bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Cupin Protein, Dehydratase Pac13 is a Homodimer
Authors: Zhang Rundong 
Published: April 2019

ABSTRACTCupin proteins share a double-stranded β-helix fold, form one of the largest superfamilies and possess remarkable functional diversity. They usually form homooligomeric states. Michailidou et al. recently reported that a cupin protein Pac13, which is a dehydratase mediating the formation of the 3’-deoxy nucleoside of pacidamycins, is an unusual, small monomer. However, a careful analysis of the biophysical and structural data provided by the authors clearly indicates that Pac13 is a homodimer.
Neurophysiological correlates of collective perceptual decision-making
Authors: Baumgart Kristina G. , Byvshev Petr , Sliby Alexa-Nicole , Strube Andreas , König Peter , Wahn Basil 
Published: April 2019

AbstractHumans frequently coordinate with others in daily life. A recent study on perceptual decision-making showed that dyad members with similar individual performances attain a higher joint performance than the better dyad member (i.e., a collective benefit). However, little is known about the physiological basis of these results. Here, we replicate this earlier work and also investigate the neurophysiological correlates of decision-making using EEG.In a two interval forced choice task, co-actors individually indicated presence of a target stimulus with a higher contrast and then indicated their confidence on a rating scale. Viewing the individual ratings, dyads made a joint decision. Replicating earlier work, we found a positive correlation between the similarity of individual performances and collective benefit.We analyzed event related potentials (ERPs) in three phases (i.e., stimulus onset, response, and feedback) using explorative cluster mass permutation tests. At stimulus onset, ERPs were significantly linearly related to our manipulation of contrast differences, validating our manipulation of task difficulty. For individual and joint responses, we found a significant centro-parietal error-related positivity for correct versus incorrect responses, which suggests that accuracy is already evaluated at the response level. At feedback presentation, we found a significant late positive fronto-central potential elicited by incorrect joint responses, suggesting a stronger emotional response to negative as compared to positive feedback. In sum, these results demonstrate that response- and feedback-related components elicited by an error-monitoring system differentially integrate conflicting information exchanged during the joint decision-making process.
Endophytic Virome
Authors: Das Saurav , Barooah Madhumita , Thakur Nagendra 
Published: April 2019

AbstractEndophytic microorganisms are well established for their mutualistic relationship and plant growth promotion through production of different metabolites. Bacteria and fungi are the major group of endophytes which were extensively studied. Virus are badly named for centuries and their symbiotic relationship was vague. Recent development of omics tools especially next generation sequencing has provided a new perspective towards the mutualistic viral relationship. Endogenous virus which has been much studied in animal and are less understood in plants. In this study, we described the endophytic viral population of tea plant root. Viral population (9%) were significantly less while compared to bacterial population (90%). Viral population of tea endophytes were mostly dominated by endogenous pararetroviral sequences (EPRV) derived from Caulimoviridae and Geminiviridae. Subclassification of Caulimoviridae showed the dominance of Badnavirus (42%), Caulimovirus (29%), Soymovirus (3%), Tungrovirus (3%), while Geminviridae was only represented by genus Bagmovirus. Interestingly, the endophytic virome sequence from root also showed the presence of phage virus from order Caudovirales. Identified sequence from Caudovirales were Myoviridae and Siphoviridae. Sequence comparison with viral population of soil and root showed the possibility of horizontal transfer of Caudovirales from soil to root environment. This study will expand the knowledge on endogenous viruses especially for tea plant. This study will also help us to understand the symbiotic integration of viral particle with plant which could be used in broader sense to tackle different agronomic problems.Significance StatementVirus were badly named for centuries and mostly known for their disease-causing abilities. But recent development of omics tools has focused another facet which is symbiotic. This paper discusses about viral community identified from shotgun sequence of tea root samples which are endogenous in origin. Interestingly, we also identified sequences of phage virus from Caudovirales family which possibly have transmitted from soil. Here we also compared the soil virome community with tea virome to establish the hypothesis. This research will broaden the current knowledge on symbiotic relationship of virus and plant.
Modeling place cells and grid cells in multi-compartment environments: hippocampal-entorhinal loop as a multisensory integration circuit
Authors: Li Tianyi , Arleo Angelo , Sheynikhovich Denis 
Published: April 2019

AbstractHippocampal place cells and entorhinal grid cells are thought to form a representation of space by integrating internal and external sensory cues. Experimental studies show that different subsets of place cells are controlled by vision, self-motion or a combination of both. Moreover, recent studies in environments with a high degree of visual aliasing suggest that a continuous interaction between place cells and grid cells can result in a deformation of hexagonal grids or in a progressive loss of visual cue control. The computational nature of such a bidirectional interaction remains unclear. In this work we present a neural network model of a dynamic loop between place cells and grid cells. The model is tested in two recent experimental paradigms involving double-room environments that provide conflicting evidence about visual cue control over self-motion-based spatial codes. Analysis of the model behavior in the two experiments suggests that the strength of hippocampal-entorhinal dynamical loop is the key parameter governing differential cue control in multi-compartment environments. Construction of spatial representations in visually identical environments requires weak visual cue control, while synaptic plasticity is regulated by the mismatch between visual- and self-motion representations. More gener-ally our results suggest a functional segregation between plastic and dynamic processes in hippocampal processing.
Disruption of large-scale electrophysiological networks in stroke patients with visuospatial neglect
Authors: Ros Tomas , Michela Abele , Meyer Anaïs , Bellman Anne , Vuadens Philippe , Zermatten Victorine , Saj Arnaud , Vuilleumier Patrik 
Published: April 2019

AbstractStroke frequently produces attentional dysfunctions including symptoms of hemispatial neglect, which is characterized by a breakdown of awareness for the contralesional hemispace. Recent studies with functional MRI (fMRI) suggest that hemineglect patients display abnormalintra-andinter-hemisphericfunctional connectivity. However, since stroke is a vascular disorder and fMRI signals remain sensitive to non-neuronal (i.e. vascular) coupling, more direct demonstrations of neural network dysfunction in hemispatial neglect are warranted. Here, we utilize electroencephalogram (EEG) source imaging to uncover differences in resting-state network organization between patients with right-hemispheric stroke (N = 15) and age-matched, healthy controls (N = 27), and determine the relationship between hemineglect symptoms and brain network organization. We estimatedintra-andinter-regional differences in cortical communication, by calculating the spectral power and amplitude envelope correlations (AEC) of narrow-band EEG oscillations. We firstly observed focal frequency-slowing within the right posterior cortical regions, reflected in relative delta/theta power increases and alpha/beta/gamma decreases. Secondly, nodes within the right temporal and parietal cortex consistently displayed anomalous intra- and inter- hemispheric coupling, stronger in delta and gamma bands, and weaker in theta, alpha, and beta bands. Finally, a significant association was observed between the severity of left-hemispace search deficits (e.g. cancellation test omissions) and reduced functional connectivity within the alpha and beta bands. In sum, our novel results validate the hypothesis of large-scale cortical network disruption following stroke, and reinforce the proposal that abnormal brain oscillations may be intimately involved in the pathophysiology of visuospatial neglect.
A global perspective on microbial diversity in the terrestrial deep subsurface
Authors: Soares A. , Edwards A. , An D. , Bagnoud A. , Bomberg M. , Budwill K. , Caffrey S. M. , Fields M. , Gralnick J. , Kadnikov V. , Momper L. , Osburn M. , Moreau J.W. , Moser D. , Mu A. , Purkamo L. , Rassner S. M. , Sheik C. S. , Sherwood Lollar B. , Toner B. M. , Voordouw G. , Wouters K. , Mitchell A. C. 
Published: April 2019

SummaryWhile recent efforts to catalogue Earth’s microbial diversity have focused upon surface and marine habitats, 12% to 20% of Earth’s bacterial and archaeal biomass is suggested to inhabit the terrestrial deep subsurface, compared to ∼1.8% in the deep subseafloor1–3. Metagenomic studies of the terrestrial deep subsurface have yielded a trove of divergent and functionally important microbiomes from a range of localities4–6. However, a wider perspective of microbial diversity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Here, we show the diversity of bacterial communities in deep subsurface groundwater is controlled by aquifer lithology globally, by using 16S rRNA gene datasets collected across five countries on two continents and from fifteen rock types over the past decade. Furthermore, our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated by Betaproteobacteria, Gammaproteobacteria and Firmicutes, likely as a function of the diverse metabolic strategies of these taxa. Despite this similarity, evidence was found not only for aquifer-specific microbial communities, but also for a common small consortium of prevalent Betaproteobacteria and Gammaproteobacterial OTUs across the localities. This finding implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, that may play an important role in colonising and sustaining microbial habitats in the deep terrestrial subsurface. Anin-silicocontamination-aware approach to analysing this dataset underscores the importance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial diversity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling.
Nuclear gene transformation in a dinoflagellate
Authors: Sprecher Brittany N. , Zhang Huan , Lin Senjie 
Published: April 2019

ABSTRACTThe lack of a robust gene transformation tool that allows functional testing of the vast number of nuclear genes in dinoflagellates has greatly hampered our understanding of fundamental biology in this ecologically important and evolutionarily unique lineage. Here we report the development of a dinoflagellate expression vector, an electroporation protocol, and successful expression of introduced genes in the dinoflagellateOxyrrhis marina. This protocol, involving the use of Lonza’s Nucleofector and a codon optimized antibiotic resistance gene, has been successfully used to produce consistent results in several independent experiments. It is anticipated that this protocol will be adaptable for other dinoflagellates and will allow characterization of many novel dinoflagellate genes.
The N-Glycome regulates the endothelial-to-hematopoietic transition
Authors: Kasper Dionna M. , Hintzen Jared , Wu Yinyu , Ghersi Joey J. , Mandl Hanna K. , Salinas Kevin E. , Armero William , He Zhiheng , Sheng Ying , Xie Yixuan , Heindel Daniel W. , Park Eon Joo , Sessa William C. , Mahal Lara K. , Lebrilla Carlito , Hirschi Karen K. , Nicoli Stefania 
Published: April 2019

AbstractHematopoietic stem and progenitor cells (HSPCs) that establish and maintain the blood system in adult vertebrates arise from the transdifferentiation of hemogenic endothelial cells (hemECs) during embryogenesis. This endothelial-to-hematopoietic transition (EHT) is tightly regulated, but the mechanisms are poorly understood. Here, we show that microRNA (miR)-223-mediated regulation of N-glycan biosynthesis in endothelial cells (ECs) regulates EHT. Single cell RNA-sequencing revealed that miR-223 is enriched in hemECs and in oligopotent nascent HSPCs. miR-223 restricts the EHT of lymphoid/myeloid lineages by suppressing the expression of mannosyltransferase alg2 and sialyltransferase st3gal2, two enzymes involved in N-linked protein glycosylation. High-throughput glycomics of ECs lacking miR-223 showed a decrease of high mannose versus sialylated complex/hybrid sugars on N-glycoproteins involved in EHT such as the metalloprotease Adam10. Endothelial-specific expression of an N-glycan Adam10 mutant or of the N-glycoenzymes phenocopied the aberrant HSPC production of miR-223 mutants. Thus, the N-glycome plays a previously unappreciated role as an intrinsic regulator of EHT, with specific mannose and sialic acid modifications serving as key endothelial determinants of their hematopoietic fate.One Sentence SummaryThe N-glycan “sugar code” governs the hematopoietic fate of endothelial cells and regulates blood stem cell production in vivo.
Composition of the holdfast polysaccharide fromCaulobacter crescentus
Authors: Hershey David M. , Porfírio Sara , Jaehrig Bernhard , Heiss Christian , Azadi Parastoo , Fiebig Aretha , Crosson Sean 
Published: April 2019

AbstractSurface colonization is central to the lifestyles of many bacteria. Exploiting surface niches requires sophisticated systems for sensing and attaching to solid materials.Caulobacter crescentussynthesizes a polysaccharide-based adhesin known as the holdfast at one of its cell poles, which enables tight attachment to exogenous surfaces. The genes required for holdfast biosynthesis have been analyzed in detail, but an inability to isolate sufficient quantities of holdfast has limited efforts to characterize its composition and structure. In this report we describe a method to extract the holdfast fromC. crescentuscultures and present a survey of its carbohydrate content. Glucose, 3-O-methylglucose, mannose, N-acetylglucosamine and xylose were detected in our extracts. Our results suggest that the holdfast contains a 1,4-linked backbone of glucose, mannose, N-acetylglucosamine and xylose that is decorated with branches at the C-6 positions of glucose and mannose. By defining the monosaccharide components in the polysaccharide, our work establishes a framework for characterizing enzymes in the holdfast pathway and provides a broader understanding of how polysaccharide adhesins are built.
Dorsoventral dissociation of Hox gene expression underpins the diversification of molluscs
Authors: Huan Pin , Wang Qian , Tan Sujian , Liu Baozhong 
Published: April 2019

AbstractUnlike the Hox genes in arthropods and vertebrates, those in molluscs show diverse expression patterns and, with some exceptions, have generally been described as lacking the canonical staggered pattern along the anterior-posterior (AP) axis. This difference is unexpected given that almost all molluscs share highly conserved early development. Here, we show that molluscan Hox expression can undergo dynamic changes, which may explain why previous research observed different expression patterns. Moreover, we reveal that a key character of molluscan Hox expression is that the dorsal and ventral expression is dissociated. We then deduce a generalized molluscan Hox expression model, including conserved staggered Hox expression in the neuroectoderm on the ventral side and lineage-specific dorsal expression that strongly correlates with shell formation. This generalized model clarifies a long-standing debate over whether molluscs possess staggered Hox expression and it can be used to explain the diversification of molluscs. In this scenario, the dorsoventral dissociation of Hox expression allows lineage-specific dorsal and ventral patterning in different clades, which may have permitted the evolution of diverse body plans in different molluscan clades.
Joint species distribution modelling with HMSC-R
Authors: Tikhonov Gleb , Opedal Øystein , Abrego Nerea , Lehikoinen Aleksi , Ovaskainen Otso 
Published: April 2019

AbstractJoint Species Distribution Modelling (JSDM) is becoming an increasingly popular statistical method for analyzing data in community ecology. JSDM allow the integration of community ecology data with data on environmental covariates, species traits, phylogenetic relationships, and the spatio-temporal context of the study, providing predictive insights into community assembly processes from non-manipulative observational data of species communities. Hierarchical Modelling of Species Communities (HMSC) is a general and flexible framework for fitting JSDMs, yet its full range of functionality has remained restricted to Matlab users only.To make HMSC accessible to the wider community of ecologists, we introduce HMSC-R 3.0, a user-friendly R implementation of the framework described in Ovaskainen et al (Ecology Letters, 20 (5), 561-576, 2017) and further extended in several later publications.We illustrate the use of the package by providing a series of five vignettes that apply HMSC-R 3.0 to simulated and real data. HMSC-R applications to simulated data involve single-species models, models of small communities, and models of large species communities. They demonstrate the estimation of species responses to environmental covariates and how these depend on species traits, as well as the estimation of residual species associations. They further demonstrate how HMSC-R can be applied to normally distributed data, count data, and presence-absence data. The real data consist of bird counts in a spatio-temporally structured dataset, environmental covariates, species traits and phylogenetic relationships. The vignettes demonstrate how to construct and fit many kinds of models, how to examine MCMC convergence, how to examine the explanatory and predictive powers of the models, how to assess parameter estimates, and how to make predictions.The package, along with the extended vignettes, makes JSDM fitting and post-processing easily accessible to ecologists familiar with R.
First report of reference guided genome assembly of Black Bengal goat (Capra hircus)
Authors: Siddiki Amam Z. , Baten A. , Billah M. , Alam MAU. , Shawrob KSM. , Saha S. , Chowdhury M. , Rahman A.H. , Stear M. , Miah G. , Kumkum M. , Hossain M.A. , Mollah AKM. , Islam M.S. , Khan MKI. 
Published: April 2019

AbstractObjectivesBlack Bengal goat (Capra hircus), a member of the Bovidae family with the unique traits of high prolificacy, skin quality and low demand for food is the most socioeconomically significant goat breed in Bangladesh. Furthermore, the aptitude of adaptation and disease resistance capacity of it is highly notable which makes its whole genome information an area of research interest.Data descriptionThe genomic DNA of local (Chittagong, Bangladesh) healthy Black Bengal goat (Capra hircus) was extracted and then sequenced. The de novo assembly and structural annotations are being presented here. Sequencing was done using Illumina sequencing platform and the draft genome assembled is about 3.04 Gb. 26458 Genes were annotated using Maker gene annotations tool which predicted BUSCO Gene models. Universal Single Copy Orthologs refer 82.5% completeness of the assembled genome.
Local parasite pressures and host genotype may modulate epigenetic diversity in a mixed-mating fish
Authors: Berbel-Filho Waldir M. , de Leaniz Carlos Garcia , Morán Paloma , Cable Jo , Lima Sergio M. Q. , Consuegra Sofia 
Published: April 2019

AbstractParasite-mediated selection is one of the main drivers of genetic variation in natural populations. The persistence of asexual reproduction and self-fertilization, however, challenges the notion that low genetic variation and inbreeding compromise the host’s ability to respond to pathogens. DNA methylation represents a potential mechanism for generating additional adaptive variation under low genetic diversity. We compared genetic diversity (microsatellites and AFLPs), variation in DNA methylation (MSAFLPs), and parasite loads in three populations of Kryptolebias hermaphroditus, a unique mixed-mating (partially self-fertilising) fish, to analyse the potential adaptive value of DNA methylation in relation to genetic diversity and parasite loads. We found strong genetic population structuring, as well as differences in parasite loads and methylation levels among sampling sites and selfing lineages. Globally, the interaction between parasites and inbreeding with selfing lineages influenced DNA methylation, but parasites seemed more important in determining methylation levels at the local scale.
Identification of target candidate in Polycystic ovarian syndrome and invitro evaluation of therapeutic activity of the designed RNA Aptamer
Authors: Subramanian Manibalan , Ayyachamy Shobana , Manickam Kiruthika , Madasamy Swathi , Renganathan Venkatalakshmi , Achary Anant , Kandasamy Thirukumaran , Suhasini K , Roopathy Sharon 
Published: April 2019

AbstractPrevalence of poly cystic ovary syndrome has been gradually increasing among adult females and Laparoscopy drilling on the ovary is only available temporary solution with high incidence of reoccurrence. Confidential gene disease association studies combined with various graph theory analysis on the biological protein interaction network of this syndrome has resulted, the 15 genes are overexpressed as central nodes among 434 proteins of disease specific proteome network. Through the Intensive Structural and functional prioritization analysis we have identified S100A8, calprotectin is the ideal drug target protein. In this research, we have constructed RNA library of consensus DNA sequence of Glucocorticoid Response Element (GRE) and screened the best RNA Aptamer fragment which competitively binds with minimal energy to inhibit the cell migration activity of S100A8. In order to prove this computational research, Lipofectamine mediated RNA aptamer delivered and Wound scrap assay in cell lines confirms that the synthesized 18mer oligo has significant molecular level inhibition activity toward cyst formation and spreading in poly cystic condition in ovary.
High-Throughput Single-Molecule Analysis via Divisive Segmentation and Clustering
Authors: White David S. , Goldschen-Ohm Marcel P. , Goldsmith Randall H. , Chanda Baron 
Published: April 2019

ABSTRACTSingle-molecule approaches provide insight into the dynamics of biomolecules, yet analysis methods have not scaled with the growing size of data sets acquired in high-throughput experiments. We present a new analysis platform (DISC) that uses divisive clustering to accelerate unsupervised analysis of single-molecule trajectories by up to three orders of magnitude with improved accuracy. Using DISC, we reveal an inherent lack of cooperativity between cyclic nucleotide binding domains from HCN pacemaker ion channels embedded in nanophotonic zero-mode waveguides.