bluuebunny/crossref_metadata_2025_split huggingface dataset:
The C. elegans 3’-UTRome V2: an updated genomic resource to study 3’-UTR biology
Authors: Steber HS , Gallante C , O’Brien S , Chiu P.-L , Mangone M 
Published: July 2019

ABSTRACT3’-Untranslated Regions (3’-UTRs) of mRNAs emerged as central regulators of cellular function as they contain important but poorly-characterized cis-regulatory elements targeted by a multitude of regulatory factors. The model nematode C. elegans is ideal to study these interactions since it possesses a well-defined 3’-UTRome. In order to improve its annotation, we have used a genomics approach to download raw transcriptome data for 1,088 transcriptome datasets corresponding to the entire collection of C. elegans trancriptomes from 2015 to 2018 from the Sequence Read Archive at the NCBI. We then extracted and mapped high-quality 3’-UTR data at ultra-deep coverage. Here we describe and release to the community the updated version of the worm 3’-UTRome, which we named 3’-UTRome v2. This resource contains high-quality 3’-UTR data mapped at single base ultra-resolution for 23,084 3’-UTR isoform variants corresponding to 14,788 protein-coding genes and is updated to the latest release of WormBase. We used this dataset to study and probe principles of mRNA cleavage and polyadenylation in C. elegans. The worm 3’-UTRome v2 represents the most comprehensive and high-resolution 3’-UTR dataset available in C. elegans and provides a novel resource to investigate the mRNA cleavage and polyadenylation reaction, 3’-UTR biology and miRNA targeting in a living organism.
A genetic screen for genes that impact peroxisomes in Drosophila identifies candidate genes for human disease
Authors: Graves Hillary K. , Jangam Sharayu , Tan Kai Li , Pignata Antonella , Seto Elaine S. , Yamamoto Shinya , Wangler Michael F. 
Published: July 2019

AbstractPeroxisomes are sub-cellular organelles that are essential for proper function of eukaryotic cells. In addition to being the sites of a variety of oxidative reactions, they are crucial regulators of lipid metabolism. Peroxisome loss or dysfunction leads to multisystem diseases in humans that strongly affects the nervous system. In order to uncover previously unidentified genes and mechanisms that impact peroxisomes, we conducted a genetic screen on a collection of lethal mutations on the X chromosome in Drosophila. Using the number, size and morphology of GFP tagged peroxisomes as a readout, we screened for mutations that altered the number and morphology of peroxisomes based on clonal analysis and confocal microscopy. From this screen, we identified 18 genes that cause increases in peroxisome number or altered morphology when mutated. We examined the human homologs of these genes and found that they are involved in a diverse array of cellular processes. Interestingly, the human homologs from the X-chromosome collection are under selective constraint in human populations and are good candidate genes particularly for dominant genetic disease. This in vivo screening approach for peroxisome defects allows identification of novel genes that impact peroxisomes in vivo in a multicellular organism and is a valuable platform to discover genes potentially involved in dominant disease that could affect peroxisomes.
A binning tool to reconstruct viral haplotypes from assembled contigs
Authors: Chen Jiao , Shang Jiayu , Wang Jianrong , Sun Yanni 
Published: July 2019

AbstractMotivationInfections by RNA viruses such as Influenza, HIV still pose a serious threat to human health despite extensive research on viral diseases. One challenge for producing effective prevention and treatment strategies is high intra-species genetic diversity. As different strains may have different biological properties, characterizing the genetic diversity is thus important to vaccine and drug design. Next-generation sequencing technology enables comprehensive characterization of both known and novel strains and has been widely adopted for sequencing viral populations. However, genome-scale reconstruction of haplotypes is still a challenging problem. In particular, haplotype assembly programs often produce contigs rather than full genomes. As a mutation in one gene can mask the phenotypic effects of a mutation at another locus, clustering these contigs into genome-scale haplotypes is still needed.ResultsWe developed a contig binning tool, VirBin, which clusters contigs into different groups so that each group represents a haplotype. Commonly used features based on sequence composition and contig coverage cannot effectively distinguish viral haplotypes because of their high sequence similarity and heterogeneous sequencing coverage for RNA viruses. VirBin applied prototype-based clustering to cluster regions that are more likely to contain mutations specific to a haplotype. The tool was tested on multiple simulated sequencing data with different haplotype abundance distributions and contig sizes, and also on mock quasispecies sequencing data. The benchmark results with other contig binning tools demonstrated the superior sensitivity and precision of VirBin in contig binning for viral haplotype reconstruction.Availabilityhttps://github.com/chjiao/VirBinContactyannisun@cityu.edu.hk
Kinase-mediated RAS signaling via membraneless cytoplasmic protein granules
Authors: Tulpule Asmin , Guan Juan , Neel Dana S. , Lin Yone Phar , Heslin Ann , Allegakoen Hannah R. , Perati Shriya , Ramirez Alejandro D. , Shi Xiaoyu , Yang Bin , Feng Siyu , Makhija Suraj , Brown David , Huang Bo , Bivona Trever G. 
Published: July 2019

SummaryReceptor tyrosine kinase (RTK)-mediated activation of downstream effector pathways such as the RAS GTPase/MAP kinase (MAPK) signaling cascade is thought to occur exclusively from lipid membrane compartments in mammalian cells. Here, we uncover a membraneless, protein granule-based subcellular structure that can organize RTK/RAS/MAPK signaling in cancer. Chimeric (fusion) oncoproteins involving certain RTKs including ALK and RET undergo de novo higher-order assembly into membraneless cytoplasmic protein granules. These pathogenic biomolecular condensates locally concentrate the RAS activating complex GRB2/SOS1 and activate RAS in a lipid membrane-independent manner to initiate MAPK signaling. Formation of membraneless protein granules by RTK oncoproteins is both necessary and sufficient for RAS/MAPK signaling output in cells. Our findings reveal membraneless, higher-order cytoplasmic protein assembly as a distinct subcellular platform to activate RTKs and RAS GTPases and a general principle by which cells can organize oncogenic signaling.HighlightsRTK oncoproteins can form de novo membraneless cytoplasmic protein granulesRTK protein granules activate RAS in lipid membrane-independent mannerHigher-order protein assembly is critical for oncogenic RAS/MAPK signalingProtein granules are a distinct subcellular platform for organizing RTK signaling
XPRESSyourself: Enhancing, Standardizing, and Automating Ribosome Profiling Computational Analyses Yields Improved Insight into Data
Authors: Berg Jordan A. , Belyeu Jonathan R. , Morgan Jeffrey T. , Ouyang Yeyun , Bott Alex J. , Quinlan Aaron R. , Gertz Jason , Rutter Jared 
Published: July 2019

AbstractRibosome profiling, an application of nucleic acid sequencing for monitoring ribosome activity, has revolutionized our understanding of protein translation dynamics. This technique has been available for a decade, yet the current state and standardization of publicly available computational tools for these data is bleak. We introduce XPRESSyourself, an analytical toolkit that eliminates barriers and bottlenecks associated with this specialized data type by filling gaps in the computational toolset for both experts and non-experts of ribosome profiling. XPRESSyourself automates and standardizes analysis procedures, decreasing time-to-discovery and increasing reproducibility. This toolkit acts as a reference implementation of current best practices in ribosome profiling analysis. We demonstrate this toolkit’s performance on publicly available ribosome profiling data by rapidly identifying hypothetical mechanisms related to neurodegenerative phenotypes and neuroprotective mechanisms of the small-molecule ISRIB during acute cellular stress. XPRESSyourself brings robust, rapid analysis of ribosome-profiling data to a broad and ever-expanding audience and will lead to more reproducible and accessible measurements of translation regulation. XPRESSyourself software is perpetually open-source under the GPL-3.0 license and is hosted at https://github.com/XPRESSyourself, where users can access additional documentation and report software issues.
Polarella glacialis genomes encode tandem repeats of single-exon genes with functions critical to adaptation of dinoflagellates
Authors: Stephens Timothy G. , González-Pech Raúl A. , Cheng Yuanyuan , Mohamed Amin R. , Burt David W. , Bhattacharya Debashish , Ragan Mark A. , Chan Cheong Xin 
Published: July 2019

AbstractDinoflagellates are taxonomically diverse, ecologically important phytoplankton in marine and freshwater environments. Here, we present two draft diploid genome assemblies of the free-living dinoflagellate Polarella glacialis, isolated from the Arctic and Antarctica. For each genome, guided using full-length transcriptome data, we predicted >50,000 high-quality genes. About 68% of the genome is repetitive sequence; long terminal repeats likely contribute to intra-species structural divergence and distinct genome sizes (3.0 and 2.7 Gbp). Of all genes, ∼40% are encoded unidirectionally, ∼25% comprised of single exons. Multi-genome comparison unveiled genes specific to P. glacialis and a common, putatively bacterial, origin of ice-binding domains in cold-adapted dinoflagellates. Our results elucidate how selection acts within the context of a complex genome structure to facilitate local adaptation. Since most dinoflagellate genes are constitutively expressed, Polarella glacialis has enhanced transcriptional responses via unidirectional, tandem duplication of single-exon genes that encode functions critical to survival in cold, low-light environments.
Non-Redundant Roles in Sister Chromatid Cohesion of the DNA Helicase DDX11 and the SMC3 Acetyl Transferases ESCO1/2
Authors: Faramarz Atiq , Balk Jesper A. , Oostra Anneke B. , Ghandour Cherien A. , Rooimans Martin A. , Wolthuis Rob M.F. , Lange Job de 
Published: July 2019

AbstractIn a process linked to DNA replication, duplicated chromosomes are co-entrapped into large, circular cohesin complexes and functional sister chromatid cohesion (SCC) is established by acetylation of the SMC3 cohesin subunit. Several rare human developmental syndromes are characterized by defective SCC. Roberts Syndrome (RBS) is caused by mutations in the SMC3 acetyl transferase ESCO2, whereas mutations in the DNA helicase DDX11 lead to Warsaw Breakage Syndrome (WABS). We found that WABS-derived cells predominantly rely on ESCO2, not ESCO1, for residual SCC, growth and survival. Reciprocally, RBS-derived cells depend on DDX11 to maintain low levels of SCC. Synthetic lethality between DDX11 and ESCO2 correlated with a prolonged delay in mitosis, and was rescued by knock down of the cohesion remover WAPL. Rescue experiments using mouse or human cDNAs revealed that DDX11, ESCO1 and ESCO2 act on differential aspects of DNA replication-coupled SCC establishment. Importantly, DDX11 is required for normal DNA replication fork speed without clearly affecting SMC3 acetylation. We propose that DDX11 and ESCO2 control spatially separated fractions of cohesin, with supportive roles for DDX11 in replication-associated cohesion establishment, and for ESCO2 in cohesin complexes located around centromeres, respectively.
Agroecosystem resilience. A conceptual and methodological framework for evaluation
Authors: Córdoba Cindy , Triviño Catalina , Toro Javier 
Published: July 2019

AbstractThis article proposes a conceptual and methodological framework for analyzing agroecosystem resilience, which incorporates agrarian structure and peasant community agency. The methodology is applied to a comparison of two peasant communities in Latin America (Brazil and Colombia), emphasizing the capacity to transform unsustainable power structures in place of adapting to them. This application demonstrates that when agency is strongly developed, as in the case of Brazil, it is possible to transform structural conditions that restrict resilience. The inclusion and consideration of biophysical variables, management practices, agrarian structure and agency, through a participatory approach, allows for the identification of factors that inhibit or potentiate the resilience of agroecosystems.
Analysis of the Mutant Selection Window and Killing of Mycoplasma hyopneumoniae for Doxycycline, Tylosin, Danofloxacin, Tiamulin, and Valnemulin
Authors: Huang Zilong , Mao Chunxiao , Wei Yanzhe , Gu Xiaoyan , Cai Qinren , Shen Xiangguang , Ding Huanzhong 
Published: July 2019

AbstractMycoplasma hyopneumoniae is the major pathogenic microorganism causing enzootic pneumonia in pigs. With increasing resistance of M. hyopneumoniae to conventional antibiotics, treatment is becoming complicated. Herein, we investigated the mutant selection window (MSW) of doxycycline, tylosin, danofloxacin, tiamulin, and valnemulin for treating M. hyopneumoniae strain (ATCC 25934) to determine the likelihood of promoting resistance with continued use of these antibiotics. Minimum inhibitory concentration (MIC) values against M. hyopneumoniae were determined for each antimicrobial agent and ranged from 105 colony-forming units (CFU)/mL to 109 CFU/mL based on microdilution broth and agar dilution methods. The minimal concentration inhibiting colony formation by 99% (MIC99) and the mutant prevention concentration (MPC) were determined by the agar dilution method with three inoculum sizes. Antimicrobial killing was determined based on MIC99 and MPC values for all five agents. MIC values ranged from 0.001 to 0.25 μg/mL based on the microdilution broth method, and from 0.008 to 1.0 μg/mL based on the agar dilution method. MPC values ranged from 0.0016 to 10.24 μg/mL. MPC/MIC99 values were ordered tylosin >doxycycline >danofloxacin >tiamulin >valnemulin. MPC achieved better bactericidal action than MIC99. Based on pharmacodynamic analyses, danofloxacin, tylosin, and doxycycline are more likely to select resistant mutants than tiamulin and valnemulin.
Genomewide analysis of biomass responses to water withholding in young plants of maize inbred lines with expired plant variety protection certificate
Authors: Mazur Maja , Brkić Andrija , Šimić Domagoj , Brkić Josip , Jambrović Antun , Zdunić Zvonimir , Galic Vlatko 
Published: July 2019

AbstractPatterns of seasonal variations in rainfall are changing which affects rain-fed agricultural areas. Water deficit during the early vegetative growth poses threat as it causes variability in plant development, makes plant susceptible to other stresses and deteriorates the stands. Plant’s responses to water deficit are reflected in biomass traits which represent the morpho-physiological adjustments of plant to new conditions. The aims of this study were to assess the biomass responses of maize inbred lines with expired plant variety protection certificate that are freely distributed worldwide using genomewide analysis approach. The collection of 109 maize inbred lines, genotyped using genotyping-by-sequencing, was planted in controlled conditions (16/8 day/night, 25°C, 50% RH, 200 μMol/m2/s) in trays filled with soil in three replicates. Plants in control (C) were watered every two days with 8 mlH2O, while watering was stopped for 10 days in water withholding (WW) treatment. Fourteen days old plants were harvested and fresh weight (FW), dry weight (DW) and dry matter content (DMC, % of FW) were measured. Different responses to WW were detected in two genetic subgroups: Stiff Stalk and Non-Stiff Stalk. Totally 29 QTLs were detected, and it was shown that genetic regulation of DMC is different than regulation of FW and DW. This was further supported with correlations of rrBLUP marker effects among the traits. It was concluded that measurements of biomass traits in this manner are fast and reliable indicator of plant’s response to water deficit and can be used for effective screening of breeding progenies.
The observation of birds as informative tools to develop citizen science: Contributions of a 10-year record in the state of Chihuahua, Mexico
Authors: González-Quiñones Fidel , Granados Luis Roberto , Ruiz José Manuel Jurado , Tarango Javier , Machin-Mastromatteo Juan D. , Romo-González José Refugio 
Published: July 2019

AbstractThis article analyses historical data from observations made to birds in breeding, throughout two routes with urban characteristics and during a consecutive period of 10 years (2009-2018), following a precise methodology designed by the North American Breeding Bird Survey. The analyzed routes are officially registered in the Mexican Commission for Biodiversity’s Knowledge and Use, the United States Geological Survey Patuxent Wildlife Research Center, and the Canadian Wildlife Service Research Centre. The observations were made by citizens without formal professional education; hence the results may be considered within the framework of citizen science. Their contributions provided important data for decision-making regarding environmental issues, since the presence of birds is considered one of the main indicators on health conditions of an ecosystem. Data analysis identified two basic conditions: (i) a reduction of the 23% in the number of species found, as many of them disappeared during counting; and (ii) the significant increase in population of other species, three of pigeons among them. Apart from the study of bird behavior in the routes with urban characteristics, the article acknowledges the lack of connection and use of the information produced from monitoring for decision-making and education regarding environmental issues. Therefore, we consider crucial to create scientific observatories, both available to experts in the field and to the general population, as the ultimate purpose would be the production of citizen science.
Higher-order patterns of aquatic species spread through the global shipping network
Authors: Saebi Mandana , Xu Jian , Grey Erin K. , Lodge David M. , Chawla Nitesh 
Published: July 2019

AbstractThe introduction and establishment of non-indigenous species (NIS) through global ship movements is a significant threat to marine ecosystems and economies. While ballast-vectored invasions have been partly addressed by some national policies and an international agreement regulating the concentrations of organisms in ballast water, biofouling-vectored invasions remain a large risk. Development of additional realistic and cost-effective ship-borne NIS policies requires an accurate estimation of NIS spread risk from both ballast water and biofouling. In this paper, we demonstrate that first-order Markov assumptions limit accurate modeling of NIS spread risks through the global shipping network. In contrast, we show that higher-order patterns overcome this limitation by revealing indirect pathways of NIS transfer. We accomplish this by developing Species Flow Higher-Order Networks (SF-HON), which we developed independently for ballast and biofouling, for comparison with first-order Markovian models of ballast and biofouling. We evaluated SF-HON predictions using the largest available datasets of invasive species for Europe and the United States. We show that not only does SF-HON yield more accurate NIS spread risk predictions than first-order models and existing higher-order models, but also that there are important differences in NIS spread via the ballast and biofouling vectors. Our work provides information that policymakers can use to develop more efficient and targeted prevention strategies for ship-borne NIS spread management, especially as management of biofouling is of increasing concern.
Selection for imperfection: A review of asymmetric genitalia in araneomorph spiders (Araneae: Araneomorphae)
Authors: Rivera-Quiroz F. Andres , Schilthuizen Menno , Petcharad Boopa , Miller Jeremy A. 
Published: July 2019

AbstractBilateral asymmetry in the genitalia is a rare but widely dispersed phenomenon in the animal tree of life. In arthropods, occurrences vary greatly from one group to another and there seems to be no common explanation for all the independent origins. In spiders, genital asymmetry appears to be especially rare. Few examples have been studied in detail but isolated reports are scattered in the taxonomic literature. Based on a broad literature study, we found several species in thirteen families with evidence of genital asymmetry, mostly expressed only in females. Our review suggests that spider genital asymmetries, although rare, are more common than previously thought and taxonomic descriptions and illustrations are a useful but not entirely reliable tool for studying them. Here we also document thoroughly the case of the liocranid spiderTeutamus politus. We collected live specimens to observe male-female interactions and document their genital morphology. We considerT. politusto be the first known case of directional asymmetry and the first report of developmentally asymmetric male genitals in Entelegynae spiders. Generalities, evolution and categorization of asymmetry in spiders are further discussed.
Nucleolar stress inDrosophilaneuroblasts, a model for human ribosomopathies
Authors: Baral Sonu Shrestha , Lieux Molly E. , DiMario Patrick J. 
Published: July 2019

ABSTRACTDifferent stem cells or progenitor cells display variable threshold requirements for functional ribosomes. For instance, select embryonic neural crest cells or adult bone marrow stem cells, but not others, show lethality due to failures in ribosome biogenesis or function (known as nucleolar stress) in several human ribosomopathies. To determine if variousDrosophilaneuroblasts display differential sensitivities to nucleolar stress, we used CRISPR-Cas9 to disrupt theNopp140gene that encodes two ribosome biogenesis factors (RBFs). Disruption ofNopp140induced nucleolar stress that arrested larvae in the second instar stage. While the majority of larval neuroblasts arrested development, the Mushroom Body (MB) neuroblasts continued to proliferate as shown by their maintenance of deadpan, a neuroblast-specific transcription factor, and by their continued EdU incorporation. MB neuroblasts in wild type larvae contained more fibrillarin and Nopp140 in their nucleoli as compared to other neuroblasts, indicating that MB neuroblasts stockpile RBFs as they proliferate in late embryogenesis while other neuroblasts normally enter quiescence. A greater abundance of Nopp140 encoded by maternal transcripts inNopp140−/−MB neuroblasts likely rendered these cells more resilient to nucleolar stress.Summary StatementNucleolar stress (loss of ribosome production/function) in certain human stem cells or progenitor cells results in disease. In fruit flies, larval Mushroom Body neuroblasts are relatively resilient to nucleolar stress.