bioimaging.

PubMed

Soenen, Stefaan J; Manshian, Bella B; Aubert, Tangi; Himmelreich, Uwe; Demeester, Jo; De Smedt, Stefaan C; Hens, Zeger; Braeckmans, Kevin

2014-06-16

The use of quantum dots (QDots) as bright and photostable probes for long-term fluorescence imaging is gaining more interest. Thus far, (pre)clinical use of QDots remains limited, which is primarily caused by the potential toxicity of QDots. Most QDots consist of Cd2+ ions, which are known to cause high levels of toxicity. In order to overcome this problem, several strategies have been tested, such as the generation of cadmium-free QDots. In the present study, two types of cadmium-free QDots, composed of ZnSe/ZnS (QDotZnSe) and InP/ZnS (QDotInP), were studied with respect to their cytotoxicity and cellular uptake in a variety of cell types. A multiparametric cytotoxicity approach is used, where the QDots are studied with respect to cell viability, oxidative stress, cell morphology, stem cell differentiation, and neurite outgrowth. The data reveal slight differences in uptake levels for both types of QDots (maximal for QDotZnSe), but clear differences in cytotoxicity and cell functionality effects exist, with highest toxicity for QDotZnSe. Differences between cell types and between both types of QDots can be explained by the intrinsic sensitivity of certain cell types and chemical composition of the QDots. At concentrations at which no toxic effects can be observed, the functionality of the QDots for fluorescence cell visualization is evaluated, revealing that the higher brightness of QDotZnSe overcomes most of the toxicity issues compared to that of QDotInP. Comparing the results obtained with common Cd2+-containing QDots tested under identical conditions, the importance of particle functionality is demonstrated, revealing that cadmium-free QDots tested in this study are not significantly better than Cd2+-containing QDots for long-term cell imaging and that more work needs to be performed in optimizing the brightness and surface chemistry of cadmium-free QDots for them to replace currently used Cd2+-containing QDots.

Effects of emotion regulation strategy on brain responses to the valence and social content of visual scenes.

PubMed

Vrtička, Pascal; Sander, David; Vuilleumier, Patrik

2011-04-01

Emotion Regulation (ER) includes different mechanisms aiming at volitionally modulating emotional responses, including cognitive re-evaluation (re-appraisal; REAP) or inhibition of emotion expression and behavior (expressive suppression; ESUP). However, despite the importance of these ER strategies, previous functional magnetic resonance imaging (fMRI) studies have not sufficiently disentangled the specific neural impact of REAP versus ESUP on brain responses to different kinds of emotion-eliciting events. Moreover, although different effects have been reported for stimulus valence (positive vs. negative), no study has systematically investigated how ER may change emotional processing as a function of particular stimulus content variables (i.e., social vs. nonsocial). Our fMRI study directly compared brain activation to visual scenes during the use of different ER strategies, relative to a "natural" viewing condition, but also examined the effects of ER as a function of the social versus nonsocial content of scenes, in addition to their negative versus positive valence (by manipulating these factors orthogonally in a 2×2 factorial design). Our data revealed that several prefrontal cortical areas were differentially recruited during either REAP or ESUP, independent of the valence and content of images. In addition, selective modulations by either REAP or ESUP were found depending on the negative valence of scenes (medial fusiform gyrus, anterior insula, dmPFC), and on their nonsocial (middle insula) or social (bilateral amygdala, mPFC, posterior cingulate) significance. Furthermore, we observed a significant lateralization in the amygdala for the effect of the two different ER strategies, with a predominant modulation by REAP on the left side but by ESUP on the right side. Taken together, these results do not only highlight the distributed nature of neural changes induced by ER, but also reveal the specific impact of different strategies (REAP or ESUP), and the specific sites implicated by different dimensions of emotional information (social or negative). Copyright © 2011 Elsevier Ltd. All rights reserved.

Myocardial aging as a T-cell–mediated phenomenon

PubMed Central

Ramos, Gustavo Campos; van den Berg, Anne; Nunes-Silva, Vânia; Weirather, Johannes; Peters, Laura; Burkard, Matthias; Friedrich, Mike; Pinnecker, Jürgen; Abeßer, Marco; Heinze, Katrin G.; Schuh, Kai; Beyersdorf, Niklas; Kerkau, Thomas; Demengeot, Jocelyne; Frantz, Stefan; Hofmann, Ulrich

2017-01-01

In recent years, the myocardium has been rediscovered under the lenses of immunology, and lymphocytes have been implicated in the pathogenesis of cardiomyopathies with different etiologies. Aging is an important risk factor for heart diseases, and it also has impact on the immune system. Thus, we sought to determine whether immunological activity would influence myocardial structure and function in elderly mice. Morphological, functional, and molecular analyses revealed that the age-related myocardial impairment occurs in parallel with shifts in the composition of tissue-resident leukocytes and with an accumulation of activated CD4+ Foxp3− (forkhead box P3) IFN-γ+ T cells in the heart-draining lymph nodes. A comprehensive characterization of different aged immune-deficient mouse strains revealed that T cells significantly contribute to age-related myocardial inflammation and functional decline. Upon adoptive cell transfer, the T cells isolated from the mediastinal lymph node (med-LN) of aged animals exhibited increased cardiotropism, compared with cells purified from young donors or from other irrelevant sites. Nevertheless, these cells caused rather mild effects on cardiac functionality, indicating that myocardial aging might stem from a combination of intrinsic and extrinsic (immunological) factors. Taken together, the data herein presented indicate that heart-directed immune responses may spontaneously arise in the elderly, even in the absence of a clear tissue damage or concomitant infection. These observations might shed new light on the emerging role of T cells in myocardial diseases, which primarily affect the elderly population. PMID:28255084

Molecular recognition in poly(epsilon-caprolactone)-based thermoplastic elastomers.

PubMed

Wisse, Eva; Spiering, A J H; van Leeuwen, Ellen N M; Renken, Raymond A E; Dankers, Patricia Y W; Brouwer, Linda A; van Luyn, Marja J A; Harmsen, Martin C; Sommerdijk, Nico A J M; Meijer, E W

2006-12-01

The molecular recognition properties of the hydrogen bonding segments in biodegradable thermoplastic elastomers were explored, aiming at the further functionalization of these potentially interesting biomaterials. A poly(epsilon-caprolactone)-based poly(urea) 2 was synthesized and characterized in terms of mechanical properties, processibility and histocompatibility. Comparison of the data with those obtained from the structurally related poly(urethane urea) 1 revealed that the difference in hard segment structure does not significantly affect the potency for application as a biomaterial. Nevertheless, the small differences in hard block composition had a strong effect on the molecular recognition properties of the hydrogen bonding segments. High selectivity was found for poly(urea) 2 in which bisureidobutylene-functionalized azobenzene dye 3 was selectively incorporated while bisureidopentylene-functionalized azobenzene dye 4 was completely released. In contrast, the incorporation of both dyes in poly(urethane urea) 1 led in both cases to their gradual release in time. Thermal analysis of the polymers in combination with variable temperature infrared experiments indicated that the hard blocks in 1 showed a sharp melting point, whereas those in 2 showed a very broad melting trajectory. This suggests a more precise organization of the hydrogen bonding segments in the hard blocks of poly(urea) 2 compared to poly(urethane urea) 1 and explains the results from the molecular recognition experiments. Preliminary results revealed that a bisureidobutylene-functionalized GRGDS peptide showed more supramolecular interaction with the PCL-based poly(urea), containing the bisureidobutylene recognition unit, as compared to HMW PCL, lacking this recognition unit.

The joint moderating effect of health consciousness and healthy lifestyle on consumers' willingness to use functional foods in Taiwan.

PubMed

Chen, Mei-Fang

2011-08-01

Functional foods marketed as promoting health or reducing the risk of disease open a promising avenue for consumers to pursue a healthier life. Despite the stable growth in functional foods in Taiwan, at present little is known about whether or not consumers with varying degrees of health consciousness and different healthy lifestyles will have dissimilar attitudes toward functional foods and will vary in their willingness to use them. Regression analysis of this empirical study verifies that consumers' attitudes toward functional foods do have an impact on their willingness to use such foods. Moreover, moderated regression analysis (MRA) reveals that the joint moderator of health consciousness and healthy lifestyle indeed exerts an impact on consumers' willingness to consume functional foods. Finally, one-way ANOVA tests show that there are some differences between the consumers of the "Healthy Life Attentive" group and those of the "Healthy Life Inattentive" one both in attitudes toward and in willingness to consume functional foods. The empirical results and findings from this study would be valuable for the marketers in the functional food industry to formulate marketing communication strategies and facilitate this industry's development. Copyright © 2011 Elsevier Ltd. All rights reserved.

Gastric microbial community profiling reveals a dysbiotic cancer-associated microbiota

PubMed Central

Pereira-Marques, Joana; Pinto-Ribeiro, Ines; Costa, Jose L; Carneiro, Fatima; Machado, Jose C

2018-01-01

Objective Gastric carcinoma development is triggered by Helicobacter pylori. Chronic H. pylori infection leads to reduced acid secretion, which may allow the growth of a different gastric bacterial community. This change in the microbiome may increase aggression to the gastric mucosa and contribute to malignancy. Our aim was to evaluate the composition of the gastric microbiota in chronic gastritis and in gastric carcinoma. Design The gastric microbiota was retrospectively investigated in 54 patients with gastric carcinoma and 81 patients with chronic gastritis by 16S rRNA gene profiling, using next-generation sequencing. Differences in microbial composition of the two patient groups were assessed using linear discriminant analysis effect size. Associations between the most relevant taxa and clinical diagnosis were validated by real-time quantitative PCR. Predictive functional profiling of microbial communities was obtained with PICRUSt. Results The gastric carcinoma microbiota was characterised by reduced microbial diversity, by decreased abundance of Helicobacter and by the enrichment of other bacterial genera, mostly represented by intestinal commensals. The combination of these taxa into a microbial dysbiosis index revealed that dysbiosis has excellent capacity to discriminate between gastritis and gastric carcinoma. Analysis of the functional features of the microbiota was compatible with the presence of a nitrosating microbial community in carcinoma. The major observations were confirmed in validation cohorts from different geographic origins. Conclusions Detailed analysis of the gastric microbiota revealed for the first time that patients with gastric carcinoma exhibit a dysbiotic microbial community with genotoxic potential, which is distinct from that of patients with chronic gastritis. PMID:29102920

Unraveling Core Functional Microbiota in Traditional Solid-State Fermentation by High-Throughput Amplicons and Metatranscriptomics Sequencing

PubMed Central

Song, Zhewei; Du, Hai; Zhang, Yan; Xu, Yan

2017-01-01

Fermentation microbiota is specific microorganisms that generate different types of metabolites in many productions. In traditional solid-state fermentation, the structural composition and functional capacity of the core microbiota determine the quality and quantity of products. As a typical example of food fermentation, Chinese Maotai-flavor liquor production involves a complex of various microorganisms and a wide variety of metabolites. However, the microbial succession and functional shift of the core microbiota in this traditional food fermentation remain unclear. Here, high-throughput amplicons (16S rRNA gene amplicon sequencing and internal transcribed space amplicon sequencing) and metatranscriptomics sequencing technologies were combined to reveal the structure and function of the core microbiota in Chinese soy sauce aroma type liquor production. In addition, ultra-performance liquid chromatography and headspace-solid phase microextraction-gas chromatography-mass spectrometry were employed to provide qualitative and quantitative analysis of the major flavor metabolites. A total of 10 fungal and 11 bacterial genera were identified as the core microbiota. In addition, metatranscriptomic analysis revealed pyruvate metabolism in yeasts (genera Pichia, Schizosaccharomyces, Saccharomyces, and Zygosaccharomyces) and lactic acid bacteria (genus Lactobacillus) classified into two stages in the production of flavor components. Stage I involved high-level alcohol (ethanol) production, with the genus Schizosaccharomyces serving as the core functional microorganism. Stage II involved high-level acid (lactic acid and acetic acid) production, with the genus Lactobacillus serving as the core functional microorganism. The functional shift from the genus Schizosaccharomyces to the genus Lactobacillus drives flavor component conversion from alcohol (ethanol) to acid (lactic acid and acetic acid) in Chinese Maotai-flavor liquor production. Our findings provide insight into the effects of the core functional microbiota in soy sauce aroma type liquor production and the characteristics of the fermentation microbiota under different environmental conditions. PMID:28769888

Cognitive and motor function of neurologically impaired extremely low birth weight children.

PubMed

Bernardo, Janine; Friedman, Harriet; Minich, Nori; Taylor, H Gerry; Wilson-Costello, Deanne; Hack, Maureen

2015-01-01

Rates of neurological impairment among extremely low birth weight children (ELBW [<1 kg]) have decreased since 2000; however, their functioning is unexamined. To compare motor and cognitive functioning of ELBW children with neurological impairment, including cerebral palsy and severe hypotonia/hypertonia, between two periods: 1990 to 1999 (n=83) and 2000 to 2005 (n=34). Measures of function at 20 months corrected age included the Mental and Psychomotor Developmental Indexes of the Bayley Scales of Infant Development and the Gross Motor Functional Classification System as primary outcomes and individual motor function items as secondary outcomes. Analysis failed to reveal significant differences for the primary outcomes, although during 2000 to 2005, sitting significantly improved in children with neurological impairment (P=0.003). Decreases in rates of neurological impairment among ELBW children have been accompanied by a suggestion of improved motor function, although cognitive function has not changed.

Bioinformatics functional analysis of let-7a, miR-34a, and miR-199a/b reveals novel insights into immune system pathways and cancer hallmarks for hepatocellular carcinoma.

PubMed

Soliman, Bangly; Salem, Ahmed; Ghazy, Mohamed; Abu-Shahba, Nourhan; El Hefnawi, Mahmoud

2018-05-01

Let-7a, miR-34a, and miR-199 a/b have gained a great attention as master regulators for cellular processes. In particular, these three micro-RNAs act as potential onco-suppressors for hepatocellular carcinoma. Bioinformatics can reveal the functionality of these micro-RNAs through target prediction and functional annotation analysis. In the current study, in silico analysis using innovative servers (miRror Suite, DAVID, miRGator V3.0, GeneTrail) has demonstrated the combinatorial and the individual target genes of these micro-RNAs and further explored their roles in hepatocellular carcinoma progression. There were 87 common target messenger RNAs (p ≤ 0.05) that were predicted to be regulated by the three micro-RNAs using miRror 2.0 target prediction tool. In addition, the functional enrichment analysis of these targets that was performed by DAVID functional annotation and REACTOME tools revealed two major immune-related pathways, eight hepatocellular carcinoma hallmarks-linked pathways, and two pathways that mediate interconnected processes between immune system and hepatocellular carcinoma hallmarks. Moreover, protein-protein interaction network for the predicted common targets was obtained by using STRING database. The individual analysis of target genes and pathways for the three micro-RNAs of interest using miRGator V3.0 and GeneTrail servers revealed some novel predicted target oncogenes such as SOX4, which we validated experimentally, in addition to some regulated pathways of immune system and hepatocarcinogenesis such as insulin signaling pathway and adipocytokine signaling pathway. In general, our results demonstrate that let-7a, miR-34a, and miR-199 a/b have novel interactions in different immune system pathways and major hepatocellular carcinoma hallmarks. Thus, our findings shed more light on the roles of these miRNAs as cancer silencers.

Complexity of EEG-signal in Time Domain - Possible Biomedical Application

NASA Astrophysics Data System (ADS)

Klonowski, Wlodzimierz; Olejarczyk, Elzbieta; Stepien, Robert

2002-07-01

Human brain is a highly complex nonlinear system. So it is not surprising that in analysis of EEG-signal, which represents overall activity of the brain, the methods of Nonlinear Dynamics (or Chaos Theory as it is commonly called) can be used. Even if the signal is not chaotic these methods are a motivating tool to explore changes in brain activity due to different functional activation states, e.g. different sleep stages, or to applied therapy, e.g. exposure to chemical agents (drugs) and physical factors (light, magnetic field). The methods supplied by Nonlinear Dynamics reveal signal characteristics that are not revealed by linear methods like FFT. Better understanding of principles that govern dynamics and complexity of EEG-signal can help to find `the signatures' of different physiological and pathological states of human brain, quantitative characteristics that may find applications in medical diagnostics.

Why are the seed cones of conifers so diverse at pollination?

PubMed

Losada, Juan M; Leslie, Andrew B

2018-06-08

Form and function relationships in plant reproductive structures have long fascinated biologists. Although the intricate associations between specific pollinators and reproductive morphology have been widely explored among animal-pollinated plants, the evolutionary processes underlying the diverse morphologies of wind-pollinated plants remain less well understood. Here we study how this diversity may have arisen by focusing on two conifer species in the pine family that have divergent reproductive cone morphologies at pollination. Standard histology methods, artificial wind pollination assays and phylogenetic analyses were used in this study. A detailed study of cone ontogeny in these species reveals that variation in the rate at which their cone scales mature means that pollination occurs at different stages in their development, and thus in association with different specific morphologies. Pollination experiments nevertheless indicate that both species effectively capture pollen. In wind-pollinated plants, morphological diversity may result from simple variation in development among lineages rather than selective pressures for any major differences in function or performance. This work also illustrates the broader importance of developmental context in understanding plant form and function relationships; because plant reproductive structures perform many different functions over their lifetime, subtle differences in development may dramatically alter the specific morphologies that they use to meet these demands.

Does Older Adults' Cognitive Function Disrupt the Malleability of Their Attitudes toward Outgroup Members?: An fMRI Investigation.

PubMed

Krendl, Anne C; Kensinger, Elizabeth A

2016-01-01

In the current study we examine how individual differences in older adults' global cognitive function impacts the extent to which their attitudes toward stigmatized individuals are malleable. Because prior research has elucidated the neural processes that are involved in evaluating stigmatized individuals who are responsible or not responsible for their condition, a cognitive neuroscience approach may be well-suited to answer this question. In the current study, 36 older and 17 young adults underwent functional magnetic resonance imaging while evaluating images of homeless people who were described as being responsible or not responsible for their condition. They also indicated how much pity they felt for each of the individuals in order to determine the extent to which their attitudes were malleable (e.g., more pity for not-responsible as compared to responsible individuals). Participants' cognitive function and baseline measure of their attitudes toward stigmatized individuals (including homeless individuals) were assessed. Results revealed that although older adults' attitudes were malleable, the extent to which this was true varied due to individual differences in their global cognitive function. Specifically, the difference in the magnitude of older adults' self-reported pity for not-responsible as compared to responsible homeless individuals was predicted by their global cognitive function. Moreover, the difference in pity that older adults expressed toward not-responsible as compared to responsible homeless individuals was related to activity in the left insula and the anterior cingulate cortex (regions implicated in empathy). These results suggest that attitude malleability is affected by individual differences in global cognitive function.

Does Older Adults’ Cognitive Function Disrupt the Malleability of Their Attitudes toward Outgroup Members?: An fMRI Investigation

PubMed Central

Krendl, Anne C.; Kensinger, Elizabeth A.

2016-01-01

In the current study we examine how individual differences in older adults’ global cognitive function impacts the extent to which their attitudes toward stigmatized individuals are malleable. Because prior research has elucidated the neural processes that are involved in evaluating stigmatized individuals who are responsible or not responsible for their condition, a cognitive neuroscience approach may be well-suited to answer this question. In the current study, 36 older and 17 young adults underwent functional magnetic resonance imaging while evaluating images of homeless people who were described as being responsible or not responsible for their condition. They also indicated how much pity they felt for each of the individuals in order to determine the extent to which their attitudes were malleable (e.g., more pity for not-responsible as compared to responsible individuals). Participants’ cognitive function and baseline measure of their attitudes toward stigmatized individuals (including homeless individuals) were assessed. Results revealed that although older adults’ attitudes were malleable, the extent to which this was true varied due to individual differences in their global cognitive function. Specifically, the difference in the magnitude of older adults’ self-reported pity for not-responsible as compared to responsible homeless individuals was predicted by their global cognitive function. Moreover, the difference in pity that older adults expressed toward not-responsible as compared to responsible homeless individuals was related to activity in the left insula and the anterior cingulate cortex (regions implicated in empathy). These results suggest that attitude malleability is affected by individual differences in global cognitive function. PMID:27074046

Incomplete inhibition of platelet function as assessed by the platelet function analyzer (PFA-100) identifies a subset of cardiovascular patients with high residual platelet response while on aspirin.

PubMed

Crescente, M; Mezzasoma, A M; Del Pinto, M; Palmerini, F; Di Castelnuovo, A; Cerletti, C; De Gaetano, G; Gresele, P

2011-01-01

Sixty-six patients with a history of ischemic events (myocardial infarction, unstable angina, or stroke) on chronic aspirin therapy were studied by different platelet function tests: 37 patients had suffered a recurrent event while on aspirin and 29 were without recurrences. Based on results from light transmission aggregometry (LTA) induced by arachidonic acid (AA) and serum TxB(2) both COX-1-dependent methods, only one patient could be identified as aspirin "resistant". However, when methods only partially-dependent on platelet COX-1 activity were considered, the prevalence of aspirin non-responders ranged, according to the different tests, from 0 to 52%. No difference was observed between patients with recurrences and those without. Among patients with recurrent events, those with an incomplete inhibition of platelet function, as assessed by the PFA-100, had significantly higher residual serum TxB(2) (2.4 ± 2.4 ng/mL vs 0.4 ± 0.1 ng/mL, p = 0.03), residual LTA-AA (9.2 ± 10.6% vs 2.0 ± 1.6%, p = 0.008), LTA-Coll (49.3 ± 14.6% vs 10.2 ± 8.3%, p = 0.007) and LTA-ADP (50.9 ± 16.2% vs 34.3 ± 11.0%, p = 0.04). In conclusion, laboratory tests solely exploring the AA-mediated pathway of platelet function, while being the most appropriate to detect the effect of aspirin on its pharmacologic target (platelet COX-1), may fail to reveal the functional interactions between minimal residual TxA(2) and additional stimuli or primers potentially leading to aspirin-insensitive platelet aggregation. High residual platelet response in platelet function tests only partially dependent on COX-1 may reveal a condition of persistent platelet reactivity in a subset of aspirin-treated patients characterizing them as a subgroup at higher vascular risk.

Do differences in visuospatial ability between senile dementias of the Alzheimer and Lewy body types reflect differences solely in mnemonic function?

PubMed

Sahgal, A; McKeith, I G; Galloway, P H; Tasker, N; Steckler, T

1995-02-01

Visuospatial memory was investigated in two groups of patients suffering from senile dementias of the Alzheimer (SDAT) or Lewy body (SDLT) types; a, third, age-matched, healthy control group was also included. The two patient groups were mildly demented and could not be distinguished from each other by traditional tests of cognitive function. A different pattern of performance emerged in the two groups on a computerised test of spatial working memory, which is a self-ordered pointing task requiring the subject to search for hidden tokens. An analysis of the pattern of errors revealed that the SDLT group made more of both possible types of error ("Within Search" and "Between Search") than the SDAT group. Neither patient groups' performance differed from each other when assessed on a computerised Corsi spatial span task. A measure of planning ability was obtained by examining search strategies. Although an index previously developed to measure the subject's use of a particular strategy in the spatial working memory task failed to detect any differences between the three groups, a novel index was calculated which focuses on performance within a search, and this revealed deficits in both demented groups. Since the two patient groups differed from each other in the spatial working memory, but not the Corsi spatial span, task, it is suggested that the differences between the two demented groups are not due to a specific mnemonic impairment, but reflect dysfunctions in non-mnemonic processes mediated by fronto-subcortical circuits, which are more severely damaged in SDLT.

Functional and rheological properties of proteins in frozen turkey breast meat with different ultimate pH.

PubMed

Chan, J T Y; Omana, D A; Betti, M

2011-05-01

Functional and rheological properties of proteins from frozen turkey breast meat with different ultimate pH at 24 h postmortem (pH(24)) have been studied. Sixteen breast fillets from Hybrid Tom turkeys were initially selected based on lightness (L*) values for each color group (pale, normal, and dark), with a total of 48 breast fillets. Further selection of 8 breast samples was made within each class of meat according to the pH(24). The average L* and pH values of the samples were within the following range: pale (L* >52; pH ≤5.7), normal (46 < L* < 52; 5.9 < pH <6.1), and dark (L* <46; pH ≥6.3), referred to as low, normal, and high pH meat, respectively. Ultimate pH did not cause major changes in the emulsifying and foaming properties of the extracted sarcoplasmic and myofibrillar proteins. An SDS-PAGE profile of proteins from low and normal pH meat was similar, which revealed that the extent of protein denaturation was the same. Low pH meat had the lowest water-holding capacity compared with normal and high pH meat as shown by the increase in cooking loss, which can be explained by factors other than protein denaturation. Gel strength analysis and folding test revealed that gel-forming ability was better for high pH meat compared with low and normal pH meat.Dynamic viscoelastic behavior showed that myosin denaturation temperature was independent of pH(24). Normal and high pH meat had similar hardness, springiness, and chewiness values as revealed by texture profile analysis. The results from this study indicate that high pH meat had similar or better functional properties than normal pH meat. Therefore, high pH meat is suitable for further processed products, whereas low pH meat may need additional treatment or ingredient formulations to improve its functionality.

Frontal lobe function in chess players.

PubMed

Nejati, Majid; Nejati, Vahid

2012-01-01

Chess is considered as a cognitive game because of severe engagement of the mental resources during playing. The purpose of this study is evaluation of frontal lobe function of chess players with matched non-players. Wisconsin Card Sorting Test (WCST) data showed no difference between the player and non-player groups in preservation error and completed categories but surprisingly showed significantly lower grade of the player group in correct response. Our data reveal that chess players don't have any preference in any stage of Stroop test. Chess players don't have any preference in selective attention, inhibition and executive cognitive function. Chess players' have lower shifting abilities than non-players.

View Point: Semaphorin-3E: An Emerging Modulator of Natural Killer Cell Functions?

PubMed Central

Alamri, Abdulaziz; Soussi Gounni, Abdelilah; Kung, Sam K. P.

2017-01-01

Semaphorin-3E (Sema-3E) is a member of a large family of proteins originally identified as axon guidance cues in neural development. It is expressed in different cell types, such as immune cells, cancer cells, neural cells, and epithelial cells. Subsequently, dys-regulation of Sema-3E expression has been reported in various biological processes that range from cancers to autoimmune and allergic diseases. Recent work in our laboratories revealed a critical immunoregulatory role of Sema-3E in experimental allergic asthma. We further speculate possible immune modulatory function(s) of Sema-3E on natural killer (NK) cells. PMID:29113093

How multi-partner endosymbioses function.

PubMed

Douglas, Angela E

2016-12-01

Various animals are associated with specific endosymbiotic microorganisms that provide the host with essential nutrients or confer protection against natural enemies. Genomic analyses of the many endosymbioses that are found in plant sap-feeding hemipteran insects have revealed independent acquisitions - and occasional replacements - of endosymbionts, such that many of these endosymbioses involve two or more microbial partners. In this Review, I discuss how partitioning of the genetic capacity for metabolic function between different endosymbionts has sustained nutritional function in multi-partner endosymbioses, and how the phenotypic traits of these endosymbionts can be shaped by co-evolutionary interactions with both co-occurring microbial taxa and the host, which often operate over long evolutionary timescales.

Evidence for a possible role of oxygen free radicals in the abnormal functional arterial vasomotion in insulin dependent diabetes.

PubMed

Ceriello, A; Quatraro, A; Caretta, F; Varano, R; Giugliano, D

1990-01-01

A functional arterial spasm, revealed by reduced post-ischemic response, is present in diabetic subjects with no overt evidence of vascular damage. The administration of three different antioxidant agents, vitamin C, thiopronine and glutathione, produces an increase of basal blood flow in both diabetic and normal subjects, and ameliorates significantly the vascular functional response in diabetes. These data suggest that free radicals may play a role in the regulation of arterial resistance in humans, and that a de-regulation of their action may be involved in the development of arterial dysfunction in diabetes.

A Culturally-Specific Dance Intervention to Increase Functional Capacity in African American Women

PubMed Central

Murrock, Carolyn J.; Gary, Faye A.

2013-01-01

This study examined a culturally-specific dance intervention on functional capacity in African American women at three time points. The intervention was two times per week for 8 weeks using two African American churches randomly assigned to either the experimental or comparison group, had 126 participants, ages 36–82 years. Analysis of covariance revealed that both groups improved over time and the only significant difference between groups was at 18 weeks. The increase at 18 weeks in the experimental group remained when controlling for baseline covariates. This study supported culturally-specific dance as an intervention to improve functional capacity in African American women. PMID:19202718

A culturally-specific dance intervention to increase functional capacity in African American women.

PubMed

Murrock, Carolyn J; Gary, Faye A

2008-01-01

This study examined a culturally-specific dance intervention on functional capacity in African American women at three time points. The intervention was two times per week for 8 weeks using two African American churches randomly assigned to either the experimental or comparison group, had 126 participants, ages 36-82 years. Analysis of covariance revealed that both groups improved over time and the only significant difference between groups was at 18 weeks. The increase at 18 weeks in the experimental group remained when controlling for baseline covariates. This study supported culturally-specific dance as an intervention to improve functional capacity in African American women.

Functional Redundancy Patterns Reveal Non-Random Assembly Rules in a Species-Rich Marine Assemblage

PubMed Central

Guillemot, Nicolas; Kulbicki, Michel; Chabanet, Pascale; Vigliola, Laurent

2011-01-01

The relationship between species and the functional diversity of assemblages is fundamental in ecology because it contains key information on functional redundancy, and functionally redundant ecosystems are thought to be more resilient, resistant and stable. However, this relationship is poorly understood and undocumented for species-rich coastal marine ecosystems. Here, we used underwater visual censuses to examine the patterns of functional redundancy for one of the most diverse vertebrate assemblages, the coral reef fishes of New Caledonia, South Pacific. First, we found that the relationship between functional and species diversity displayed a non-asymptotic power-shaped curve, implying that rare functions and species mainly occur in highly diverse assemblages. Second, we showed that the distribution of species amongst possible functions was significantly different from a random distribution up to a threshold of ∼90 species/transect. Redundancy patterns for each function further revealed that some functions displayed fast rates of increase in redundancy at low species diversity, whereas others were only becoming redundant past a certain threshold. This suggested non-random assembly rules and the existence of some primordial functions that would need to be fulfilled in priority so that coral reef fish assemblages can gain a basic ecological structure. Last, we found little effect of habitat on the shape of the functional-species diversity relationship and on the redundancy of functions, although habitat is known to largely determine assemblage characteristics such as species composition, biomass, and abundance. Our study shows that low functional redundancy is characteristic of this highly diverse fish assemblage, and, therefore, that even species-rich ecosystems such as coral reefs may be vulnerable to the removal of a few keystone species. PMID:22039543

Functional brain networks in Alzheimer's disease: EEG analysis based on limited penetrable visibility graph and phase space method

NASA Astrophysics Data System (ADS)

Wang, Jiang; Yang, Chen; Wang, Ruofan; Yu, Haitao; Cao, Yibin; Liu, Jing

2016-10-01

In this paper, EEG series are applied to construct functional connections with the correlation between different regions in order to investigate the nonlinear characteristic and the cognitive function of the brain with Alzheimer's disease (AD). First, limited penetrable visibility graph (LPVG) and phase space method map single EEG series into networks, and investigate the underlying chaotic system dynamics of AD brain. Topological properties of the networks are extracted, such as average path length and clustering coefficient. It is found that the network topology of AD in several local brain regions are different from that of the control group with no statistically significant difference existing all over the brain. Furthermore, in order to detect the abnormality of AD brain as a whole, functional connections among different brain regions are reconstructed based on similarity of clustering coefficient sequence (CCSS) of EEG series in the four frequency bands (delta, theta, alpha, and beta), which exhibit obvious small-world properties. Graph analysis demonstrates that for both methodologies, the functional connections between regions of AD brain decrease, particularly in the alpha frequency band. AD causes the graph index complexity of the functional network decreased, the small-world properties weakened, and the vulnerability increased. The obtained results show that the brain functional network constructed by LPVG and phase space method might be more effective to distinguish AD from the normal control than the analysis of single series, which is helpful for revealing the underlying pathological mechanism of the disease.

The Development of Metaphor Comprehension and Its Relationship with Relational Verbal Reasoning and Executive Function.

PubMed

Carriedo, Nuria; Corral, Antonio; Montoro, Pedro R; Herrero, Laura; Ballestrino, Patricia; Sebastián, Iraia

2016-01-01

Our main objective was to analyse the different contributions of relational verbal reasoning (analogical and class inclusion) and executive functioning to metaphor comprehension across development. We postulated that both relational reasoning and executive functioning should predict individual and developmental differences. However, executive functioning would become increasingly involved when metaphor comprehension is highly demanding, either because of the metaphors' high difficulty (relatively novel metaphors in the absence of a context) or because of the individual's special processing difficulties, such as low levels of reading experience or low semantic knowledge. Three groups of participants, 11-year-olds, 15-year-olds and young adults, were assessed in different relational verbal reasoning tasks-analogical and class-inclusion-and in executive functioning tasks-updating information in working memory, inhibition, and shifting. The results revealed clear progress in metaphor comprehension between ages 11 and 15 and between ages 15 and 21. However, the importance of executive function in metaphor comprehension was evident by age 15 and was restricted to updating information in working memory and cognitive inhibition. Participants seemed to use two different strategies to interpret metaphors: relational verbal reasoning and executive functioning. This was clearly shown when comparing the performance of the "more efficient" participants in metaphor interpretation with that of the "less efficient" ones. Whereas in the first case none of the executive variables or those associated with relational verbal reasoning were significantly related to metaphor comprehension, in the latter case, both groups of variables had a clear predictor effect.

The processing of mispredicted and unpredicted sensory inputs interact differently with attention.

PubMed

Hsu, Yi-Fang; Hämäläinen, Jarmo A; Waszak, Florian

2018-03-01

Prediction and attention are fundamental brain functions in the service of perception. Interestingly, previous investigations found prediction effects independent of attention in some cases but attention-dependent in other cases. The discrepancy might be related to whether the prediction effect was revealed by comparing mispredicted event (where there is incorrect prediction) or unpredicted event (where there is no precise prediction) against predicted event, which are associated with different precision-weighted prediction error. Here we conducted a joint analysis on four published electroencephalography (EEG) datasets which allow for proper dissociation of mispredicted and unpredicted conditions when there was orthogonal manipulation of prediction and attention. We found that the mispredicted-versus-predicted contrast revealed an attention-independent effect of prediction suppression, whereas the unpredicted-versus-predicted contrast revealed a prediction effect that was reversed by attention on auditory N1. The results suggest that mispredicted and unpredicted processing interact with attention in distinct manners. Copyright © 2018 Elsevier Ltd. All rights reserved.

Interspecific metabolic diversity of root-colonizing endophytic fungi revealed by enzyme activity tests.

PubMed

Knapp, Dániel G; Kovács, Gábor M

2016-12-01

Although dark septate endophytes (DSE) represent a worldwide dispersed form group of root-colonizing endophytic fungi, our knowledge on their role in ecosystem functioning is far limited. In this study, we aimed to test if functional diversity exists among DSE fungi representing different lineages of root endophytic fungal community of semiarid sandy grasslands. To address this question and to gain general information on function of DSE fungi, we adopted api-ZYM and BioLog FF assays to study those non-sporulating filamentous fungi and characterized the metabolic activity of 15 different DSE species. Although there were striking differences among the species, all of the substrates tested were utilized by the DSE fungi. When endophytes characteristic to grasses and non-grass host plants were separately considered, we found that the whole substrate repertoire was used by both groups. This might illustrate the complementary functional diversity of the communities root endophytic plant-associated fungi. The broad spectra of substrates utilized by these root endophytes illustrate the functional importance of their diversity, which can play role not only in nutrient mobilization and uptake of plants from with nutrient poor soils, but also in general plant performance and ecosystem functioning. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Cell type-specific long-range connections of basal forebrain circuit.

PubMed

Do, Johnny Phong; Xu, Min; Lee, Seung-Hee; Chang, Wei-Cheng; Zhang, Siyu; Chung, Shinjae; Yung, Tyler J; Fan, Jiang Lan; Miyamichi, Kazunari; Luo, Liqun; Dan, Yang

2016-09-19

The basal forebrain (BF) plays key roles in multiple brain functions, including sleep-wake regulation, attention, and learning/memory, but the long-range connections mediating these functions remain poorly characterized. Here we performed whole-brain mapping of both inputs and outputs of four BF cell types - cholinergic, glutamatergic, and parvalbumin-positive (PV+) and somatostatin-positive (SOM+) GABAergic neurons - in the mouse brain. Using rabies virus -mediated monosynaptic retrograde tracing to label the inputs and adeno-associated virus to trace axonal projections, we identified numerous brain areas connected to the BF. The inputs to different cell types were qualitatively similar, but the output projections showed marked differences. The connections to glutamatergic and SOM+ neurons were strongly reciprocal, while those to cholinergic and PV+ neurons were more unidirectional. These results reveal the long-range wiring diagram of the BF circuit with highly convergent inputs and divergent outputs and point to both functional commonality and specialization of different BF cell types.

Microbial community structure in fermentation process of Shaoxing rice wine by Illumina-based metagenomic sequencing.

PubMed

Xie, Guangfa; Wang, Lan; Gao, Qikang; Yu, Wenjing; Hong, Xutao; Zhao, Lingyun; Zou, Huijun

2013-09-01

To understand the role of the community structure of microbes in the environment in the fermentation of Shaoxing rice wine, samples collected from a wine factory were subjected to Illumina-based metagenomic sequencing. De novo assembly of the sequencing reads allowed the characterisation of more than 23 thousand microbial genes derived from 1.7 and 1.88 Gbp of sequences from two samples fermented for 5 and 30 days respectively. The microbial community structure at different fermentation times of Shaoxing rice wine was revealed, showing the different roles of the microbiota in the fermentation process of Shaoxing rice wine. The gene function of both samples was also studied in the COG database, with most genes belonging to category S (function unknown), category E (amino acid transport and metabolism) and unclassified group. The results show that both the microbial community structure and gene function composition change greatly at different time points of Shaoxing rice wine fermentation. © 2013 Society of Chemical Industry.

Mechanical Properties of Nylon Harp Strings

PubMed Central

Lynch-Aird, Nicolas; Woodhouse, Jim

2017-01-01

Monofilament nylon strings with a range of diameters, commercially marketed as harp strings, have been tested to establish their long-term mechanical properties. Once a string had settled into a desired stress state, the Young’s modulus was measured by a variety of methods that probe different time-scales. The modulus was found to be a strong function of testing frequency and also a strong function of stress. Strings were also subjected to cyclical variations of temperature, allowing various thermal properties to be measured: the coefficient of linear thermal expansion and the thermal sensitivities of tuning, Young’s modulus and density. The results revealed that the particular strings tested are divided into two groups with very different properties: stress-strain behaviour differing by a factor of two and some parametric sensitivities even having the opposite sign. Within each group, correlation studies allowed simple functional fits to be found to the key properties, which have the potential to be used in automated tuning systems for harp strings. PMID:28772858

Mechanical Properties of Nylon Harp Strings.

PubMed

Lynch-Aird, Nicolas; Woodhouse, Jim

2017-05-04

Monofilament nylon strings with a range of diameters, commercially marketed as harp strings, have been tested to establish their long-term mechanical properties. Once a string had settled into a desired stress state, the Young's modulus was measured by a variety of methods that probe different time-scales. The modulus was found to be a strong function of testing frequency and also a strong function of stress. Strings were also subjected to cyclical variations of temperature, allowing various thermal properties to be measured: the coefficient of linear thermal expansion and the thermal sensitivities of tuning, Young's modulus and density. The results revealed that the particular strings tested are divided into two groups with very different properties: stress-strain behaviour differing by a factor of two and some parametric sensitivities even having the opposite sign. Within each group, correlation studies allowed simple functional fits to be found to the key properties, which have the potential to be used in automated tuning systems for harp strings.

EEG Cortical Connectivity Analysis of Working Memory Reveals Topological Reorganization in Theta and Alpha Bands

PubMed Central

Dai, Zhongxiang; de Souza, Joshua; Lim, Julian; Ho, Paul M.; Chen, Yu; Li, Junhua; Thakor, Nitish; Bezerianos, Anastasios; Sun, Yu

2017-01-01

Numerous studies have revealed various working memory (WM)-related brain activities that originate from various cortical regions and oscillate at different frequencies. However, multi-frequency band analysis of the brain network in WM in the cortical space remains largely unexplored. In this study, we employed a graph theoretical framework to characterize the topological properties of the brain functional network in the theta and alpha frequency bands during WM tasks. Twenty-eight subjects performed visual n-back tasks at two difficulty levels, i.e., 0-back (control task) and 2-back (WM task). After preprocessing, Electroencephalogram (EEG) signals were projected into the source space and 80 cortical brain regions were selected for further analysis. Subsequently, the theta- and alpha-band networks were constructed by calculating the Pearson correlation coefficients between the power series (obtained by concatenating the power values of all epochs in each session) of all pairs of brain regions. Graph theoretical approaches were then employed to estimate the topological properties of the brain networks at different WM tasks. We found higher functional integration in the theta band and lower functional segregation in the alpha band in the WM task compared with the control task. Moreover, compared to the 0-back task, altered regional centrality was revealed in the 2-back task in various brain regions that mainly resided in the frontal, temporal and occipital lobes, with distinct presentations in the theta and alpha bands. In addition, significant negative correlations were found between the reaction time with the average path length of the theta-band network and the local clustering of the alpha-band network, which demonstrates the potential for using the brain network metrics as biomarkers for predicting the task performance during WM tasks. PMID:28553215

Functional anatomic studies of memory retrieval for auditory words and visual pictures.

PubMed

Buckner, R L; Raichle, M E; Miezin, F M; Petersen, S E

1996-10-01

Functional neuroimaging with positron emission tomography was used to study brain areas activated during memory retrieval. Subjects (n = 15) recalled items from a recent study episode (episodic memory) during two paired-associate recall tasks. The tasks differed in that PICTURE RECALL required pictorial retrieval, whereas AUDITORY WORD RECALL required word retrieval. Word REPETITION and REST served as two reference tasks. Comparing recall with repetition revealed the following observations. (1) Right anterior prefrontal activation (similar to that seen in several previous experiments), in addition to bilateral frontal-opercular and anterior cingulate activations. (2) An anterior subdivision of medial frontal cortex [pre-supplementary motor area (SMA)] was activated, which could be dissociated from a more posterior area (SMA proper). (3) Parietal areas were activated, including a posterior medial area near precuneus, that could be dissociated from an anterior parietal area that was deactivated. (4) Multiple medial and lateral cerebellar areas were activated. Comparing recall with rest revealed similar activations, except right prefrontal activation was minimal and activations related to motor and auditory demands became apparent (e.g., bilateral motor and temporal cortex). Directly comparing picture recall with auditory word recall revealed few notable activations. Taken together, these findings suggest a pathway that is commonly used during the episodic retrieval of picture and word stimuli under these conditions. Many areas in this pathway overlap with areas previously activated by a different set of retrieval tasks using stem-cued recall, demonstrating their generality. Examination of activations within individual subjects in relation to structural magnetic resonance images provided an-atomic information about the location of these activations. Such data, when combined with the dissociations between functional areas, provide an increasingly detailed picture of the brain pathways involved in episodic retrieval tasks.

Chemical Functionalization of Germanium with Dextran Brushes for Immobilization of Proteins Revealed by Attenuated Total Reflection Fourier Transform Infrared Difference Spectroscopy.

PubMed

Schartner, Jonas; Hoeck, Nina; Güldenhaupt, Jörn; Mavarani, Laven; Nabers, Andreas; Gerwert, Klaus; Kötting, Carsten

2015-07-21

Protein immobilization studied by attenuated total reflection Fourier transform infrared (ATR-FT-IR) difference spectroscopy is an emerging field enabling the study of proteins at atomic detail. Gold or glass surfaces are frequently used for protein immobilization. Here, we present an alternative method for protein immobilization on germanium. Because of its high refractive index and broad spectral window germanium is the best material for ATR-FT-IR spectroscopy of thin layers. So far, this technique was mainly used for protein monolayers, which lead to a limited signal-to-noise ratio. Further, undesired protein-protein interactions can occur in a dense layer. Here, the germanium surface was functionalized with thiols and stepwise a dextran brush was generated. Each step was monitored by ATR-FT-IR spectroscopy. We compared a 70 kDa dextran with a 500 kDa dextran regarding the binding properties. All surfaces were characterized by atomic force microscopy, revealing thicknesses between 40 and 110 nm. To analyze the capability of our system we utilized N-Ras on mono-NTA (nitrilotriacetic acid) functionalized dextran, and the amount of immobilized Ras corresponded to several monolayers. The protein stability and loading capacity was further improved by means of tris-NTA for immobilization. Small-molecule-induced changes were revealed with an over 3 times higher signal-to-noise ratio compared to monolayers. This improvement may allow the observation of very small and so far hidden changes in proteins upon stimulus. Furthermore, we immobilized green fluorescent protein (GFP) and mCherry simultaneously enabling an analysis of the surface by fluorescence microscopy. The absence of a Förster resonance energy transfer (FRET) signal demonstrated a large protein-protein distance, indicating an even distribution of the protein within the dextran.

EEG Cortical Connectivity Analysis of Working Memory Reveals Topological Reorganization in Theta and Alpha Bands.

PubMed

Dai, Zhongxiang; de Souza, Joshua; Lim, Julian; Ho, Paul M; Chen, Yu; Li, Junhua; Thakor, Nitish; Bezerianos, Anastasios; Sun, Yu

2017-01-01

Numerous studies have revealed various working memory (WM)-related brain activities that originate from various cortical regions and oscillate at different frequencies. However, multi-frequency band analysis of the brain network in WM in the cortical space remains largely unexplored. In this study, we employed a graph theoretical framework to characterize the topological properties of the brain functional network in the theta and alpha frequency bands during WM tasks. Twenty-eight subjects performed visual n -back tasks at two difficulty levels, i.e., 0-back (control task) and 2-back (WM task). After preprocessing, Electroencephalogram (EEG) signals were projected into the source space and 80 cortical brain regions were selected for further analysis. Subsequently, the theta- and alpha-band networks were constructed by calculating the Pearson correlation coefficients between the power series (obtained by concatenating the power values of all epochs in each session) of all pairs of brain regions. Graph theoretical approaches were then employed to estimate the topological properties of the brain networks at different WM tasks. We found higher functional integration in the theta band and lower functional segregation in the alpha band in the WM task compared with the control task. Moreover, compared to the 0-back task, altered regional centrality was revealed in the 2-back task in various brain regions that mainly resided in the frontal, temporal and occipital lobes, with distinct presentations in the theta and alpha bands. In addition, significant negative correlations were found between the reaction time with the average path length of the theta-band network and the local clustering of the alpha-band network, which demonstrates the potential for using the brain network metrics as biomarkers for predicting the task performance during WM tasks.

Effects of reward and punishment on task performance, mood and autonomic nervous function, and the interaction with personality.

PubMed

Sakuragi, Sokichi; Sugiyama, Yoshiki

2009-06-01

The effects of reward and punishment are different, and there are individual differences in sensitivity to reward and punishment. The purpose of this study was to investigate the effects of reward and punishment on task performance, mood, and autonomic nervous function, along with the interaction with personality. Twenty-one healthy female subjects volunteered for the experiment. The task performance was evaluated by required time and total errors while performing a Wisconsin Card Sorting Test. We assessed their personalities using the Minnesota Multiphasic Personality Inventory (MMPI) questionnaire, and mood states by a profile of mood states. Autonomic nervous function was estimated by a spectral analysis of heart rate variability, baroreflex sensitivity, and blood pressure. Repeated measures analysis of variance (ANOVA) revealed significant interaction of condition x time course on mood and autonomic nervous activity, which would indicate a less stressed state under the rewarding condition, but revealed no significant interaction of condition x time course on the task performance. The interactions with personality were further analyzed by repeated measures ANOVA applying the clinical scales of MMPI as independent variables, and significant interactions of condition x time course x Pt (psychasthenia) on task performance, mood, and blood pressure, were revealed. That is, the high Pt group, whose members tend to be sensitive and prone to worry, showed gradual improvement of task performance under the punishing situation with slight increase in systolic blood pressure, while showed no improvement under the rewarding situation with fatigue sense attenuation. In contrast, the low Pt group, whose members tend to be adaptive and self-confident, showed gradual improvement under the rewarding situation. Therefore, we should carefully choose the strategy of reward or punishment, considering the interaction with personality as well as the context in which it is given.

Auditory hallucinations and the temporal cortical response to speech in schizophrenia: a functional magnetic resonance imaging study.

PubMed

Woodruff, P W; Wright, I C; Bullmore, E T; Brammer, M; Howard, R J; Williams, S C; Shapleske, J; Rossell, S; David, A S; McGuire, P K; Murray, R M

1997-12-01

The authors explored whether abnormal functional lateralization of temporal cortical language areas in schizophrenia was associated with a predisposition to auditory hallucinations and whether the auditory hallucinatory state would reduce the temporal cortical response to external speech. Functional magnetic resonance imaging was used to measure the blood-oxygenation-level-dependent signal induced by auditory perception of speech in three groups of male subjects: eight schizophrenic patients with a history of auditory hallucinations (trait-positive), none of whom was currently hallucinating; seven schizophrenic patients without such a history (trait-negative); and eight healthy volunteers. Seven schizophrenic patients were also examined while they were actually experiencing severe auditory verbal hallucinations and again after their hallucinations had diminished. Voxel-by-voxel comparison of the median power of subjects' responses to periodic external speech revealed that this measure was reduced in the left superior temporal gyrus but increased in the right middle temporal gyrus in the combined schizophrenic groups relative to the healthy comparison group. Comparison of the trait-positive and trait-negative patients revealed no clear difference in the power of temporal cortical activation. Comparison of patients when experiencing severe hallucinations and when hallucinations were mild revealed reduced responsivity of the temporal cortex, especially the right middle temporal gyrus, to external speech during the former state. These results suggest that schizophrenia is associated with a reduced left and increased right temporal cortical response to auditory perception of speech, with little distinction between patients who differ in their vulnerability to hallucinations. The auditory hallucinatory state is associated with reduced activity in temporal cortical regions that overlap with those that normally process external speech, possibly because of competition for common neurophysiological resources.

Human bloodstains on bone artefacts: an SEM intra- and inter-sample comparative study using ratite bird tibiotarsus.

PubMed

Hortolà, Policarp

2016-11-01

Apart from their forensic significance in crime investigation, human bloodstains have an anthropological interest due to their occurrence on certain traditional weapons and ritual objects. Previously, a guiding study of erythrocytes in experimental samples including domestic sheep (Ovis aries) tibia was carried out using a scanning electron microscope (SEM). Here, a comparative SEM study to reveal the potential differences in bloodstain surface morphology as a function of intra-sample (smear region) and inter-sample (individual smear, smearing mechanism, bone origin) parameters is reported. A fragment of emu (Dromaius novaehollandiae) tibiotarsus was smeared with an adult man's peripheral blood. After air-drying and storing indoors, the boundary and neighbouring inner areas of the three individual bloodstains obtained were examined via secondary electrons in a variable-pressure SEM working in low-vacuum mode. As a whole, desiccation microcracks were present, the limits between the smear and the substrate appeared poorly defined, and no erythrocyte negative replicas were observed in the examined areas. In addition, a putative fibrin network, more or less embedded in the dried plasma matrix, was observed in the smears' boundary. Regarding the smear region in sliding smears, the periphery and boundary revealed to be different, while the head and tail were similar. Considering individual sliding smears, they had similar characteristics. Relating to the smear region as a function of the smearing mechanism, the periphery was different whether sliding or touching, while the boundary was similar in sliding and touching smears. Concerning the smear region as a function of the bone origin, the periphery revealed to be similar in both ratite and mammalian bone, while the boundary did different in ratite and mammalian bone. The results of this study show that SEM examination can be used fruitfully to detect bloodstains on ratite bone. Combined with previous SEM results in domestic sheep bone, they suggest, further, that blood remains can be detected on objects made of bone irrespectively of the mammalian or ratite origin of this raw material. Copyright © 2016 Elsevier Ltd. All rights reserved.

One Size Fits All? Applying Theoretical Predictions about Age and Emotional Experience to People with Functional Disabilities

PubMed Central

Piazza, Jennifer R.; Charles, Susan T.; Luong, Gloria; Almeida, David M.

2015-01-01

The current study examined whether commonly observed age differences in affective experience among community samples of healthy adults would generalize to a group of adults who live with significant functional disability. Age differences in daily affect and affective reactivity to daily stressors among a sample of participants with spinal cord injury were compared to a non-injured sample. Results revealed that patterns of affective experience varied by sample. Among non-injured adults, older age was associated with lower levels of daily negative affect (NA), higher levels of daily positive affect (PA), and less negative affective reactivity in response to daily stressors. In contrast, among participants with spinal cord injury, no age differences emerged. Findings, which support the model of Strength and Vulnerability Integration (SAVI), underscore the importance of taking life context into account when predicting age differences in affective well-being. PMID:26322552

Is the fluency of language outputs related to individual differences in intelligence and executive function?

PubMed

Engelhardt, Paul E; Nigg, Joel T; Ferreira, Fernanda

2013-10-01

There has been little research on the fluency of language production and individual difference variables, such as intelligence and executive function. In this study, we report data from 106 participants who completed a battery of standardized cognitive tasks and a sentence production task. For the sentence production task, participants were presented with two objects and a verb and their task was to formulate a sentence. Four types of disfluency were examined: filled pauses (e.g. uh, um), unfilled pauses, repetitions, and repairs. Repetitions occur when the speaker suspends articulation and then repeats the previous word/phrase, and repairs occur when the speaker suspends articulation and then starts over with a different word/phrase. Hierarchical structural equation modeling revealed a significant relationship between repair disfluencies and inhibition. Conclusions focus on the role of individual differences in cognitive ability and their role in models and theories of language production. © 2013.

Is the fluency of language outputs related to individual differences in intelligence and executive function?

PubMed Central

Engelhardt, Paul E.; Nigg, Joel T.; Ferreira, Fernanda

2013-01-01

There has been little research on the fluency of language production and individual differences variables, such as intelligence and executive function. In this study, we report data from 106 participants who completed a battery of standardized cognitive tasks and a sentence production task. For the sentence production task, participants were presented with two objects and a verb and their task was to formulate a sentence. Four types of disfluency were examined: filled pauses (e.g. uh, um), unfilled pauses, repetitions, and repairs. Repetitions occur when the speaker suspends articulation and then repeats the previous word/phrase, and repairs occur when the speaker suspends articulation and then starts over with a different word/phrase. Hierarchical structural equation modeling revealed a significant relationship between repair disfluencies and inhibition. Conclusions focus on the role of individual differences in cognitive ability and their role in models and theories of language production. PMID:24018099

Contrasting species and functional beta diversity in montane ant assemblages.

PubMed

Bishop, Tom R; Robertson, Mark P; van Rensburg, Berndt J; Parr, Catherine L

2015-09-01

Beta diversity describes the variation in species composition between sites and can be used to infer why different species occupy different parts of the globe. It can be viewed in a number of ways. First, it can be partitioned into two distinct patterns: turnover and nestedness. Second, it can be investigated from either a species identity or a functional-trait point of view. We aim to document for the first time how these two aspects of beta diversity vary in response to a large environmental gradient. Maloti-Drakensberg Mountains, southern Africa. We sampled ant assemblages along an extensive elevational gradient (900-3000 m a.s.l.) twice yearly for 7 years, and collected functional-trait information related to the species' dietary and habitat-structure preferences. We used recently developed methods to partition species and functional beta diversity into their turnover and nestedness components. A series of null models were used to test whether the observed beta diversity patterns differed from random expectations. Species beta diversity was driven by turnover, but functional beta diversity was composed of both turnover and nestedness patterns at different parts of the gradient. Null models revealed that deterministic processes were likely to be responsible for the species patterns but that the functional changes were indistinguishable from stochasticity. Different ant species are found with increasing elevation, but they tend to represent an increasingly nested subset of the available functional strategies. This finding is unique and narrows down the list of possible factors that control ant existence across elevation. We conclude that diet and habitat preferences have little role in structuring ant assemblages in montane environments and that some other factor must be driving the non-random patterns of species turnover. This finding also highlights the importance of distinguishing between different kinds of beta diversity.

Structure and function of the adhesive type IV pilus of Sulfolobus acidocaldarius

PubMed Central

Henche, Anna-Lena; Ghosh, Abhrajyoti; Yu, Xiong; Jeske, Torsten; Egelman, Edward; Albers, Sonja-Verena

2014-01-01

Archaea display a variety of type IV pili on their surface and employ them in different physiological functions. In the crenarchaeon Sulfolobus acidocaldarius the most abundant surface structure is the aap pilus (archaeal adhesive pilus). The construction of in frame deletions of the aap genes revealed that all the five genes (aapA, aapX, aapE, aapF, aapB) are indispensible for assembly of the pilus and an impact on surface motility and biofilm formation was observed. Our analyses revealed that there exists a regulatory cross-talk between the expression of aap genes and archaella (formerly archaeal flagella) genes during different growth phases. The structure of the aap pilus is entirely different from the known bacterial type IV pili as well as other archaeal type IV pili. An aap pilus displayed 3 stranded helices where there is a rotation per subunit of ~ 138° and a rise per subunit of ~ 5.7 Å. The filaments have a diameter of ~ 110 Å and the resolution was judged to be ~ 9 Å. We concluded that small changes in sequence might be amplified by large changes in higher-order packing. Our finding of an extraordinary stability of aap-pili possibly represents an adaptation to harsh environments that S. acidocaldarius encounters. PMID:23078543

Serine Protease Inhibitors Specifically Defend Solanum nigrum against Generalist Herbivores but Do Not Influence Plant Growth and Development[C][W

PubMed Central

Hartl, Markus; Giri, Ashok P.; Kaur, Harleen; Baldwin, Ian T.

2010-01-01

Solanaceaeous taxa produce diverse peptide serine proteinase inhibitors (SPIs), known antidigestive defenses that might also control endogenous plant proteases. If and how a plant coordinates and combines its different SPIs for the defense against herbivores and if these SPIs simultaneously serve developmental functions is unknown. We examine Solanum nigrum’s SPI profile, comprising four different active inhibitors, of which the most abundant proved to be novel, to understand their functional specialization in an ecological context. Transcript and activity characterization revealed tissue-specific and insect-elicited accumulation patterns. Stable and transient gene silencing of all four SPIs revealed different specificities for target proteinases: the novel SPI2c displayed high specificity for trypsin and chymotrypsin, while two other SPI2 homologs were highly active against subtilisin. In field and lab experiments, we found all four SPIs to display herbivore- and gene-specific defensive properties, with dissimilar effects on closely related species. However, we did not observe any clear developmental phenotype in SPI-silenced plants, suggesting that SPIs do not play a major role in regulating endogenous proteases under the conditions studied. In summary, specific single SPIs or their combinations defend S. nigrum against generalist herbivores, while the defense against herbivores specialized on SPI-rich diets requires other unknown defense mechanisms. PMID:21177479

Methylation of zebularine investigated using density functional theory calculations.

PubMed

Selvam, Lalitha; Chen, Fang Fang; Wang, Feng

2011-07-30

Deoxyribonucleic acid (DNA) methylation is an epigenetic phenomenon, which adds methyl groups into DNA. This study reveals methylation of a nucleoside antibiotic drug 1-(β-D-ribofuranosyl)-2-pyrimidinone (zebularine or zeb) with respect to its methylated analog, 1-(β-D-ribofuranosyl)-5-methyl-2-pyrimidinone (d5) using density functional theory calculations in valence electronic space. Very similar infrared spectra suggest that zeb and d5 do not differ by types of the chemical bonds, but distinctly different Raman spectra of the nucleoside pair reveal that the impact caused by methylation of zeb can be significant. Further valence orbital-based information details on valence electronic structural changes caused by methylation of zebularine. Frontier orbitals in momentum space and position space of the molecules respond differently to methylation. Based on the additional methyl electron density concentration in d5, orbitals affected by the methyl moiety are classified into primary and secondary contributors. Primary methyl contributions include MO8 (57a), MO18 (47a), and MO37 (28a) of d5, which concentrates on methyl and the base moieties, suggest certain connection to their Frontier orbitals. The primary and secondary methyl affected orbitals provide useful information on chemical bonding mechanism of the methylation in zebularine. Copyright © 2011 Wiley Periodicals, Inc.

The Structure of Working Memory Abilities across the Adult Life Span

PubMed Central

Hale, Sandra; Rose, Nathan S.; Myerson, Joel; Strube, Michael J; Sommers, Mitchell; Tye-Murray, Nancy; Spehar, Brent

2010-01-01

The present study addresses three questions regarding age differences in working memory: (1) whether performance on complex span tasks decreases as a function of age at a faster rate than performance on simple span tasks; (2) whether spatial working memory decreases at a faster rate than verbal working memory; and (3) whether the structure of working memory abilities is different for different age groups. Adults, ages 20–89 (n=388), performed three simple and three complex verbal span tasks and three simple and three complex spatial memory tasks. Performance on the spatial tasks decreased at faster rates as a function of age than performance on the verbal tasks, but within each domain, performance on complex and simple span tasks decreased at the same rates. Confirmatory factor analyses revealed that domain-differentiated models yielded better fits than models involving domain-general constructs, providing further evidence of the need to distinguish verbal and spatial working memory abilities. Regardless of which domain-differentiated model was examined, and despite the faster rates of decrease in the spatial domain, age group comparisons revealed that the factor structure of working memory abilities was highly similar in younger and older adults and showed no evidence of age-related dedifferentiation. PMID:21299306

Resting state fMRI: A review on methods in resting state connectivity analysis and resting state networks.

PubMed

Smitha, K A; Akhil Raja, K; Arun, K M; Rajesh, P G; Thomas, Bejoy; Kapilamoorthy, T R; Kesavadas, Chandrasekharan

2017-08-01

The inquisitiveness about what happens in the brain has been there since the beginning of humankind. Functional magnetic resonance imaging is a prominent tool which helps in the non-invasive examination, localisation as well as lateralisation of brain functions such as language, memory, etc. In recent years, there is an apparent shift in the focus of neuroscience research to studies dealing with a brain at 'resting state'. Here the spotlight is on the intrinsic activity within the brain, in the absence of any sensory or cognitive stimulus. The analyses of functional brain connectivity in the state of rest have revealed different resting state networks, which depict specific functions and varied spatial topology. However, different statistical methods have been introduced to study resting state functional magnetic resonance imaging connectivity, yet producing consistent results. In this article, we introduce the concept of resting state functional magnetic resonance imaging in detail, then discuss three most widely used methods for analysis, describe a few of the resting state networks featuring the brain regions, associated cognitive functions and clinical applications of resting state functional magnetic resonance imaging. This review aims to highlight the utility and importance of studying resting state functional magnetic resonance imaging connectivity, underlining its complementary nature to the task-based functional magnetic resonance imaging.

Age-dependent trade-offs between immunity and male, but not female, reproduction.

PubMed

McNamara, Kathryn B; van Lieshout, Emile; Jones, Therésa M; Simmons, Leigh W

2013-01-01

Immune function is costly and must be traded off against other life-history traits, such as gamete production. Studies of immune trade-offs typically focus on adult individuals, yet the juvenile stage can be a highly protracted period when reproductive resources are acquired and immune challenges are ubiquitous. Trade-offs during development are likely to be important, yet no studies have considered changes in adult responses to immune challenges imposed at different stages of juvenile development. By manipulating the timing of a bacterial immune challenge to the larvae of the cotton bollworm moth, we examined potential trade-offs between investment into immunity at different stages of juvenile development (early or late) and subsequent adult reproductive investment into sperm or egg production. Our data reveal an age-dependent trade-off between juvenile immune function and adult male reproductive investment. Activation of the immune response during late development resulted in a reduced allocation of resources to eupyrene (fertilizing) sperm production. Immune activation from the injection procedure itself (irrespective of whether individuals were injected with an immune elicitor or a control solution) also caused reproductive trade-offs; males injected early in development produced fewer apyrene (nonfertilizing) sperm. Contrary to many other studies, our study demonstrates these immune trade-offs under ad libitum nutritional conditions. No trade-offs were observed between female immune activation and adult reproductive investment. We suggest the differences in trade-offs observed between male sperm types and the absence of reproductive trade-offs in females may be the result of ontogenetic differences in gamete production in this species. Our data reveal developmental windows when trade-offs between immune function and gametic investment are made, and highlight the importance of considering multiple developmental periods when making inferences regarding the fundamental trade-offs expected between immune function and reproduction. © 2012 The Authors. Journal of Animal Ecology © 2012 British Ecological Society.

A convergent functional architecture of the insula emerges across imaging modalities.

PubMed

Kelly, Clare; Toro, Roberto; Di Martino, Adriana; Cox, Christine L; Bellec, Pierre; Castellanos, F Xavier; Milham, Michael P

2012-07-16

Empirical evidence increasingly supports the hypothesis that patterns of intrinsic functional connectivity (iFC) are sculpted by a history of evoked coactivation within distinct neuronal networks. This, together with evidence of strong correspondence among the networks defined by iFC and those delineated using a variety of other neuroimaging techniques, suggests a fundamental brain architecture detectable across multiple functional and structural imaging modalities. Here, we leverage this insight to examine the functional organization of the human insula. We parcellated the insula on the basis of three distinct neuroimaging modalities - task-evoked coactivation, intrinsic (i.e., task-independent) functional connectivity, and gray matter structural covariance. Clustering of these three different covariance-based measures revealed a convergent elemental organization of the insula that likely reflects a fundamental brain architecture governing both brain structure and function at multiple spatial scales. While not constrained to be hierarchical, our parcellation revealed a pseudo-hierarchical, multiscale organization that was consistent with previous clustering and meta-analytic studies of the insula. Finally, meta-analytic examination of the cognitive and behavioral domains associated with each of the insular clusters obtained elucidated the broad functional dissociations likely underlying the topography observed. To facilitate future investigations of insula function across healthy and pathological states, the insular parcels have been made freely available for download via http://fcon_1000.projects.nitrc.org, along with the analytic scripts used to perform the parcellations. Copyright © 2012 Elsevier Inc. All rights reserved.

Executive functioning predicts reading, mathematics, and theory of mind during the elementary years.

PubMed

Cantin, Rachelle H; Gnaedinger, Emily K; Gallaway, Kristin C; Hesson-McInnis, Matthew S; Hund, Alycia M

2016-06-01

The goal of this study was to specify how executive functioning components predict reading, mathematics, and theory of mind performance during the elementary years. A sample of 93 7- to 10-year-old children completed measures of working memory, inhibition, flexibility, reading, mathematics, and theory of mind. Path analysis revealed that all three executive functioning components (working memory, inhibition, and flexibility) mediated age differences in reading comprehension, whereas age predicted mathematics and theory of mind directly. In addition, reading mediated the influence of executive functioning components on mathematics and theory of mind, except that flexibility also predicted mathematics directly. These findings provide important details about the development of executive functioning, reading, mathematics, and theory of mind during the elementary years. Copyright © 2016 Elsevier Inc. All rights reserved.

Neural sex modifies the function of a C. elegans sensory circuit.

PubMed

Lee, Kyunghwa; Portman, Douglas S

2007-11-06

Though sex differences in animal behavior are ubiquitous, their neural and genetic underpinnings remain poorly understood. In particular, the role of functional differences in the neural circuitry that is shared by both sexes has not been extensively investigated. We have addressed these issues with C. elegans olfaction, a simple innate behavior mediated by sexually isomorphic neurons. Though males respond to the same olfactory attractants as do hermaphrodites, we find that each sex has a characteristic repertoire of olfactory preferences. These are not secondary to other sex-specific behaviors and do not require signaling from the gonad. Sex-specific olfactory preferences are controlled by tra-1, the master regulator of C. elegans sexual differentiation. Moreover, the genetic masculinization of neurons in an otherwise wild-type hermaphrodite is sufficient to switch the sexual phenotype of olfactory preference behavior. These studies reveal novel and unexpected sex differences in a C. elegans sensory behavior that is exhibited by both sexes. Our results indicate that these differences are a function of the chromosomally determined sexual identity of shared neural circuitry.

Current Progress in Tonoplast Proteomics Reveals Insights into the Function of the Large Central Vacuole

PubMed Central

Trentmann, Oliver; Haferkamp, Ilka

2013-01-01

Vacuoles of plants fulfill various biologically important functions, like turgor generation and maintenance, detoxification, solute sequestration, or protein storage. Different types of plant vacuoles (lytic versus protein storage) are characterized by different functional properties apparently caused by a different composition/abundance and regulation of transport proteins in the surrounding membrane, the tonoplast. Proteome analyses allow the identification of vacuolar proteins and provide an informative basis for assigning observed transport processes to specific carriers or channels. This review summarizes techniques required for vacuolar proteome analyses, like e.g., isolation of the large central vacuole or tonoplast membrane purification. Moreover, an overview about diverse published vacuolar proteome studies is provided. It becomes evident that qualitative proteomes from different plant species represent just the tip of the iceberg. During the past few years, mass spectrometry achieved immense improvement concerning its accuracy, sensitivity, and application. As a consequence, modern tonoplast proteome approaches are suited for detecting alterations in membrane protein abundance in response to changing environmental/physiological conditions and help to clarify the regulation of tonoplast transport processes. PMID:23459586

Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme.

PubMed Central

Jeruzalmi, D; Steitz, T A

1998-01-01

The T7 RNA polymerase-T7 lysozyme complex regulates phage gene expression during infection of Escherichia coli. The 2.8 A crystal structure of the complex reveals that lysozyme binds at a site remote from the polymerase active site, suggesting an indirect mechanism of inhibition. Comparison of the T7 RNA polymerase structure with that of the homologous pol I family of DNA polymerases reveals identities in the catalytic site but also differences specific to RNA polymerase function. The structure of T7 RNA polymerase presented here differs significantly from a previously published structure. Sequence similarities between phage RNA polymerases and those from mitochondria and chloroplasts, when interpreted in the context of our revised model of T7 RNA polymerase, suggest a conserved fold. PMID:9670025

Integrated Analysis of Alzheimer's Disease and Schizophrenia Dataset Revealed Different Expression Pattern in Learning and Memory.

PubMed

Li, Wen-Xing; Dai, Shao-Xing; Liu, Jia-Qian; Wang, Qian; Li, Gong-Hua; Huang, Jing-Fei

2016-01-01

Alzheimer's disease (AD) and schizophrenia (SZ) are both accompanied by impaired learning and memory functions. This study aims to explore the expression profiles of learning or memory genes between AD and SZ. We downloaded 10 AD and 10 SZ datasets from GEO-NCBI for integrated analysis. These datasets were processed using RMA algorithm and a global renormalization for all studies. Then Empirical Bayes algorithm was used to find the differentially expressed genes between patients and controls. The results showed that most of the differentially expressed genes were related to AD whereas the gene expression profile was little affected in the SZ. Furthermore, in the aspects of the number of differentially expressed genes, the fold change and the brain region, there was a great difference in the expression of learning or memory related genes between AD and SZ. In AD, the CALB1, GABRA5, and TAC1 were significantly downregulated in whole brain, frontal lobe, temporal lobe, and hippocampus. However, in SZ, only two genes CRHBP and CX3CR1 were downregulated in hippocampus, and other brain regions were not affected. The effect of these genes on learning or memory impairment has been widely studied. It was suggested that these genes may play a crucial role in AD or SZ pathogenesis. The different gene expression patterns between AD and SZ on learning and memory functions in different brain regions revealed in our study may help to understand the different mechanism between two diseases.

Levels of integration in cognitive control and sequence processing in the prefrontal cortex.

PubMed

Bahlmann, Jörg; Korb, Franziska M; Gratton, Caterina; Friederici, Angela D

2012-01-01

Cognitive control is necessary to flexibly act in changing environments. Sequence processing is needed in language comprehension to build the syntactic structure in sentences. Functional imaging studies suggest that sequence processing engages the left ventrolateral prefrontal cortex (PFC). In contrast, cognitive control processes additionally recruit bilateral rostral lateral PFC regions. The present study aimed to investigate these two types of processes in one experimental paradigm. Sequence processing was manipulated using two different sequencing rules varying in complexity. Cognitive control was varied with different cue-sets that determined the choice of a sequencing rule. Univariate analyses revealed distinct PFC regions for the two types of processing (i.e. sequence processing: left ventrolateral PFC and cognitive control processing: bilateral dorsolateral and rostral PFC). Moreover, in a common brain network (including left lateral PFC and intraparietal sulcus) no interaction between sequence and cognitive control processing was observed. In contrast, a multivariate pattern analysis revealed an interaction of sequence and cognitive control processing, such that voxels in left lateral PFC and parietal cortex showed different tuning functions for tasks involving different sequencing and cognitive control demands. These results suggest that the difference between the process of rule selection (i.e. cognitive control) and the process of rule-based sequencing (i.e. sequence processing) find their neuronal underpinnings in distinct activation patterns in lateral PFC. Moreover, the combination of rule selection and rule sequencing can shape the response of neurons in lateral PFC and parietal cortex.

Individual differences reveal correlates of hidden hearing deficits.

PubMed

Bharadwaj, Hari M; Masud, Salwa; Mehraei, Golbarg; Verhulst, Sarah; Shinn-Cunningham, Barbara G

2015-02-04

Clinical audiometry has long focused on determining the detection thresholds for pure tones, which depend on intact cochlear mechanics and hair cell function. Yet many listeners with normal hearing thresholds complain of communication difficulties, and the causes for such problems are not well understood. Here, we explore whether normal-hearing listeners exhibit such suprathreshold deficits, affecting the fidelity with which subcortical areas encode the temporal structure of clearly audible sound. Using an array of measures, we evaluated a cohort of young adults with thresholds in the normal range to assess both cochlear mechanical function and temporal coding of suprathreshold sounds. Listeners differed widely in both electrophysiological and behavioral measures of temporal coding fidelity. These measures correlated significantly with each other. Conversely, these differences were unrelated to the modest variation in otoacoustic emissions, cochlear tuning, or the residual differences in hearing threshold present in our cohort. Electroencephalography revealed that listeners with poor subcortical encoding had poor cortical sensitivity to changes in interaural time differences, which are critical for localizing sound sources and analyzing complex scenes. These listeners also performed poorly when asked to direct selective attention to one of two competing speech streams, a task that mimics the challenges of many everyday listening environments. Together with previous animal and computational models, our results suggest that hidden hearing deficits, likely originating at the level of the cochlear nerve, are part of "normal hearing." Copyright © 2015 the authors 0270-6474/15/352161-12$15.00/0.

Levels of Integration in Cognitive Control and Sequence Processing in the Prefrontal Cortex

PubMed Central

Bahlmann, Jörg; Korb, Franziska M.; Gratton, Caterina; Friederici, Angela D.

2012-01-01

Cognitive control is necessary to flexibly act in changing environments. Sequence processing is needed in language comprehension to build the syntactic structure in sentences. Functional imaging studies suggest that sequence processing engages the left ventrolateral prefrontal cortex (PFC). In contrast, cognitive control processes additionally recruit bilateral rostral lateral PFC regions. The present study aimed to investigate these two types of processes in one experimental paradigm. Sequence processing was manipulated using two different sequencing rules varying in complexity. Cognitive control was varied with different cue-sets that determined the choice of a sequencing rule. Univariate analyses revealed distinct PFC regions for the two types of processing (i.e. sequence processing: left ventrolateral PFC and cognitive control processing: bilateral dorsolateral and rostral PFC). Moreover, in a common brain network (including left lateral PFC and intraparietal sulcus) no interaction between sequence and cognitive control processing was observed. In contrast, a multivariate pattern analysis revealed an interaction of sequence and cognitive control processing, such that voxels in left lateral PFC and parietal cortex showed different tuning functions for tasks involving different sequencing and cognitive control demands. These results suggest that the difference between the process of rule selection (i.e. cognitive control) and the process of rule-based sequencing (i.e. sequence processing) find their neuronal underpinnings in distinct activation patterns in lateral PFC. Moreover, the combination of rule selection and rule sequencing can shape the response of neurons in lateral PFC and parietal cortex. PMID:22952762

Alexithymia is related to differences in gray matter volume: a voxel-based morphometry study.

PubMed

Ihme, Klas; Dannlowski, Udo; Lichev, Vladimir; Stuhrmann, Anja; Grotegerd, Dominik; Rosenberg, Nicole; Kugel, Harald; Heindel, Walter; Arolt, Volker; Kersting, Anette; Suslow, Thomas

2013-01-23

Alexithymia has been characterized as the inability to identify and describe feelings. Functional imaging studies have revealed that alexithymia is linked to reactivity changes in emotion- and face-processing-relevant brain areas. In this respect, anterior cingulate cortex (ACC), amygdala, anterior insula and fusiform gyrus (FFG) have been consistently reported. However, it remains to be clarified whether alexithymia is also associated with structural differences. Voxel-based morphometry on T1-weighted magnetic resonance images was used to investigate gray matter volume in 17 high alexithymics (HA) and 17 gender-matched low alexithymics (LA), which were selected from a sample of 161 healthy volunteers on basis of the 20-item Toronto Alexithymia Scale. Data were analyzed as statistic parametric maps for the comparisons LA>HA and HA>LA in a priori determined regions of interests (ROIs), i.e., ACC, amygdala, anterior insula and FFG. Moreover, an exploratory whole brain analysis was accomplished. For the contrast LA>HA, significant clusters were detected in the ACC, left amygdala and left anterior insula. Additionally, the whole brain analysis revealed volume differences in the left middle temporal gyrus. No significant differences were found for the comparison HA>LA. Our findings suggest that high compared to low alexithymics show less gray matter volume in several emotion-relevant brain areas. These structural differences might contribute to the functional alterations found in previous imaging studies in alexithymia. Copyright © 2012 Elsevier B.V. All rights reserved.

Family Functioning and Adolescent Psychological Maladjustment: The Mediating Role of Coping Strategies.

PubMed

Francisco, Rita; Loios, Sara; Pedro, Marta

2016-10-01

This study aims to analyze the mediating role of coping strategies in the relationship between family functioning and youth maladjustment. A community sample of 341 adolescents (M = 15.11 years old; SD = 1.71) completed self-report measures about such variables. Results showed that a perception of an inadequate family functioning was associated with the use of maladaptive coping strategies, as well as with youth psychological maladjustment. The results also revealed that rumination and support-seeking mediated the relationship between family functioning and internalizing behavior, and hostile expression of feelings played a mediating role between family functioning and externalizing behavior. No gender differences were found in the relationship between variables. This study emphasizes the importance of coping strategies used by adolescents to understand the relationship between family functioning and youth psychological maladjustment.

Contribution of Theory of Mind, Executive Functioning, and Pragmatics to Socialization Behaviors of Children with High-Functioning Autism.

PubMed

Berenguer, Carmen; Miranda, Ana; Colomer, Carla; Baixauli, Inmaculada; Roselló, Belén

2018-02-01

Social difficulties are a key aspect of autism, but the intervening factors are still poorly understood. This study had two objectives: to compare the profile of ToM skills, executive functioning (EF), and pragmatic competence (PC) of children with high-functioning autism (HFA) and children with typical development (TD), and analyze their mediator role in social functioning. The participants were 52 children with HFA and 37 children with TD matched on age, intelligence quotient, and expressive vocabulary. Significant differences were found on measures of ToM, both explicit and applied, EF, and PC between children with HFA and TD. Multiple mediation analysis revealed that applied ToM skills and PC mediated the relations between autism symptoms and social functioning. Implications for social cognitive interventions to address these findings are discussed.

Why women use makeup: implication of psychological traits in makeup functions.

PubMed

Korichi, Rodolphe; Pelle-de-Queral, Delphine; Gazano, Germaine; Aubert, Arnaud

2008-01-01

Makeup acts and stimulates three of our senses: touch (which encompasses all sensations from the body surface), smell (fragrance), and sight (the process of becoming and looking beautiful). The positive stimulation of these senses by makeup can induce sensory as well as psychological pleasure. In order to understand the relationship of women to their makeup, we interviewed different groups of women on their quality of life and makeup habits. Then, through four standard well-validated psychometric self-questionnaires, we examined the possible relation between the need to make up oneself and specific psychological features. Our first results clearly showed that makeup could support two opposite "up" functions, i.e., "camouflage" vs "seduction." Concerning their psychological profiles, results showed that women of the functional class "camouflage" are more anxious, defensive, and emotionally unstable compared to those of the functional class "seduction," who appear to be more sociable, assertive, and extroverted. Further analyses revealed a division of the two classes into subclasses of volunteers with opposed personality and psychological profiles. This new classification allowed us to define more precisely the relations existing within the subjective experience of women during the makeup process. In conclusion, our study revealed that beyond the simple application of colorful products on the face, makeup has two major functional implications depending on specific psychological profiles of women.

Connectivity dynamics in typical development and its relationship to autistic traits and autism spectrum disorder.

PubMed

Rashid, Barnaly; Blanken, Laura M E; Muetzel, Ryan L; Miller, Robyn; Damaraju, Eswar; Arbabshirani, Mohammad R; Erhardt, Erik B; Verhulst, Frank C; van der Lugt, Aad; Jaddoe, Vincent W V; Tiemeier, Henning; White, Tonya; Calhoun, Vince

2018-03-30

Recent advances in neuroimaging techniques have provided significant insights into developmental trajectories of human brain function. Characterizations of typical neurodevelopment provide a framework for understanding altered neurodevelopment, including differences in brain function related to developmental disorders and psychopathology. Historically, most functional connectivity studies of typical and atypical development operate under the assumption that connectivity remains static over time. We hypothesized that relaxing stationarity assumptions would reveal novel features of both typical brain development related to children on the autism spectrum. We employed a "chronnectomic" (recurring, time-varying patterns of connectivity) approach to evaluate transient states of connectivity using resting-state functional MRI in a population-based sample of 774 6- to 10-year-old children. Dynamic connectivity was evaluated using a sliding-window approach, and revealed four transient states. Internetwork connectivity increased with age in modularized dynamic states, illustrating an important pattern of connectivity in the developing brain. Furthermore, we demonstrated that higher levels of autistic traits and ASD diagnosis were associated with longer dwell times in a globally disconnected state. These results provide a roadmap to the chronnectomic organization of the developing brain and suggest that characteristics of functional brain connectivity are related to children on the autism spectrum. © 2018 Wiley Periodicals, Inc.

Morphological and functional evaluation of chronic pancreatitis with magnetic resonance imaging

PubMed Central

Hansen, Tine Maria; Nilsson, Matias; Gram, Mikkel; Frøkjær, Jens Brøndum

2013-01-01

Magnetic resonance imaging (MRI) techniques for assessment of morphology and function of the pancreas have been improved dramatically the recent years and MRI is very often used in diagnosing and follow-up of chronic pancreatitis (CP) patients. Standard MRI including fat-suppressed T1-weighted and T2-weighted imaging techniques reveal decreased signal and glandular atrophy of the pancreas in CP. In contrast-enhanced MRI of the pancreas in CP the pancreatic signal is usually reduced and delayed due to decreased perfusion as a result of chronic inflammation and fibrosis. Thus, morphological changes of the ductal system can be assessed by magnetic resonance cholangiopancreatography (MRCP). Furthermore, secretin-stimulated MRCP is a valuable technique to evaluate side branch pathology and the exocrine function of the pancreas and diffusion weighted imaging can be used to quantify both parenchymal fibrotic changes and the exocrine function of the pancreas. These standard and advanced MRI techniques are supplementary techniques to reveal morphological and functional changes of the pancreas in CP. Recently, spectroscopy has been used for assessment of metabolite concentrations in-vivo in different tissues and may have the potential to offer better tissue characterization of the pancreas. Hence, the purpose of the present review is to provide an update on standard and advanced MRI techniques of the pancreas in CP. PMID:24259954

Functional versus Nonfunctional Rehabilitation in Chronic Ischemic Stroke: Evidences from a Randomized Functional MRI Study

PubMed Central

Pelicioni, Maristela C. X.; Novaes, Morgana M.; Peres, Andre S. C.; Lino de Souza, Altay A.; Minelli, Cesar; Fabio, Soraia R. C.; Pontes-Neto, Octavio M.; Santos, Antonio C.; de Araujo, Draulio B.

2016-01-01

Motor rehabilitation of stroke survivors may include functional and/or nonfunctional strategy. The present study aimed to compare the effect of these two rehabilitation strategies by means of clinical scales and functional Magnetic Resonance Imaging (fMRI). Twelve hemiparetic chronic stroke patients were selected. Patients were randomly assigned a nonfunctional (NFS) or functional (FS) rehabilitation scheme. Clinical scales (Fugl-Meyer, ARA test, and modified Barthel) and fMRI were applied at four moments: before rehabilitation (P1) and immediately after (P2), 1 month after (P3), and three months after (P4) the end of rehabilitation. The NFS group improved significantly and exclusively their Fugl-Meyer scores at P2, P3, and P4, when compared to P1. On the other hand, the FS group increased significantly in Fugl-Meyer at P2, when compared to P1, and also in their ARA and Barthel scores. fMRI inspection at the individual level revealed that both rehabilitation schemes most often led to decreased activation sparseness, decreased activity of contralesional M1, increased asymmetry of M1 activity to the ipsilesional side, decreased perilesional activity, and decreased SMA activity. Increased M1 asymmetry with rehabilitation was also confirmed by Lateralization Indexes. Our clinical analysis revealed subtle differences between FS and NFS. PMID:26839716

Mineral and organic growing media have distinct community structure, stability and functionality in soilless culture systems.

PubMed

Grunert, Oliver; Hernandez-Sanabria, Emma; Vilchez-Vargas, Ramiro; Jauregui, Ruy; Pieper, Dietmar H; Perneel, Maaike; Van Labeke, Marie-Christine; Reheul, Dirk; Boon, Nico

2016-01-05

The choice of soilless growing medium for plant nutrition, growth and support is crucial for improving the eco-sustainability of the production in horticultural systems. As our current understanding of the functional microbial communities inhabiting this ecosystem is still limited, we examined the microbial community development of the two most important growing media (organic and mineral) used in open soilless horticultural systems. We aimed to identify factors that influence community composition over time, and to compare the distribution of individual taxa across growing media, and their potential functionality. High throughput sequencing analysis revealed a distinctive and stable microbial community in the organic growing medium. Humidity, pH, nitrate-N, ammonium-N and conductivity were uncovered as the main factors associated with the resident bacterial communities. Ammonium-N was correlated with Rhizobiaceae abundance, while potential competitive interactions among both Methylophilaceae and Actinobacteridae with Rhizobiaceae were suggested. Our results revealed that soilless growing media are unique niches for diverse bacterial communities with temporal functional stability, which may possibly impact the resistance to external forces. These differences in communities can be used to develop strategies to move towards a sustainable horticulture with increased productivity and quality.

Anxiety Modulates Insula Recruitment in Resting-State Functional Magnetic Resonance Imaging in Youth and Adults

PubMed Central

Gotlib, Ian H.; Thompson, Paul M.; Thomason, Moriah E.

2011-01-01

Abstract Research on resting-state functional connectivity reveals intrinsically connected networks in the brain that are largely consistent across the general population. However, there are individual differences in these networks that have not been elucidated. Here, we measured the influence of naturally occurring mood on functional connectivity. In particular, we examined the association between self-reported levels of anxiety and connectivity in the default mode network (DMN). Healthy youth (n=43; ages 10–18) and adult participants (n=24, ages 19–59) completed a 6-min resting-state functional magnetic resonance imaging scan, then immediately completed questionnaires assessing their mood and thoughts during the scan. Regression analyses conducted separately for the youth and adult samples revealed brain regions in which increases in connectivity differentially corresponded to higher anxiety in each group. In one area, the left insular cortex, both groups showed similar increased connectivity to the DMN (youth: -30, 26, 14; adults: -33, 12, 14) with increased anxiety. State anxiety assessed during scanning was not correlated with trait anxiety, so our results likely reflect state levels of anxiety. To our knowledge, this is the first study to relate naturally occurring mood to resting state connectivity. PMID:22433052

Formula Budgeting for Higher Education: State Practices in 1979-80. Working Paper Series.

ERIC Educational Resources Information Center

Gross, Francis M.

Budget formulas used by states for state-supported colleges and universities are described, along with budgeting guidelines. A comparative analysis of the budget formulas in use in 1979-1980 reveals the similarities and differences in design among 19 states. Functional areas of expenditure used in the formula calculation are also compared for each…

Aspects of Theme in the Method and Discussion Sections of Biology Journal Articles in English.

ERIC Educational Resources Information Center

Martinez, Iliana A.

2003-01-01

Analyzes the thematic structure of the method and Discussion section of biology research articles. A corpus of 30 journal articles was analyzed using the categories of systematic functional linguistics and a semantic categorization for unmarked themes realized by subject. Revealed differences in the semantic construction of the sections. (VWL)

Inequality: Race Differences in the Distribution of Earnings. Rand Paper Series P5481-1.

ERIC Educational Resources Information Center

Smith, James P.; Welch, Finis

Characteristics and determinants of earnings distributions for black and white males are revealed in samples from the 1960 and 1970 censuses. Using this data, this paper describes and contrasts the properties of black and white male earnings distributions. It also uses earnings functions estimated from the census to identify and rank variables in…

Comparing return to sport activities after short metaphyseal femoral arthroplasty with resurfacing and big femoral head arthroplasties.

PubMed

Karampinas, Panagiotis K; Papadelis, Eustratios G; Vlamis, John A; Basiliadis, Hlias; Pneumaticos, Spiros G

2017-07-01

Young patients feel that maintaining sport activities after total hip arthroplasty constitutes an important part of their quality of life. The majority of hip surgeons allow patients to return to low-impact activities, but significant caution is advised to taking part in high-impact activities. The purpose of this study is to compare and evaluate the post-operative return to daily living habits and sport activities following short-metaphyseal hip and high functional total hip arthroplasties (resurfacing and big femoral head arthroplasties). In a study design, 48 patients (55 hips) were enrolled in three different comparative groups, one with the short-metaphyseal arthroplasties, a second with high functional resurfacing arthroplasties and a third of big femoral head arthroplasties. Each patient experienced a clinical examination and evaluated with Harris Hip Score, WOMAC, Sf-36, UCLA activity score, satisfaction VAS, anteroposterior and lateral X-rays of the hip and were followed in an outpatient setting for 2 years. Statistical analysis revealed no notable differences between the three groups regarding their demographic data however significant differences have been found between preoperative and postoperative clinical scores of each group. Also, we fail to reveal any significant differences when comparing data of all three groups at the final 2 years postoperative control regarding their clinical scores. The overall outcome of all three groups was similar, all the patients were satisfied and returned to previous level of sport activities. Short metaphyseal hip arthroplasties in young patients intending to return to previous and even high impact sport activities, similar to high functional resurfacing, big femoral head arthroplasties. Short stems with hard on hard bearing surfaces might become an alternative to standard stems and hip resurfacing.

Individual Differences in Amygdala-Medial Prefrontal Anatomy Link Negative Affect, Impaired Social Functioning, and Polygenic Depression Risk

PubMed Central

Holmes, Avram J.; Lee, Phil H.; Hollinshead, Marisa O.; Bakst, Leah; Roffman, Joshua L.; Smoller, Jordan W.; Buckner, Randy L.

2013-01-01

Individual differences in affective and social processes may arise from variability in amygdala-medial prefrontal (mPFC) circuitry and related genetic heterogeneity. To explore this possibility in humans, we examined the structural correlates of trait negative affect in a sample of 1050 healthy young adults with no history of psychiatric illness. Analyses revealed that heightened negative affect was associated with increased amygdala volume and reduced thickness in a left mPFC region encompassing the subgenual and rostral anterior cingulate cortex. The most extreme individuals displayed an inverse correlation between amygdala volume and mPFC thickness, suggesting that imbalance between these structures is linked to negative affect in the general population. Subgroups of participants were further evaluated on social (n = 206) and emotional (n = 533) functions. Individuals with decreased mPFC thickness exhibited the poorest social cognition and were least able to correctly identify facial emotion. Given prior links between disrupted amygdala–mPFC circuitry and the presence of major depressive disorder (MDD), we explored whether the individual differences in anatomy observed here in healthy young adults were associated with polygenic risk for MDD (n = 438) using risk scores derived from a large genome-wide association analysis (n = 18,759). Analyses revealed associations between increasing polygenic burden for MDD and reduced cortical thickness in the left mPFC. These collective findings suggest that, within the healthy population, there is significant variability in amygdala–mPFC circuitry that is associated with poor functioning across affective and social domains. Individual differences in this circuitry may arise, in part, from common genetic variability that contributes to risk for MDD. PMID:23238724

Comprehensive molecular profiling of 718 Multiple Myelomas reveals significant differences in mutation frequencies between African and European descent cases

PubMed Central

Christofferson, Austin; Aldrich, Jessica; Jewell, Scott; Kittles, Rick A.; Derome, Mary; Craig, David Wesley; Carpten, John D.

2017-01-01

Multiple Myeloma (MM) is a plasma cell malignancy with significantly greater incidence and mortality rates among African Americans (AA) compared to Caucasians (CA). The overall goal of this study is to elucidate differences in molecular alterations in MM as a function of self-reported race and genetic ancestry. Our study utilized somatic whole exome, RNA-sequencing, and correlated clinical data from 718 MM patients from the Multiple Myeloma Research Foundation CoMMpass study Interim Analysis 9. Somatic mutational analyses based upon self-reported race corrected for ancestry revealed significant differences in mutation frequency between groups. Of interest, BCL7A, BRWD3, and AUTS2 demonstrate significantly higher mutation frequencies among AA cases. These genes are all involved in translocations in B-cell malignancies. Moreover, we detected a significant difference in mutation frequency of TP53 and IRF4 with frequencies higher among CA cases. Our study provides rationale for interrogating diverse tumor cohorts to best understand tumor genomics across populations. PMID:29166413

[EEG correlates of geno-phenotypical features of the brain development in children of the native and newcomers' population of the Russian North-East].

PubMed

Soroko, S I; Bekshaev, S S; Rozhkov, V P

2012-01-01

Traditional and original methods of EEG analysis were used to study the brain electrical activity maturation in 156 children and adolescents from 7 to 17 years old who represented the native (Koryaks and Evenks) and newcomers' populations living in severe climatic and geographic conditions of the Russian North-East. New data revealing age-, sex- and ethnic-related features in quantitative EEG parameters are presented. Markers are obtained that characterize alterations in the structure of interaction between different EEG rhythms. The results demonstrate age-dependent transformation of this structure separated in time for both different cortical areas and different EEG frequency bands. These alterations show time lag from 2 to 3 years in children of native population compared to the newcomers. The revealed differences are assumed to reflect geno-phenotypical features of morpho-functional CNS development in children of the native and newcomers' population that depend on strong adaptation tension for extreme environmental conditions.

Mining for hemicellulases in the fungus-growing termite Pseudacanthotermes militaris using functional metagenomics.

PubMed

Bastien, Géraldine; Arnal, Grégory; Bozonnet, Sophie; Laguerre, Sandrine; Ferreira, Fernando; Fauré, Régis; Henrissat, Bernard; Lefèvre, Fabrice; Robe, Patrick; Bouchez, Olivier; Noirot, Céline; Dumon, Claire; O'Donohue, Michael

2013-05-14

The metagenomic analysis of gut microbiomes has emerged as a powerful strategy for the identification of biomass-degrading enzymes, which will be no doubt useful for the development of advanced biorefining processes. In the present study, we have performed a functional metagenomic analysis on comb and gut microbiomes associated with the fungus-growing termite, Pseudacanthotermes militaris. Using whole termite abdomens and fungal-comb material respectively, two fosmid-based metagenomic libraries were created and screened for the presence of xylan-degrading enzymes. This revealed 101 positive clones, corresponding to an extremely high global hit rate of 0.49%. Many clones displayed either β-d-xylosidase (EC 3.2.1.37) or α-l-arabinofuranosidase (EC 3.2.1.55) activity, while others displayed the ability to degrade AZCL-xylan or AZCL-β-(1,3)-β-(1,4)-glucan. Using secondary screening it was possible to pinpoint clones of interest that were used to prepare fosmid DNA. Sequencing of fosmid DNA generated 1.46 Mbp of sequence data, and bioinformatics analysis revealed 63 sequences encoding putative carbohydrate-active enzymes, with many of these forming parts of sequence clusters, probably having carbohydrate degradation and metabolic functions. Taxonomic assignment of the different sequences revealed that Firmicutes and Bacteroidetes were predominant phyla in the gut sample, while microbial diversity in the comb sample resembled that of typical soil samples. Cloning and expression in E. coli of six enzyme candidates identified in the libraries provided access to individual enzyme activities, which all proved to be coherent with the primary and secondary functional screens. This study shows that the gut microbiome of P. militaris possesses the potential to degrade biomass components, such as arabinoxylans and arabinans. Moreover, the data presented suggests that prokaryotic microorganisms present in the comb could also play a part in the degradation of biomass within the termite mound, although further investigation will be needed to clarify the complex synergies that might exist between the different microbiomes that constitute the termitosphere of fungus-growing termites. This study exemplifies the power of functional metagenomics for the discovery of biomass-active enzymes and has provided a collection of potentially interesting biocatalysts for further study.

Whole-Genome Duplication and the Functional Diversification of Teleost Fish Hemoglobins

PubMed Central

Opazo, Juan C.; Butts, G. Tyler; Nery, Mariana F.; Storz, Jay F.; Hoffmann, Federico G.

2013-01-01

Subsequent to the two rounds of whole-genome duplication that occurred in the common ancestor of vertebrates, a third genome duplication occurred in the stem lineage of teleost fishes. This teleost-specific genome duplication (TGD) is thought to have provided genetic raw materials for the physiological, morphological, and behavioral diversification of this highly speciose group. The extreme physiological versatility of teleost fish is manifest in their diversity of blood–gas transport traits, which reflects the myriad solutions that have evolved to maintain tissue O2 delivery in the face of changing metabolic demands and environmental O2 availability during different ontogenetic stages. During the course of development, regulatory changes in blood–O2 transport are mediated by the expression of multiple, functionally distinct hemoglobin (Hb) isoforms that meet the particular O2-transport challenges encountered by the developing embryo or fetus (in viviparous or oviparous species) and in free-swimming larvae and adults. The main objective of the present study was to assess the relative contributions of whole-genome duplication, large-scale segmental duplication, and small-scale gene duplication in producing the extraordinary functional diversity of teleost Hbs. To accomplish this, we integrated phylogenetic reconstructions with analyses of conserved synteny to characterize the genomic organization and evolutionary history of the globin gene clusters of teleosts. These results were then integrated with available experimental data on functional properties and developmental patterns of stage-specific gene expression. Our results indicate that multiple α- and β-globin genes were present in the common ancestor of gars (order Lepisoteiformes) and teleosts. The comparative genomic analysis revealed that teleosts possess a dual set of TGD-derived globin gene clusters, each of which has undergone lineage-specific changes in gene content via repeated duplication and deletion events. Phylogenetic reconstructions revealed that paralogous genes convergently evolved similar functional properties in different teleost lineages. Consistent with other recent studies of globin gene family evolution in vertebrates, our results revealed evidence for repeated evolutionary transitions in the developmental regulation of Hb synthesis. PMID:22949522

Do tasks make a difference? Accounting for heterogeneity of performance of children with reading difficulties on tasks of executive function: findings from a meta-analysis.

PubMed

Booth, Josephine N; Boyle, James M E; Kelly, Steve W

2010-03-01

Research studies have implicated executive functions in reading difficulties (RD). But while some studies have found children with RD to be impaired on tasks of executive function other studies report unimpaired performance. A meta-analysis was carried out to determine whether these discrepant findings can be accounted for by differences in the tasks of executive function that are utilized. A total of 48 studies comparing the performance on tasks of executive function of children with RD with their typically developing peers were included in the meta-analysis, yielding 180 effect sizes. An overall effect size of 0.57 (SE .03) was obtained, indicating that children with RD have impairments on tasks of executive function. However, effect sizes varied considerably suggesting that the impairment is not uniform. Moderator analysis revealed that task modality and IQ-achievement discrepancy definitions of RD influenced the magnitude of effect; however, the age and gender of participants and the nature of the RD did not have an influence. While the children's RD were associated with executive function impairments, variation in effect size is a product of the assessment task employed, underlying task demands, and definitional criteria.

Minimal invasive epicardial lead implantation: optimizing cardiac resynchronization with a new mapping device for epicardial lead placement.

PubMed

Maessen, J G; Phelps, B; Dekker, A L A J; Dijkman, B

2004-05-01

To optimize resynchronization in biventricular pacing with epicardial leads, mapping to determine the best pacing site, is a prerequisite. A port access surgical mapping technique was developed that allowed multiple pace site selection and reproducible lead evaluation and implantation. Pressure-volume loops analysis was used for real time guidance in targeting epicardial lead placement. Even the smallest changes in lead position revealed significantly different functional results. Optimizing the pacing site with this technique allowed functional improvement up to 40% versus random pace site selection.

Determining protein function and interaction from genome analysis

DOEpatents

Eisenberg, David; Marcotte, Edward M.; Thompson, Michael J.; Pellegrini, Matteo; Yeates, Todd O.

2004-08-03

A computational method system, and computer program are provided for inferring functional links from genome sequences. One method is based on the observation that some pairs of proteins A' and B' have homologs in another organism fused into a single protein chain AB. A trans-genome comparison of sequences can reveal these AB sequences, which are Rosetta Stone sequences because they decipher an interaction between A' and B. Another method compares the genomic sequence of two or more organisms to create a phylogenetic profile for each protein indicating its presence or absence across all the genomes. The profile provides information regarding functional links between different families of proteins. In yet another method a combination of the above two methods is used to predict functional links.

Assigning protein functions by comparative genome analysis protein phylogenetic profiles

DOEpatents

Pellegrini, Matteo; Marcotte, Edward M.; Thompson, Michael J.; Eisenberg, David; Grothe, Robert; Yeates, Todd O.

2003-05-13

A computational method system, and computer program are provided for inferring functional links from genome sequences. One method is based on the observation that some pairs of proteins A' and B' have homologs in another organism fused into a single protein chain AB. A trans-genome comparison of sequences can reveal these AB sequences, which are Rosetta Stone sequences because they decipher an interaction between A' and B. Another method compares the genomic sequence of two or more organisms to create a phylogenetic profile for each protein indicating its presence or absence across all the genomes. The profile provides information regarding functional links between different families of proteins. In yet another method a combination of the above two methods is used to predict functional links.