bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trophic position derived from amino-acid nitrogen isotopes reflect physiological status of both predator and prey over four decades
Authors: Karlson Agnes ML , Ek Caroline , Jones Douglas 
Published: January 2021

AbstractNitrogen isotope analyses of amino-acids (δ15N-AA) are increasingly used to decipher food webs. Interpretation of δ15N-AA in consumers relies on the assumption that physiological status has a negligible influence on the trophic enrichment factor (TEF). Recent experiments have shown that this is not always the case and there is a need to validate derived trophic position (TP) estimates using ecological data. We analyzed δ15N-AA in cod and herring (1980-2019) from the Baltic Sea, a species-poor system where dramatic reduction in condition status of cod has occurred. We expected that TEFcod-herringin trophic AAs would increase during periods of poor cod growth, resulting in inflated TP estimates. We found that TEF and TP estimates were negatively linked to individual condition status, prey fat content and the hypoxic state of the ecosystem. Statistically adjusting for these variables resulted in lower cod TP, highlighting the importance of including ecological knowledge when interpreting TP.Scientific Significance StatementNitrogen stable isotope analyses in amino acids are increasingly used in ecology to understand how environmental change impacts food-webs. Specifically, it is used to more accurately calculate trophic position (TP) of consumers. Controlled experiments have shown that physiological status can alter amino acid isotope composition and TP interpretation, but field studies are lacking. We use 40 years of archived material to demonstrate that TP estimates in Baltic Sea cod and its prey herring are directly related to physiological status. This has important implications for interpreting the real trophic ecology of consumers under environmental stress. By simultaneously measuring condition status in both predator and prey it is possible to adjust for them as confounding variables and decipher actual consumer TP.
martini: an R package for genome-wide association studies using SNP networks
Authors: Climente-González Héctor , Azencott Chloé-Agathe 
Published: January 2021

AbstractSystems biology shows that genes related to the same phenotype are often functionally related. We can take advantage of this to discover new genes that affect a phenotype. However, the natural unit of analysis in genome-wide association studies (GWAS) is not the gene, but the single nucleotide polymorphism, or SNP. We introducemartini, an R package to build SNP co-function networks and use them to conduct GWAS. In SNP networks, two SNPs are connected if there is evidence they jointly contribute to the same biological function. By leveraging such information in GWAS, we search SNPs that are not only strongly associated with a phenotype, but also functionally related. This, in turn, boosts discovery and interpretability.Martinibuilds such networks using three sources of information: genomic position, gene annotations, and gene-gene interactions. The resulting SNP networks involve hundreds of thousands of nodes and millions of edges, making their exploration computationally intensive.Martiniimplements two network-guided biomarker discovery algorithms based on graph cuts that can handle such large networks: SConES and SigMod. They both seek a small subset of SNPs with high association scores with the phenotype of interest and densely interconnected in the network. Both algorithms use parameters that control the relative importance of the SNPs’ association scores, the number of SNPs selected, and their interconnection.Martiniincludes a cross-validation procedure to set these parameters automatically. Lastly,martiniincludes tools to visualize the selected SNPs’ network and association properties.Martiniis available on GitHub (hclimente/martini) and Bioconductor (martini).
Improved DNA-versus-Protein Homology Search for Protein Fossils
Authors: Yao Yin , Frith Martin C. 
Published: January 2021

AbstractProtein fossils, i.e. noncoding DNA descended from coding DNA, arise frequently from transposable elements (TEs), decayed genes, and viral integrations. They can reveal, and mislead about, evolutionary history and relationships. They have been detected by comparing DNA to protein sequences, but current methods are not optimized for this task. We describe a powerful DNA-protein homology search method. We use a 64×21 substitution matrix, which is fitted to sequence data, automatically learning the genetic code. We detect subtly homologous regions by considering alternative possible alignments between them, and calculate significance (probability of occurring by chance between random sequences). Our method detects TE protein fossils much more sensitively thanblastx, and > 10× faster. Of the ~7 major categories of eukaryotic TE, three have not been found in mammals: we find two of them in the human genome, polinton and DIRS/Ngaro. This method increases our power to find ancient fossils, and perhaps to detect non-standard genetic codes. The alternative-alignments and significance paradigm is not specific to DNA-protein comparison, and could benefit homology search generally.
Regulatory Modules of Human Thermogenic Adipocytes: Functional Genomics of Meta-Analyses Derived Marker-Genes
Authors: Tóth Beáta B. , Barta Zoltán , Fésüs László 
Published: January 2021

SummaryRecently, ProFAT and BATLAS scores have been offered to determine thermogenic status of adipocytes using expression pattern of brown and white marker-genes. In this work, we investigated the functional context of these genes. Although the two meta-analyses based marker-gene lists have little overlap, their enriched pathways show strong coincides suggesting they may better characterize adipocytes. We demonstrate that functional genomics of the annotated genes in common pathways enables an extended analysis of thermogenesis regulation, generates testable hypotheses supported by experimental results in human adipocytes with different browning potential and may lead to more global conclusions than single-state studies. Our results imply that different biological processes shape brown and white adipocytes with presumed transitional states. We propose that the thermogenic adipocyte phenotype require both repression of whitening and induction of browning. These simultaneous actions and hitherto unnoticed regulatory modules, such as the exemplified HIF1A that may directly act atUCP1promoter, can set new direction in obesity research.HighlightsIntegrated pathways better characterize brown adipocytes than marker-genesDifferent processes shape the brown and white adipocyte phenotypesThermogenic phenotype may require simultaneous repression of whitening and induction of browningProtein network analyses reveals unnoticed regulatory modules of adipocyte phenotypeHIF1A may regulate thermogenesis by direct control ofUCP1gene-expressionGraphical Abstract
AMMI and GGE biplot analysis of yield of different elite Wheat line under terminal heat stress and irrigated environment
Authors: K. C. Bishwas , Poudel Mukti Ram , Regmi Dipendra 
Published: January 2021

ABSTRACTWheat crop in Nepal faces terminal heat stress which accelerates the gain filling rate and shortens the filling period which leads to reduced grain weight, size, number, quality that is yield loss. For minimization of this loss, genotypic selection of high yielding lines should be performed understanding the gene-environment interaction. With the view to obtain a high yielding line with stable performance across the environments an experiment was conducted using 18 elite wheat line and 2 check varieties in alpha lattice design (2 replication and 5 blocks per replication) in different environments viz. irrigated and terminal heat stressed environment. The analysis of variance revealed that genotype, environment and their interaction had highly significant effect on the yield. Furthermore, which-won–where model indicated specific adaptation of elite lines NL-1179, NL-1420, BL-4407, NL-1368 to irrigated environment and BL-4919 and NL-1350 to terminal heat-stressed environment. Similarly, Mean-versus-stability study indicated that elite line BL-4407, NL-1368, BL-4919, NL-1350 and NL-1420 had above average yield and higher stability whereas elite lines Gautam, NL-1412, NL-1376, NL-1387, NL-1404 and N-1381 had below average yield and lower stability. Also, ranking elite lines biplot, PCA1 explaining 73.6% and PCA2 explaining 26.4% of the interaction effect, showed the rank of elite line, NL-1420 > NL-1368> NL-1350 > other lines, close to ideal line. From these findings, NL-1420 with high yield and stability can be recommended across both the environment while NL-1179 is adapted specifically for irrigated and NL-1350 adapted specifically for terminal heat-stressed environment.
Comparison of Two Illumina Whole Transcriptome RNA Sequencing Library Preparation Methods Using Human FFPE Specimens
Authors: Wang Danyi , Rolfe P. Alexander , Foernzler Dorothee , O’Rourke Dennis , Zhao Sheng , Scheuenpflug Juergen , Feng Zheng 
Published: January 2021

AbstractRNA extraction and library preparation from formalin-fixed, paraffin-embedded (FFPE) samples are crucial pre-analytical steps towards achieving optimal downstream RNA Sequencing (RNASeq) results. We assessed the Illumina TruSeq Stranded Total RNA library preparation method and the Illumina TruSeq RNA Access library preparation method for RNA-Seq analysis using 25 FFPE samples from human cancer indications (NSCLC, CRC, RC, BC and HCC) at two independent vendors. These FFPE samples covered a wide range of sample storage durations (3-25 years-old), sample qualities, and specimen types (resection vs. core needle biopsy). Our data showed that TruSeq RNA Access libraries yield over 80% exonic reads across different quality samples, indicating higher selectivity of the exome pull down by the capture approach compared to the random priming of the TruSeq Stranded Total kit. The overall QC data for FFPE RNA extraction, library preparation, and sequencing generated by the two vendors are comparable, and downstream gene expression quantification results show high concordance as well. With the TruSeq Stranded Total kit, the average Spearman correlation between vendors was 0.87 and the average Pearson correlation was 0.76. With the TruSeq RNA Access kit, the average Spearman correlation between vendors was 0.89 and the average Pearson correlation was 0.73. Interestingly, examination of the crossvendor correlations compared to various common QC statistics suggested that library concentration is better correlated with consistency between vendors than is the RNA quantity. Our analyses provide evidence to guide selection of sequencing methods for FFPE samples in which the sample quality may be severely compromised.
Hemagglutination Inhibition (HAI) Antibody Landscapes after Vaccination with diverse H7 hemagglutinin (HA) proteins
Authors: Jang Hyesun , Ross Ted M 
Published: January 2021

AbstractBackgroundA systemic evaluation of the antigenic differences of the H7 influenza hemagglutinin (HA) proteins, especially for the viruses isolated after 2016, are limited. The purpose of this study was to investigate the antigenic differences of major H7 strains with an ultimate aim to discover H7 HA proteins that can elicit protective receptor-blocking antibodies against co-circulating H7 influenza strains.MethodA panel of nine H7 influenza strains were selected from 3,633 H7 HA amino acid sequences identified over the past two decades (2000-2018). The sequences were expressed on the surface of virus like particles (VLPs) and used to vaccinate C57BL/6 mice. Serum samples were collected and tested for hemagglutination-inhibition (HAI) activity. The vaccinated mice were challenged with lethal dose of H7N9 virus, A/Anhui/1/2013.ResultsVLPs expressing the H7 HA antigens elicited broadly reactive antibodies each of the selected H7 HAs, except the A/Turkey/Italy/589/2000 (Italy/00) H7 HA. A putative glycosylation due to an A169T substitution in antigenic site B was identified as a unique antigenic profile of Italy/00. Introduction of the putative glycosylation site (H7 HA-A169T) significantly altered the antigenic profile of HA of the A/Anhui/1/2013 (H7N9) strain.ConclusionThis study identified key amino acid mutations that result in severe vaccine mismatches for future H7 epidemics. Future universal influenza vaccine candidates will need to focus on viral variants with these key mutations.
NOMIS: Quantifying morphometric deviations from normality over the lifetime of the adult human brain
Authors: Potvin Olivier , Dieumegarde Louis , Duchesne Simon ,   the Alzheimer’s Disease Neuroimaging Initiative,   the CIMA-Q,   the CCNA groups
Published: January 2021

AbstractWe present NOMIS (https://github.com/medicslab/NOMIS), a comprehensive open MRI tool to assess morphometric deviation from normality in the adult human brain. Based on MR anatomical images from 6,909 cognitively healthy individuals aged 18-100 years, we modeled 1,344 measures computed using the open accessFreeSurferpipeline, considering account personal characteristics (age, sex, intracranial volume) and image quality (resolution, contrast-to-noise ratio and surface reconstruction defect holes), and providing expected values for any new individual. Then, for each measure, the NOMIS tool was built to generate Z-score effect sizes denoting the extent of deviation from the normative sample. Depending on the user need, NOMIS offers four versions of Z-score adjusted on different sets of variables. While all versions consider head size and image quality, they can also incorporate age and/or sex, thereby facilitating multi-site neuromorphometric research across adulthood.
Deciphering the transcriptomic regulation of heat stress responses inNothofagus pumilio
Authors: Estravis-Barcala Maximiliano , Heer Katrin , Marchelli Paula , Ziegenhagen Birgit , Arana María Verónica , Bellora Nicolás 
Published: January 2021

AbstractGlobal warming is predicted to exert negative impacts on plant growth due to the damaging effect of high temperatures on plant physiology. Revealing the genetic architecture underlying the heat stress response is therefore crucial for the development of conservation strategies, and for breeding heat-resistant plant genotypes. Here we investigated the transcriptional changes induced by heat inNothofagus pumilio, an emblematic tree species of the sub-Antarctic forests of South America. Through the performance of RNA-seq of leaves of plants exposed to 20°C (control) or 34°C (heat shock), we generated the first transcriptomic resource for the species. We also studied the changes in protein-coding transcripts expression in response to heat. We found 5,214 contigs differentially expressed between temperatures. The heat treatment resulted in a down-regulation of genes related to photosynthesis and carbon metabolism, whereas secondary metabolism, protein re-folding and response to stress were up-regulated. Moreover, several transcription factor families like WRKY or ERF were promoted by heat, alongside spliceosome machinery and hormone signaling pathways. Through a comparative analysis of gene regulation in response to heat inArabidopsis thaliana, Populus tomentosaandN. pumiliowe provide evidence of the existence of shared molecular features of heat stress responses across angiosperms, and identify genes of potential biotechnological application.
Ecological habitat partitioning and feeding specialisations of coastal minke whales (Balaenoptera acutorostrata) using a designated MPA in northeast Scotland
Authors: Robinson Kevin P. , Bamford Connor C.G. , Brown William J. , Culloch Ross M. , Dolan Ciaran J. , Hall Rebecca , Russell Grace , Sidiropoulos Theofilos , Spinou Evgenia , Sim Texa M.C. , Stroud Elice , Williams Genevieve , Haskins Gary N. 
Published: January 2021

AbstractIn the design of protected areas for cetaceans, spatial maps rarely take account of the life-history and behaviour of protected species relevant to their spatial ambit, which may be important when modelling population trends or assessing susceptibility to anthropogenic threats. In the present study, we examined the distribution and feeding behaviours of minke whales by age-class (adultsversusjuveniles) from long-term studies in the Moray Firth in northeast Scotland, where a Marine Protected Area (MPA) has recently been designated. Data were collected from dedicated boat surveys between 2000 and 2019, during which 657 encounters with 774 whales of confirmed age-class (444 juveniles and 330 adults) were recorded from 50,041 km of survey effort, resulting in 224 individual follows. Feeding/foraging whales were documented in 84% of the encounters. Adults and juveniles were occasionally seen together, but their distributions were not statistically correlated, and GIS revealed spatial separation by age-class―with juveniles preferring shallow, inshore waters with sandy-gravel sediments and adults preferring deeper, offshore waters with steep benthic slope. Whilst adult minkes employed a range of “active” prey-entrapment specialisations, showing seasonal flexibility in their targeted prey with interindividual variation, juveniles almost exclusively used “passive” (low energy) feeding methods, targeting low-density patches of inshore prey. These findings corroborate the need to incorporate demographic/behavioural data into spatial models when identifying priority areas for protected cetaceans and may be important to adaptive management objectives for the species in the Moray Firth MPA.
Induction of peri-implantation stage synthetic embryos using reprogramming paradigms in ESCs
Authors: Langkabel Jan , Horne Arik , Bonaguro Lorenzo , Hesse Tatiana , Knaus Alexej , Riedel Yannick , Händler Kristian , Bassler Kevin , Reusch Nico , Yeghiazarian Leon Harootoonovtch , Pecht Tal , Aschenbrenner Anna C. , Kaiser Franziska , Kubaczka Caroline , Schultze Joachim L. , Schorle Hubert 
Published: January 2021

SummaryBlastocyst-derived stem cell lines were shown to self-organize into embryo-like structures in 3D cell culture environments. Here, we provide evidence that synthetic embryo-like structures are generated solely based on transcription factor-mediated molecular reprogramming of embryonic stem cells in a simple 3D co-culture system. ESCs in these cultures self-organize into elongated, compartmentalized synthetic embryo-like structures over the course of reprogramming exhibiting anterior visceral endoderm formation and symmetry breaking. Single-cell RNA-Seq reveals transcriptional profiles resembling epiblast, visceral endoderm, and extraembryonic ectoderm of early murine embryos around E4.5–E5.5. Within the epiblast, compartment marker gene expression supports primordial germ cell specification. After transplantation, synthetic embryo-like structures implantin uteriand initiate the formation of decidual tissues. This system allows for fast and reproducible generation of synthetic embryo-like structures, providing further insights into synthetic embryology.
miR-24:Prdx6 interactions regulate oxidative stress and viability of myogenic progenitors during ageing
Authors: Soriano-Arroquia Ana , Gostage John , Bardell David , McCloskey Eugene , Bellantuono Ilaria , Clegg Peter , McDonagh Brian , Goljanek-Whysall Katarzyna 
Published: January 2021

ABSTRACTmicroRNAs regulate a myriad of physiological processes, including skeletal muscle regeneration and homeostasis. During ageing, changes in muscle fibre microenvironment contribute to the capability of satellite cells to regenerate the muscle in response to injury and loading stressors. In this study, we isolated murine satellite cells and primary myogenic progenitors from mice and humans to demonstrate that the microRNA miR-24-3p and its target peroxiredoxin 6 (Prdx6) play an important role in muscle regeneration during ageing, regulating satellite cell viability and their differentiation potential. Our results show upregulation of miR-24 during early stages of muscle regenerationin vivoin adult mice, suggesting a potential role of miR-24 at the early stages of muscle injury. On contrary, miR-24 was downregulated during regeneration of muscle of old mice. miR-24 was also downregulated, whereas its target gene Prdx6 was upregulated, in satellite cells isolated from old mice. miR-24 consistently regulated viability and myogenic potential of myogenic progenitors from both humans and old mice, suggesting that changes in miR-24 levels during ageing may contribute to defective early stages of muscle regeneration during ageing through affecting satellite cell viability and myogenic potential. This regulation likely occursviamiR-24 counteracting the generation of reactive oxygen species through Prdx6 de-repression in primary myogenic progenitors isolated from humans and old mice. We propose that downregulation of miR-24 in muscle of old mice following injury may be a protective mechanism against elevated ROS levels to maintain satellite cell viability and myogenic potential, acting through Prdx6 upregulation. However, as miR-24 is a regulator of p16 and p21, this downregulation may lead to increased satellite cell senescence, therefore representing an age-related failed compensatory mechanism.
A preliminary study on the cistrome of human postsynaptic density from an evolutionary and network-based perspective
Authors: Kalman Zsofia E. , Gáspári Zoltán 
Published: January 2021

AbstractThe postsynaptic density (PSD) is a neuronal organelle that consists of thousands of protein complexes, having a role in signal transduction. The emergence of the complexes is dependent on the presence of proteins provided by gene expression. In this research we used Chip-seq data supported by protein level information. We developed a pipeline using data from five neuronal transcription factors, which reduces the false-positive hits of identified binding sites. In addition we found correlation between co-regulation and protein complex formation. The developed method paves the way for a future for large scale analysis utilizing a more comprehensive set of transcription factors.
Modeling Protein Association from Homogeneous to Mixed Environments: A Reaction-Diffusion Dynamics Approach
Authors: Sahu Suraj Kumar , Biswas Mithun 
Published: January 2021

AbstractProtein-protein associationin vivooccur in a crowded and complex environment. Theoretical models based on hard-core repulsion predict stabilization of the product under crowded conditions. Soft interactions, on the contrary, can either stabilize or destabilize the product formation. Here we modeled protein association in presence of crowders of varying size, shape, interaction potential and used different mixing parameters for constituent crowders to study the influence on the association reaction. It was found that size a more dominant factor in crowder-induced stabilization than the shape. Furthermore, in a mixture of crowders having different sizes but identical interaction potential, the change of free energy is additive of the free energy changes produced by individual crowders. However, the free energy change is not additive if two crowders of same size interact via different interaction potentials. These findings provide a systematic understanding of crowding influences in heterogeneous medium.