bluuebunny/crossref_metadata_2025_split huggingface dataset:
Model-based detection of whole-genome duplications in a phylogeny
Authors: Zwaenepoel Arthur , Van de Peer Yves 
Published: January 2020

AbstractAncient whole-genome duplications (WGDs) leave signatures in comparative genomic data sets that can be harnessed to detect these events of presumed evolutionary importance. Current statistical approaches for the detection of ancient WGDs in a phylogenetic context have two main drawbacks. The first is that unwarranted restrictive assumptions on the ‘background’ gene duplication and loss rates make inferences unreliable in the face of model violations. The second is that most methods can only be used to examine a limited set ofa prioriselected WGD hypotheses; and cannot be used to discover WGDs in a phylogeny. In this study we develop an approach for WGD inference using gene count data that seeks to overcome both issues. We employ a phylogenetic birth-death model that includes WGD in a flexible hierarchical Bayesian approach, and use reversible-jump MCMC to perform Bayesian inference of branch-specific duplication, loss and WGD retention rates accross the space of WGD configurations. We evaluate the proposed method using simulations, apply it to data sets from flowering plants and discuss the statistical intricacies of model-based WGD inference.
Polyamine metabolism regulates the T cell epigenome through hypusination
Authors: Puleston Daniel J. , Baixauli Francesc , Sanin David E. , Villa Matteo , Kabat Agnieszka , Kamiński Marcin M. , Weiss Hauke , Grzes Katarzyna , Flachsmann Lea , Field Cameron S. , Stanckzak Michal , Schimmelpfennig Lena , Hassler Fabian , Wang Chao , Yosef Nir , Kuchroo Vijay K. , Musa Yaarub , Mittler Gerhard , Buescher Joerg M. , Balabanov Stefan , Pearce Edward J. , Green Douglas R. , Pearce Erika L. 
Published: January 2020

SUMMARYWe report here a central role for polyamines in T cell differentiation and function. Deficiency in ornithine decarboxylase (ODC), a critical enzyme for polyamine synthesis, resulted in a profound failure of CD4+T cells to adopt correct subset specification, underscored by ectopic expression of multiple cytokines and lineage-defining transcription factors across TH1, TH2, TH17, and Tregpolarizing conditions, and enhanced colitogenic potential. T cells deficient in deoxyhypusine synthase (DHPS) or deoxyhypusine hydroxylase (DOHH), which sequentially utilize polyamines to generate hypusine, phenocopiedOdc-deficient T cells, and mice in which T cells lackedDhpsorDohhdeveloped colitis. Polyamine-hypusine pathway enzyme deficiency caused widespread chromatin and transcriptional dysregulation accompanied by alterations in histone methylation, histone acetylation, and TCA cycle metabolites. Epigenetic modulation by 2-hydroxyglutarate, or histone acetyltransferase inhibition, restored CD4+T cell subset specification. Thus, polyamine synthesis via hypusine is critical for maintaining the epigenome to focus THcell subset fidelity.
Asymmetric transcallosal conduction delay leads to finer bimanual coordination
Authors: Bortoletto Marta , Bonzano Laura , Zazio Agnese , Ferrari Clarissa , Pedullà Ludovico , Gasparotti Roberto , Miniussi Carlo , Bove Marco 
Published: January 2020

AbstractIt has been theorized that hemispheric dominance and a more segregated information processing have evolved to overcome long conduction delay through the corpus callosum (TCD) but that this may still impact behavioral performance mostly in tasks requiring high timing accuracy. Nevertheless, a thorough understanding of the temporal features of interhemispheric communication is missing due to methodological shortcomings. Here, we show in the motor system that TCD can be measured from transcranial magnetic stimulation (TMS) -evoked potentials (TEPs): by integrating TEPs with diffusion tensor imaging (DTI) and peripheral measures of interhemispheric inhibition (i.e., the ipsilateral silent period-iSP), we show that P15 TEP component reflects TCD between motor areas. Importantly, we report that better bimanual coordination is achieved when TCD between motor areas is asymmetric. These results suggest that interhemispheric communication can be optimized through asymmetric connectivity, in which information transfer is faster from the dominant hemisphere to the non-dominant hemisphere.
Differentiating between integration and non-integration strategies in perceptual decision making
Authors: Stine Gabriel M , Zylberberg Ariel , Ditterich Jochen , Shadlen Michael N 
Published: January 2020

ABSTRACTMany tasks used to study decision-making encourage subjects to integrate evidence over time. Such tasks are useful to understand how the brain operates on multiple samples of information over prolonged timescales, but only if subjects actually integrate evidence to form their decisions. We explored the behavioral observations that corroborate evidence-integration in a number of task-designs. Several commonly accepted signs of integration were also predicted by non-integration strategies. Furthermore, an integration model could fit data generated by non-integration models. We identified the features of non-integration models that allowed them to mimic integration and used these insights to design a motion discrimination task that disentangled the models. In human subjects performing the task, we falsified a non-integration strategy in each and confirmed prolonged integration in all but one subject. The findings illustrate the difficulty of identifying a decision-maker’s strategy and support solutions to achieve this goal.
Community sequencing on a natural experiment reveals little influence of host species and timing but a strong influence of compartment on the composition of root endophytes in three annual Brassicaceae
Authors: Maciá-Vicente Jose G. , Nam Bora , Thines Marco 
Published: January 2020

AbstractThe plant family Brassicaceae includes some of the most studied hosts of plant microbiomes, targeting microbial diversity, community assembly rules, and effects on host performance. Compared to bacteria, eukaryotes in the brassicaceous microbiome remain understudied, especially under natural settings. Here, we assessed the impact of host identity and age on the assembly of fungal and oomycete root communities, using DNA metabarcoding of roots and associated soil of three annual co-habiting Brassicaceae collected at two time points. Our results showed that fungal communities are more diverse and structured than those of oomycetes. In both cases, plant identity and sampling time had little influence on community variation, whereas root/soil compartment had a strong effect by exerting control on the entry of soil microorganisms into the roots. The enrichment in roots of specific fungi suggests a specialization towards the asymptomatic colonization of plant tissues, which could be relevant to host’s fitness and health.
Systematic and functional analysis of horizontal gene transfer events in diatoms
Authors: Vancaester Emmelien , Depuydt Thomas , Osuna-Cruz Cristina Maria , Vandepoele Klaas 
Published: January 2020

1.AbstractDiatoms are a diverse group of mainly photosynthetic algae, responsible for 20% of worldwide oxygen production, which can rapidly respond to favourable conditions and often outcompete other phytoplankton. We investigated the contribution of horizontal gene transfer (HGT) to its ecological success. A systematic phylogeny-based bacterial HGT detection procedure across nine sequenced diatoms showed that 3-5% of their proteome has a horizontal origin and a large influx occurred at the ancestor of diatoms. More than 90% of HGT genes are expressed, and species-specific HGT genes inPhaeodactylum tricornutumundergo strong purifying selection. They are implicated in several processes including environmental sensing, and expand the metabolic toolbox. Cobalamin (vitamin B12) is an essential cofactor for roughly half of the diatoms and is only produced by bacteria. Genes involved in its final synthesis were detected as HGT, including five consecutive enzymes inFragilariopsis cylindrus. This might give diatoms originating from the Southern Ocean, a region typically depleted in cobalamin, a competitive advantage. Overall, we show that HGT is a prevalent mechanism that is actively used in diatoms to expand its adaptive capabilities.
Evaluation of Genetic Diversity in Cultivated and Exotic Germplasm Sources of Faba Bean Using Important Morphological Traits
Authors: Kumar Praveen , Kaushik Prashant 
Published: January 2020

AbstractBackground and ObjectiveFaba bean is an important crop for achieving nutritional food security, but there is very limited diversity in the cultivated varieties of faba bean. Moreover, genetic diversity is vital for its use in faba bean genetic imporvement.Material and MethodsHere we determined the diversity in the sixty-four genotypes of faba bean of different agro-ecological origins. Plants were grown in randomized block design in three replications. Further, the genotypes were characterized based on the ten morphological traits.ResultsHighly significant differences were determined for all of the studied traits. Whereas, the number of cluster per plant was positively correlated with the pods per plants. Moreover, the trait number of cluster per plant determined the most substantial positive effect on seed yield.ConclusionsOverall, our results indicate a wide range of variability for further selection and improvement of faba bean ideotype.
Comparison of visualisation tools for single-cell RNAseq data
Authors: Çakır Batuhan , Prete Martin , Huang Ni , van Dongen Stijn , Pir Pınar , Kiselev Vladimir Yu. 
Published: January 2020

AbstractIn the last decade, single cell RNAseq (scRNAseq) datasets have grown from a single cell to millions of cells. Due to its high dimensionality, the scRNAseq data contains a lot of valuable information, however, it is not always feasible to visualise and share it in a scientific report or an article publication format. Recently, a lot of interactive analysis and visualisation tools have been developed to address this issue and facilitate knowledge transfer in the scientific community. In this study, we review and compare several of the currently available analysis and visualisation tools and benchmark those that allow to visualize the scRNAseq data on the web and share it with others. To address the problem of format compatibility for most visualisation tools, we have also developed a user-friendly R package,sceasy, which allows users to convert their own scRNAseq datasets into a specific data format for visualisation.
SBOL Visual 2 Ontology
Authors: Misirli Göksel , Beal Jacob , Gorochowski Thomas E. , Stan Guy-Bart , Wipat Anil , Myers Chris 
Published: January 2020

AbstractStandardising the visual representation of genetic parts and circuits is vital for unambiguously creating and interpreting genetic designs. To this end, an increasing number of tools are adopting well-defined glyphs from the Synthetic Biology Open Language (SBOL) Visual standard to represent various genetic parts and their relationships. However, the implementation and maintenance of the relationships between biological elements or concepts and their associated glyphs has to now been left up to tool developers. We address this need with the SBOL Visual 2 Ontology, a machine-accessible resource that provides rules for mapping from genetic parts, molecules, and interactions between them, to agreed SBOL Visual glyphs. This resource, together with a web service, can be used as a library to simplify the development of visualization tools, as a stand-alone resource to computationally search for suitable glyphs, and to help facilitate integration with existing biological ontologies and standards in synthetic biology.Graphical TOC Entry
A paleogenetic perspective of the Sabana de Bogotá (Northern South America) population history over the Holocene (9000 – 550 cal BP)
Authors: Delgado Miguel , Rodríguez Freddy , Kassadjikova Kalina , Fehren-Schmitz Lars 
Published: January 2020

ABSTRACTOn the basis of distinct lines of evidence, detailed reconstructions of the Holocene population history of the Sabana de Bogotá (SB) region, Northern South America, have been performed. Currently, there exist two competing models that support temporal continuity or, alternatively, divergence. Despite recent research that lends support to the population discontinuity model, several discrepancies remain, calling for other kinds of evidences to be explored for a more detailed picture of Holocene biocultural evolution. In this study, we analyze the mitochondrial genetic diversity of 30 individuals (including 15 newly reported complete mitochondrial genomes) recovered from several archaeological sites spanning from the late Pleistocene (12,164 cal BP) until the final late Holocene (2,751 cal BP) along with published data from the region dating ∼9,000-550 cal BP in order to investigate diachronic genetic change. Genetic diversity and distance indices were calculated, and demographic models tested in an approximate Bayesian computation (ABC) framework to evaluate whether patterns of genetic affinities of the SB prehispanic populations support genetic continuity or discontinuity. The results show that mitochondrial genomes of the complete dataset fall within the Native American haplogroups A2, B2, C1b, D1 and D4h3a. Haplotype and nucleotide diversity declined over time with further evidence of genetic drift and remarkable reduction of genetic diversity during the final late Holocene. Inter-population distances and the exact test of population differentiation, as well as demographic simulations show no population differentiation and population continuity over time. Consequently, based on the analyzed data, we cannot reject the genetic continuity in the SB region as a plausible population history scenario. However, the restriction of the analyses to the Hyper Variable Region 1 of the mitochondrial genome, and the very low sample size both constitute significant limitations to infer evolutionary history.
Extending rnaSPAdes functionality for hybrid transcriptome assembly
Authors: Prjibelski Andrey D. , Puglia Giuseppe D. , Antipov Dmitry , Bushmanova Elena , Giordano Daniela , Mikheenko Alla , Vitale Domenico , Lapidus Alla 
Published: January 2020

AbstractBackgroundDe novoRNA-Seq assembly is a powerful method for analysing transcriptomes when the reference genome is not available or poorly annotated. However, due to the short length of Illumina reads it is usually impossible to reconstruct complete sequences of complex genes and alternative isoforms. Recently emerged possibility to generate long RNA reads, such as PacBio and Oxford Nanopores, may dramatically improve the assembly quality, and thus the consecutive analysis. While reference-based tools for analysing long RNA reads were recently developed, there is no established pipeline forde novoassembly of such data.ResultsIn this work we present a novel method that allows to perform high-qualityde novotranscriptome assemblies by combining accuracy and reliability of short reads with exon structure information carried out from long error-prone reads. The algorithm is designed by incorporating existing hybridSPAdes approach into rnaSPAdes pipeline and adapting it for transcriptomic data.ConclusionTo evaluate the benefit of using long RNA reads we selected several datasets containing both Illumina and Iso-seq or Oxford Nanopore Technologies (ONT) reads. Using an existing quality assessment software, we show that hybrid assemblies performed with rnaSPAdes contain more full-length genes and alternative isoforms comparing to the case when only short-read data is used.Availability and implementationrnaSPAdes is implemented in C++ and Python and is freely available for Linux and MacOS under GPLv2 license at cab.spbu.ru/software/rnaspades/ and github.com/ablab/spades.
The two zinc fingers in the nucleocapsid domain of the HIV-1 Gag precursor are equivalent for the interaction with the genomic RNA in the cytoplasm, but not for the recruitment of the complexes at the plasma membrane
Authors: Boutant E. , Bonzi J. , Anton H. , Nasim M. B. , Cathagne R. , Réal E. , Dujardin D. , Carl P. , Didier P. , Paillart J-C. , Marquet R. , Mély Y. , de Rocquigny H. , Bernacchi S. 
Published: January 2020

ABSTRACTThe HIV-1 Gag precursor specifically selects the unspliced viral genomic RNA (gRNA) from the bulk of cellular and spliced viral RNAsviaits nucleocapsid (NC) domain and drives gRNA encapsidation at the plasma membrane (PM). To further identify the determinants governing the intracellular trafficking of Gag-gRNA complexes and their accumulation at the PM, we compared, in living and fixed cells, the interactions between gRNA and wild-type (WT) Gag or Gag mutants carrying deletions in NC zinc fingers (ZFs), or a non-myristoylated version of Gag. Our data showed that the deletion of both ZFs simultaneously or the complete NC domain completely abolished intracytoplasmic Gag-gRNA interactions. Deletion of either ZF delayed the delivery of gRNA to the PM but did not prevent Gag-gRNA interactions in the cytoplasm, indicating that the two ZFs display redundant roles in this respect. However, ZF2 played a more prominent role than ZF1 in the accumulation of the ribonucleoprotein complexes at the PM. Finally, the myristate group which is mandatory for anchoring the complexes at the MP, was found to be dispensable for the association of Gag with the gRNA in the cytosol.STATEMENT of SIGNIFICANCEFormation of HIV-1 retroviral particles relies on specific interactions between the retroviral Gag precursor and the unspliced genomic RNA (gRNA). During the late phase of replication, Gag orchestrates the assembly of newly formed viruses at the plasma membrane (PM). It has been shown that the intracellular HIV-1 gRNA recognition is governed by the two-zinc finger (ZF) motifs of the nucleocapsid (NC) domain in Gag. Here we provided a clear picture of the role of ZFs in the cellular trafficking of Gag-gRNA complexes to the PM by showing that either ZF was sufficient to efficiently promote these interactions in the cytoplasm, while interestingly, ZF2 played a more prominent role in the relocation of these ribonucleoprotein complexes at the PM assembly sites.
A comprehensive atlas of white matter tracts in the chimpanzee
Authors: Bryant Katherine L. , Li Longchuan , Eichert Nicole , Mars Rogier B. 
Published: January 2020

AbstractChimpanzees (Pan troglodytes) are, along with bonobos, humans’ closest living relatives. The advent of diffusion MRI tractography in recent years has allowed a resurgence of comparative neuroanatomical studies in humans and other primate species. Here we offer, in comparative perspective, the first chimpanzee white matter atlas, constructed fromin vivochimpanzee diffusion-weighted scans. Comparative white matter atlases provide a useful tool for identifying neuroanatomical differences and similarities between humans and other primate species. Until now, comprehensive fascicular atlases have been created for humans (Homo sapiens), rhesus macaques (Macaca mulatta), and several other nonhuman primate species, but never in a nonhuman ape. Information on chimpanzee neuroanatomy is essential for understanding the anatomical specializations of white matter organization that are unique to the human lineage.
The Effects of Copper Addition on The Structure and Antibacterial Properties of Biomedical Glasses
Authors: Mojtabavi Leyla , Razavi Amir 
Published: January 2020

AbstractIn this work, we studied the effects of copper incorporation in the composition of bioactive glass. Three different glass compositions were synthesized with 0, 3, and 6 mol% of copper addition. X-Ray Diffraction (XRD) patterns confirmed that an amorphous microstructure was obtained for all three glass compositions. Results from Differential Thermal Analysis (DTA) showed that the copper addition in the glass lowers the glass transition temperature, from 646°C to 590°C when added at 6 mol%. X-ray Photoelectron (XPS) survey and high-resolution scans were performed to study the structural effects of copper addition in the glass. Results indicated that the incorporation of copper changes the ratio of bridging to non-birding oxygens in the structure. Glasses were further analyzed for their structure with Nuclear Magnetic Resonance (NMR) spectroscopy, which indicated that copper acts as a network modifier in the glass composition and copper-containing glasses show a less connected microstructure. Antibacterial efficacy of the glasses was analyzed against E. coli and S. epidermis. Copper-containing glasses showed a significantly higher inhibition zone compared to control glass. The glass with 6 mol% copper, exhibited inhibition zones of 9 and 16mm against E. coli and S. epidermis bacteria, respectively.
Competition sensing alters antibiotic production inStreptomyces
Authors: Westhoff Sanne , Kloosterman Alexander , van Hoesel Stephan F. A. , van Wezel Gilles P. , Rozen Daniel E. 
Published: January 2020

ABSTRACTOne of the most important ways that bacteria compete for resources and space is by producing antibiotics that inhibit competitors. Because antibiotic production is costly, the biosynthetic gene clusters coordinating their synthesis are under strict regulatory control and often require “elicitors” to induce expression, including cues from competing strains. Although these cues are common, they are not produced by all competitors and so the phenotypes causing induction remain unknown. By studying interactions between 24 antibiotic-producing streptomycetes we show that inhibition between competitors is common and occurs more frequently if strains are closely related. Next, we show that antibiotic production is more likely to be induced by cues from strains that are closely related or that share secondary metabolite biosynthetic gene clusters (BGCs). Unexpectedly, antibiotic production is less likely to be induced by competitors that inhibit the growth of a focal strain, indicating that cell damage is not a general cue for induction. In addition to induction, antibiotic production often decreased in the presence of a competitor, although this response was not associated with genetic relatedness or overlap in BGCs. Finally, we show that resource limitation increases the chance that antibiotic production declines during competion. Our results reveal the importance of social cues and resource availability in the dynamics of interference competition in streptomycetes.SIGNIFICANCE STATEMENTBacteria secrete antibiotics to inhibit their competitors, but the presence of competitors can determine whether these toxins are produced. Here, we study the role of the competitive and resource environment on antibiotic production inStreptomyces, bacteria renowned for their production of antibiotics. We show thatStreptomycesare more likely to produce antibiotics when grown with closely related competitors or that share biosynthetic pathways for secondary metabolites, but not when they are threatened by competitor’s toxins, in contrast to predictions of the competition sensing hypothesis.Streptomycesalso often reduce their output of antibiotics when grown with competitors, especially under nutrient limitation. Our findings highlight that interactions between the social and resource environments strongly regulate antibiotic production in these medicinally important bacteria.