bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Arabidopsis condensin CAP-D subunits arrange interphase chromatin
Authors: Municio Celia , Antosz Wojciech , Grasser Klaus D. , Kornobis Etienne , Van Bel Michiel , Eguinoa Ignacio , Coppens Frederik , Bräutigam Andrea , Lermontova Inna , Bruckmann Astrid , Houben Andreas , Schubert Veit 
Published: December 2019

SUMMARYCondensins are best known for their role in shaping chromosomes. However, other functions as organizing interphase chromatin and transcriptional control have been reported in yeasts and animals. Yeasts encode one condensin complex, while higher eukaryotes have two of them (condensin I and II). Both, condensin I and II, are conserved inArabidopsis thaliana, but so far little is known about their function. Here we show that theA. thalianaCAP-D2 (condensin I) and CAP-D3 (condensin II) subunits are highly expressed in mitotically active tissues.In silicoand pull-down experiments indicate that both CAP-D proteins interact with the other condensin I and II subunits. Our data suggest that the expression, localization and composition of the condensin complexes inA. thalianaare similar as in other higher eukaryotes. Previous experiments showed that the lack ofA. thalianaCAP-D3 leads to centromere association during interphase. To study the function of CAP-D3 in chromatin organization more in detail we compared the nuclear distribution of rDNA, of centromeric chromocenters and of different epigenetic marks, as well as the nuclear size between wild-type andcap-d3mutants. In these mutants an association of heterochromatic sequences occurs, but nuclear size and the general methylation and acetylation patterns remain unchanged. In addition, transcriptome analyses revealed a moderate influence of CAP-D3 on general transcription, but a stronger one on transcription of stress-related genes. We propose a model for the CAP-D3 function during interphase, where CAP-D3 localizes in euchromatin loops to stiff them, and consequently separates centromeric regions and 45S rDNA repeats.
Bagworm decorations are an anti-predatory structure
Authors: Khan Md Kawsar 
Published: December 2019

AbstractMany animals decorate their exterior with environmental materials and these decorations are predicted to increase their survival. The adaptive significance of these decorations, however, has seldomly been tested experimentally under field conditions. Here, I studied the anti-predatory functions of the decoration (bag) of a bagworm moth,Eumeta crameriagainst their natural predator,Oecophylla smaragdina, the Asian weaver ant. I experimentally tested if bag removal from caterpillars resulted in more predation than bagged caterpillar under field conditions, which would support the hypothesis that bags are selected to protect the caterpillars against their predators. In support of that, I showed that caterpillars without a bag were attacked, killed and taken to ants’ nest significantly more than bagged caterpillars. My study provides rare experimental evidence for anti-predatory functions of the decoration. My study suggests that decorating behaviour has evolved in animals as an anti-predatory defence mechanism.
Introgression across evolutionary scales suggests reticulation contributes to Amazonian tree diversity
Authors: Schley Rowan J. , Pennington R. Toby , Pérez-Escobar Oscar Alejandro , Helmstetter Andrew J. , de la Estrella Manuel , Larridon Isabel , Sabino Kikuchi Izai Alberto Bruno , Barraclough Timothy , Forest Félix , Klitgård Bente 
Published: December 2019

AbstractHybridization has the potential to generate or homogenize biodiversity and is a particularly common phenomenon in plants, with an estimated 25% of species undergoing inter-specific gene flow. However, hybridization in Amazonia’s megadiverse tree flora was assumed to be extremely rare despite extensive sympatry between closely related species, and its role in diversification remains enigmatic because it has not yet been examined empirically. Using members of a dominant Amazonian tree family (Brownea, Fabaceae) as a model to address this knowledge gap, our study recovered extensive evidence of hybridization among multiple lineages across phylogenetic scales. More specifically, our results uncovered several historical introgression events betweenBrownealineages and indicated that gene tree incongruence inBrowneais best explained by introgression, rather than solely by incomplete lineage sorting. Furthermore, investigation of recent hybridization using ∼19,000 ddRAD loci recovered a high degree of shared variation between twoBrowneaspecies which co-occur in the Ecuadorian Amazon. Our analyses also showed that these sympatric lineages exhibit homogeneous rates of introgression among loci relative to the genome-wide average, implying a lack of selection against hybrid genotypes and a persistence of hybridization over time. Our results demonstrate that gene flow between multiple Amazonian tree species has occurred across temporal scales, and contrasts with the prevailing view of hybridization’s rarity in Amazonia. Overall, our results provide novel evidence that reticulate evolution influenced diversification in part of the Amazonian tree flora, which is the most diverse on Earth.
Mitigating Local Over-fitting During Single Particle Reconstruction with SIDESPLITTER
Authors: Ramlaul Kailash , Palmer Colin M. , Aylett Christopher H. S. 
Published: December 2019

AbstractSingle particle analysis of cryo-EM images enables macromolecular structure determination at resolutions approaching the atomic scale. Experimental images are extremely noisy, however, and during iterative refinement it is possible to stably incorporate noise into the reconstructed density. Such “over-fitting” can lead to misinterpretation of the structure, and thereby flawed biological results. Several strategies are routinely used to prevent the spurious incorporation of noise within reconstructed volumes, the most common being independent refinement of two sides of a split dataset.In this study, we show that over-fitting remains an issue within regions of low local signal-to-noise in reconstructed volumes refined using the half-set strategy. We propose a modified filtering process during refinement through the application of a local signal-to-noise filter, SIDESPLITTER, which we show to be capable of reducing over-fitting in both idealised and experimental settings, while maintaining independence between the two sides of a split refinement. SIDESPLITTER can also improve the final resolution in refinements of structures prone to severe over-fitting, such as membrane proteins in detergent micelles.
The effects of arbuscular mycorrhizal fungi (AMF) and Rhizophagus irregularis on soil microorganisms assessed by metatranscriptomics and metaproteomics
Authors: Lammel D.R. , Meierhofer D. , Johnston P. , Mbedi S. , Rillig M.C. 
Published: December 2019

AbstractArbuscular mycorrhizal fungi (AMF) form symbioses with approximately 80% of plant species and potentially benefit their hosts (e.g. nutrient acquisition) and the soil environment (e.g. soil aggregation). AMF also affect soil microbiota and soil multifunctionality. We manipulated AMF presence (via inoculation of non-sterile soil with Rhizophagus irregularis and using a hyphal compartment design) and used RNA-seq and metaproteomics to assess AMF roles in soil. The results indicated that AMF drove an active soil microbial community expressing transcripts and proteins related to nine metabolic functions, including the metabolism of C and N. We suggest two possible mechanisms: 1) the AMF hyphae produce exudates that select a beneficial community, or, 2) the hyphae compete with other soil microbes for available nutrients and consequently induce the community to mineralize nutrients from soil organic matter. We also identified candidate proteins that are potentially related to soil aggregation, such as Lpt and HSP60. Our results bridge microbial ecology and ecosystem functioning. We show that the AMF hyphosphere contains an active community related to soil respiration and nutrient cycling, thus potentially improving nutrient mineralization from soil organic matter and nutrient supply to the plants.
Citrusgreening.org: An open access and integrated systems biology portal for the Huanglongbing (HLB) disease complex
Authors: Flores-Gonzalez Mirella , Hosmani Prashant S , Fernandez-Pozo Noe , Mann Marina , Humann Jodi L. , Main Dorrie , Heck Michelle , Brown Susan , Mueller Lukas A , Saha Surya 
Published: December 2019

AbstractWe have created an open access web portal with pathosystem-wide resources and bioinformatics tools for the host citrus, the vector Asian citrus psyllid (ACP) and multiple pathogens including Ca. Liberibacter asiaticus. To the best of our knowledge, this is the first example of a database to use the pathosystem as a holistic framework to understand an insect transmitted plant disease. This endeavor integrates and enables the analysis of data sets generated by the community to study the citrus greening disease complex. Users can submit relevant data sets to enable sharing and allow the community to better analyze their data within an integrated system. The portal contains a variety of tools for omics data. Metabolic pathway databases, CitrusCyc and DiaphorinaCyc provide organism specific pathways that can be used to mine metabolomics, transcriptomics and proteomics results to identify pathways and regulatory mechanism involved in disease response. Psyllid Expression Network (PEN) contains expression profiles of ACP genes from multiple life stages, tissues, conditions and hosts. Citrus Expression Network (CEN) contains public expression data from multiple tissues and conditions for various citrus hosts. All tools like Apollo/JBrowse, Biocyc, Blast, CEN and PEN connect to a central database containing gene models for citrus, ACP and multiple Liberibacter pathogens. The portal also includes electrical penetration graph (EPG) recordings of ACP feeding on citrus, information about citrus rootstock trials and metabolomics data in addition to traditional omics data types with a goal of combining and mining all information related to a pathosystem. The portal includes user-friendly manual curation tools to allow the research community to continuously improve this knowledge base as more experimental research is published. Bulk downloads are available for all genome and annotation datasets from the FTP site (ftp://ftp.citrusgreening.org). The portal can be accessed at https://citrusgreening.org/.
Alignment and quantification of ChIP-exo crosslinking patterns reveal the spatial organization of protein-DNA complexes
Authors: Yamada Naomi , Rossi Matthew J. , Farrell Nina , Pugh B. Franklin , Mahony Shaun 
Published: December 2019

AbstractThe ChIP-exo assay precisely delineates protein-DNA crosslinking patterns by combining chromatin immunoprecipitation with 5′ to 3′ exonuclease digestion. Within a regulatory complex, the physical distance of a regulatory protein to DNA affects crosslinking efficiencies. Therefore, the spatial organization of a protein-DNA complex could potentially be inferred by analyzing how crosslinking signatures vary between the subunits of a regulatory complex. Here, we present a computational framework that aligns ChIP-exo crosslinking patterns from multiple proteins across a set of coordinately bound regulatory regions, and which detects and quantifies protein-DNA crosslinking events within the aligned profiles. By producing consistent measurements of protein-DNA crosslinking strengths across multiple proteins, our approach enables characterization of relative spatial organization within a regulatory complex. We demonstrate that our approach can recover aspects of regulatory complex spatial organization when applied to collections of ChIP-exo data that profile regulatory machinery at yeast ribosomal protein genes and yeast tRNA genes. We also demonstrate the ability to quantify changes in protein-DNA complex organization across conditions by applying our approach to data profiling Drosophila Pol II transcriptional components. Our results suggest that principled analyses of ChIP-exo crosslinking patterns enable inference of spatial organization within protein-DNA complexes.
kRISP-meR: A Reference-free Guide-RNA Design Tool for CRISPR/Cas9
Authors: Hera Mahmudur Rahman , Rahman Amatur , Rahman Atif 
Published: December 2019

AbstractGenome editing using the CRISPR/Cas9 system requires designing guide RNAs (sgRNA) that are efficient and specific. Guide RNAs are usually designed using reference genomes which limits their use in organisms with no or incomplete reference genomes. Here, we present kRISP-meR, a reference free method to design sgRNAs for CRISPR/Cas9 system. kRISP-meR takes as input a target region and sequenced reads from the organism to be edited and generates sgRNAs that are likely to minimize off-target effects. Our analysis indicates that kRISP-meR is able to identify majority of the guides identified by a widely used sgRNA designing tool, without any knowledge of the reference, while retaining specificity.
Latent space visualization, characterization, and generation of diverse vocal communication signals
Authors: Sainburg Tim , Thielk Marvin , Gentner Timothy Q 
Published: December 2019

ABSTRACTAnimals produce vocalizations that range in complexity from a single repeated call to hundreds of unique vocal elements patterned in sequences unfolding over hours. Characterizing complex vocalizations can require considerable effort and a deep intuition about each species’ vocal behavior. Even with a great deal of experience, human characterizations of animal communication can be affected by human perceptual biases. We present here a set of computational methods that center around projecting animal vocalizations into low dimensional latent representational spaces that are directly learned from data. We apply these methods to diverse datasets from over 20 species, including humans, bats, songbirds, mice, cetaceans, and nonhuman primates, enabling high-powered comparative analyses of unbiased acoustic features in the communicative repertoires across species. Latent projections uncover complex features of data in visually intuitive and quantifiable ways. We introduce methods for analyzing vocalizations as both discrete sequences and as continuous latent variables. Each method can be used to disentangle complex spectro-temporal structure and observe long-timescale organization in communication. Finally, we show how systematic sampling from latent representational spaces of vocalizations enables comprehensive investigations of perceptual and neural representations of complex and ecologically relevant acoustic feature spaces.
ScmR, a global regulator of gene expression, quorum sensing, pH homeostasis, and virulence inBurkholderia thailandensis
Authors: Le Guillouzer Servane , Groleau Marie-Christine , Mauffrey Florian , Déziel Eric 
Published: December 2019

AbstractThe nonpathogenic soil saprophyteBurkholderia thailandensisis a member of theBurkholderia pseudomallei-thailandensis-mallei(Bptm) group, which also comprises the closely related human pathogensBurkholderia pseudomalleiandBurkholderia malleiresponsible for the diseases melioidosis and glanders, respectively. ScmR, a recently identified LysR-type transcriptional regulator (LTTR) inB. thailandensisacts as a global transcriptional regulator throughout the stationary phase, and modulates the production of a wide range of secondary metabolites, includingN-acyl-L-homoserine lactones (AHLs) and 4-hydroxy-3-methyl-2-alkylquinoline (HMAQ), virulence in the model hostCaenorhabditis elegans, as well as several quorum sensing (QS)-dependent phenotypes. We have investigated the role of ScmR inB. thailandensisstrain E264 during the exponential phase. We used RNA-Sequencing (RNA-Seq) transcriptomic analyses to identify the ScmR regulon, which was compared to the QS-controlled regulon, showing a considerable overlap between the ScmR-regulated genes and those controlled by QS. We characterized several genes modulated by ScmR, using quantitative reverse transcription-PCR (qRT-PCR) or mini-CTX-luxtranscriptional reporters, including the oxalate biosynthetic geneobc1required for pH homeostasis, the orphan LuxR-type transcriptional regulator BtaR5-encoding gene, thebsa(Burkholderiasecretion apparatus) type III secretion system (T3SS) genes essential for bothB. pseudomalleiandB. malleipathogenicity, as well as thescmRgene itself. We confirmed that the transcription ofscmRis under QS control, presumably ensuring fine-tuned modulation of gene expression. Finally, we demonstrate that ScmR influences virulence using the fruit fly model hostDrosophila melanogaster. We conclude that ScmR represents a central component of theB. thailandensisQS regulatory network.ImportanceCoordination of the expression of genes associated with bacterial virulence and environmental adaptation is often dependent on quorum sensing (QS). The QS circuitry of the nonpathogenic bacteriumBurkholderia thailandensis, which is widely used as a model system for the study of the human pathogenBurkholderia pseudomallei, is complex. We found that the recently identified LysR-type transcriptional regulator (LTTR), ScmR, which is highly conserved and involved in the control of virulence/survival factors in theBurkholderiagenus, is a global regulator mediating gene expression through the multiple QS systems coexisting inB. thailandensis, as well as independently of QS. We conclude that ScmR represents a key QS modulatory network element, ensuring tight regulation of the transcription of QS-controlled genes, particularly those required for acclimatization to the environment.
Recombinant HcGAPDH Protein Expressed on Probiotic Bacillus subtilis Spores Protects Sheep from Haemonchus contortus Infection by Inducing both Humoral and Cell-mediated Responses
Authors: Yang Yi , Zhang Guiheng , Wu Jie , Chen Xueqiu , Tong Danni , Yang Yimin , Shi Hengzhi , Yao Chaoqun , Zhuang Lenan , Wang Jianbin , Du Aifang 
Published: December 2019

AbstractProbiotic Bacillales have been shown effective in controlling pathogens. In particular, live probiotic bacteria are thought to improve the composition of gastrointestinal microbiota, and to reduce pathogen colonization. However, how probiotics regulate immune responses and protect the host from parasitic infection remains largely unknown. In this study, we investigated whether Bacillales can be used against Haemonchus contortus, a parasitic nematode that infects small ruminants in sheep and goats worldwide. Using 16S ribosomal RNA sequencing, we found that Bacillales was highly depleted in the abomasal microbiota of sheep infected with H. contortus. We constructed a recombinant Bacillus subtilis strain (rBSCotB-HcG) that express glyceraldehyde-3-phosphate dehydrogenase of H. contortus (HcGAPDH) on its spore surface. However, mice orally administrated with the rBSCotB-HcG strain showed strong Th1-dominated immune responses; and sheep administrated per os with rBSCotB-HcG showed increased proliferation of peripheral blood mononuclear cells, elevated anti-HcGAPDH IgG levels in sera, and higher anti-HcGAPDH sIgA levels in intestinal mucus. In addition, treatment of H. contortus infected sheep with rBSCotB-HcG (Hc+rBSCotB-HcG) promoted the abundance of probiotic species in the abomasal microbiota; it also improved the average weight gain of the sheep by 27.7%. These Hc+rBSCotB-HcG sheep have reduced number of eggs per gram of feces (by 84.1%) and worm burdens (by 71.5%), with alleviated abomasal damage by H. contortus. Collectively, our data demonstrate the protective roles of CotB-HcGAPDH-expressing B. subtilis spores against H. contortus infection, suggesting a potential value of using this probiotic-based strategy in controlling parasitic nematodes of socioeconomic importance.ImportanceSequencing of the infected sheep ’s stomach flora revealed potential probiotics that could control H. contortus infection, and further genetically engineered recombinant probiotic spores expressing parasite protein, and validated their good immunogenicity in a mouse model. In the sheep infection model, the recombinant probiotics have proven to be effective against parasite infections.
Assessment of Water Stress Tolerance in Mungbean Induced by Polyethyline Glycol
Authors: Islam Mohammad Rafiqul , Islam Mohammad Sohidul , Sarker Bikash Chandra , Alam Ashraful , Akhter Masuma , Alam Mohammad Jahangir , Saneoka Hirofumi , Erman Murat , Sabagh Ayman EL 
Published: December 2019

AbstractWater scarcity is a common hindrance of crop production in the globe especially in dry regions due to low precipitation along with high air temperature. Mungbean is a valuable pulse crop faced considerable amount of water shortage during its growing periods (March-May). Thus, the study was carried out to find out the variability and diversity present in the mungbean genotypes based on genetic variation of germination and seedling growth traits induced by polyethyline glycol (PEG-6000) stress (−0.7, −1, −2 and −4 bar). Seeds of each genotype was placed in a 9 cm diameter petridish containing sand bed that moistened by respective prepared PEG solutions and allowed to grow up to 10 days after placement. The result showed that the phenotypic coefficient of variation was significantly greater than the genotypic coefficient of variation for the entire studies traits, representing that these traits was influence by the environmental factors. The heritability showed moderate to high (24.26%-99.19%) under the observed traits indicating that these traits were under the control of additive genetic effects. The clustering pattern exhibited that cluster III were the largest ones with eleven genotypes. In case of contribution of different traits, the first five components were found to contribute for 98.19 % of the total variation while only first two components contributed for 82.12 % variation. The greater inter-cluster distance was found among the cluster I with II, III, IV and V. The maximum intra-cluster distance was observed in the cluster II (0.12). The genotypes in the cluster V recorded for greater performance by giving the highest mean value for germination, coefficient of germination, speed of germination, vigor index, shoot length and root length. This mean that genotype under cluster V have any gene or mechanism which responsible for tolerant higher level of water stress. The results of the study can be caring for establishing assortment criteria for water stress tolerant mungbean genotypes under breeding program.
Variation in repeat copy number of the Epithelial adhesin 1 tandem repeat region leads to variable protein display through multiple mechanisms
Authors: Raposo Colin J. , McElroy Kyle A. , Fuchs Stephen M. 
Published: December 2019

AbstractThe pathogenic yeast Candida glabrata is reliant on a suite of cell surface adhesins that play a variety of roles necessary for transmission, establishment, and proliferation during infection. One particular adhesin, Epithelial Adhesin 1 [Epa1p], is responsible for binding to host tissue, a process which is essential for fungal propagation. Epa1p structure consists of three domains: an N-terminal intercellular binding domain responsible for epithelial cell binding, a C-terminal GPI anchor for cell wall linkage, and a serine / threonine-rich linker domain connecting these terminal domains. The linker domain contains a 40-amino acid tandem repeat region, which we have found to be variable in repeat copy number between isolates from clinical sources. We hypothesized that natural variation in Epa1p repeat copy may modulate protein function. To test this, we recombinantly expressed Epa1p with various repeat copy numbers in S. cerevisiae to determine how differences in repeat copy number affect Epa1p expression, surface display, and binding to human epithelial cells. Our data suggest that repeat copy number variation has pleiotropic effects, influencing gene expression, protein surface display, shedding from the cell surface, and host tissue adhesion of the Epa1p adhesin. Understanding these links between repeat copy number variants and mechanisms of infection provide new understanding of the variety of roles of repetitive proteins contribute to pathogenicity of C. glabrata.