bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Transcriptomic Analysis Revealed Complex Molecular Mechanisms Underlying Pests, Pathogens Resistance and Seed Development in Wild and Cultivated Blackgram
Authors: Raizada Avi , Jegadeesan Souframanien 
Published: November 2020

AbstractBlackgram is a widely cultivated pulse crop in Asia. Bruchid pests and yellow mosaic disease (YMD) causes huge loss in legume production including blackgram. Blackgram wild accession (Vigna mungo var.silvestris), Trombay wild urd (INGR10133) conferred resistance to bruchids especiallyCallosobruchus maculatus, through antibiosis. However, the mechanisms still remains uncharacterized. We performed the comparative transcriptome analysis of the developing seeds of wild and cultivated blackgram with contrasting phenotypes for 3 traits, bruchids infestation, YMD and seed size. In this study,715differentially expressed genes(DEGs) were re-annotated with reference to NCBI nr database. RNA-Seq was validated by quantitative real-time PCR for 22 DEGs. In Trombay wild, defense related components such as acid phosphatase, vicilins, trypsin inhibitor, brassinosteroid signalling components were found up-regulated. While in cultivar, transcripts forLEA, cysteine protease, autophagy related proteins(ATG3, ATG5, ATG8C and ATG1t),DnaJ, tobamovirus multiplication protein, downy mildew resistance protein, LRR/F-box proteins were found up-regulated. In TW, three transcripts were found common for both bruchids pest and geminivirus resistance (LRR receptor kinase, transmembrane protein 87b and thaumatin like protein).Our study is the first report on transcriptomic differences between wild and cultivated blackgram with new insights into the molecular networks underlying seed development, resistance to pests and pathogens.
Potential ofin vivo- andin vitro-cultured entomopathogenic nematodes to infectLobesia vanillana(Lepidoptera: Tortricidae) under laboratory conditions
Authors: du Preez Francois , Malan Antoinette Paula , Addison Pia 
Published: November 2020

AbstractThein vivo- andin vitro-cultured South African entomopathogenic nematodes (EPNs),Steinernema yirgalemenseandSteinernema jeffreyense(Rhabditida: Steinernematidae), were evaluated against larvae and pupae ofLobesia vanillanain laboratory bioassays. For larvae, high mortality was observed for all treatments:In vitro-culturedS. yirgalemense(98%) performed better thanS. jeffreyense(73%), while withinin vivocultures, there was no difference between nematode species (both 83%). No significant difference was detected betweenin vivo- andin vitrocultures of the same nematode species. The LD50of thein vitro-culturedS. yirgalemense, the best performing species, was 7.33 nematodes per larva. Mortality by infection was established by dissecting cadavers and confirming the presence of nematodes, which was > 90% for all treatments. Withinin vitrocultures, bothS. yirgalemenseandS. jeffreyensewere able to produce a new cohort of infective juveniles fromL. vanillanalarvae. Pupae, however, were found to be considerably less susceptible to EPN infection. The relative success of localin vivo- andin vitro-cultured EPN species against a tortricid species in laboratory assays is encouraging for further research and development of this technology.
Study on the efficacy ofCynodon dactylonagainst Infectious Myonecrosis Virus (IMNV) inPenaeus vannamei
Authors: Jha Rajeev Kumar , Wisoyo Soy Daniel , Kristina  , Srisombat Sarayut 
Published: November 2020

ABSTRACTInfectious myonecrosis virus (IMNV) is one of the most pathogenic viruses causing severe mortality inPenaeus vannameiin many countries. Several strategies have been implemented to inhibit the presence of IMNV disease. The present study was carried out to examine the antiviral activity ofCynodon dactylonethanolic extract on IMNV disease in shrimp byin vivotesting. TheC. dactylonplant extract was incorporated with artificial pellet feed at a concentration of 10, 15%, 20%, and 25%. For the experimental challenge shrimp were fed with IMNV-infected shrimp meat. The antiviral activity was determined by observing survival rates, and IMNV infection was confirmed at the end of the experiment through polymerase chain reaction (PCR) identification. This study showed that the plant extract ofC. dactylonwas found to be highly effective in preventing IMNV infection with up to 98% survival rate inPenaeus vannamei.
SARS-CoV-2 epitope mapping on microarrays highlights strong immune-response to N protein region
Authors: Musicò Angelo , Frigerio Roberto , Mussida Alessandro , Barzon Luisa , Sinigaglia Alessandro , Riccetti Silvia , Gobbi Federico , Piubelli Chiara , Bergamaschi Greta , Chiari Marcella , Gori Alessandro , Cretich Marina 
Published: November 2020

AbstractA workflow for SARS-CoV-2 epitope discovery on peptide microarrays is herein reported. The process started with a proteome-wide screening of immunoreactivity based on the use of a high-density microarray followed by a refinement and validation phase on a restricted panel of probes using microarrays with tailored peptide immobilization through a click-based strategy. Progressively larger, independent cohorts of Covid-19 positive sera were tested in the refinement processes, leading to the identification of immunodominant regions on SARS-CoV-2 Spike (S), Nucleocapsid (N) protein and Orf1ab polyprotein. A summary study testing 50 serum samples highlighted an epitope of the N protein (region 155-171) providing 92% sensitivity and 100% specificity of IgG detection in Covid-19 samples thus being a promising candidate for rapid implementation in serological tests.
POINT Technology Illuminates the Processing of Polymerase-Associated Intact Nascent Transcripts
Authors: Sousa-Luis Rui , Dujardin Gwendal , Zukher Inna , Kimura Hiroshi , Carmo-Fonseca Maria , Proudfoot Nick J , Nojima Takayuki 
Published: November 2020

SUMMARYMammalian chromatin is the site of both RNA polymerase II (Pol II) transcription and coupled RNA processing. However, molecular details of such co-transcriptional mechanisms remain obscure, partly due to technical limitations in purifying authentic nascent transcripts. We present a new approach to purify and profile nascent RNA, called Polymerase Intact Nascent Transcript (POINT) technology. This three-pronged methodology maps nascent RNA 5’ends (POINT-5), establishes the kinetics of co-transcriptional splicing patterns (POINT-nano) and profiles whole transcription units (POINT-seq). In particular we show by depletion of the nuclear exonuclease Xrn2 that this activity acts selectively on cleaved 5’P-RNA at polyadenylation sites. Furthermore POINT-nano reveals that splicing occurs either immediately after splice site transcription or is delayed until Pol II transcribes downstream sequences. Finally, we connect RNA cleavage and splicing with either premature or full-length transcript termination. We anticipate that POINT technology will afford full dissection of the complexity of co-transcriptional RNA processing.HIGHLIGHTSPOINT methodology dissects intact nascent RNA processingSpecificity of Xrn2 exonuclease in co-transcriptional RNA degradationSplicing suppresses Xrn2-dependent premature terminationDifferent kinetic classes of co-transcriptional splicing in human genes
PathDSP: Explainable Drug Sensitivity Prediction through Cancer Pathway Enrichment
Authors: Tang Yi-Ching , Gottlieb Assaf 
Published: November 2020

ABSTRACTComputational approaches to predict drug sensitivity can promote precision anticancer therapeutics. Generalizable and explainable models are of critical importance for translation to guide personalized treatment and are often overlooked in favor of prediction performance.Here, we propose a pathway-based model for drug sensitivity prediction that integrates chemical structure information with enrichment of cancer signaling pathways across drug-associated genes, gene expression, mutation and copy number variation data to predict drug response on the Genomics of Drug Sensitivity in Cancer (GDSC) dataset. Using a deep neural network, we outperforming state-of-the-art deep learning models, while demonstrating good generalizability a separate dataset of the Cancer Cell Line Encyclopedia (CCLE) as well as provide explainable results, demonstrated through case studies that are in line with current knowledge. Additionally, our pathway-based model achieved a good performance when predicting unseen drugs and cells, with potential utility for drug development and for guiding individualized medicine.
An End-to-end Oxford Nanopore Basecaller Using Convolution-augmented Transformer
Authors: Lv Xuan , Chen Zhiguang , Lu Yutong , Yang Yuedong 
Published: November 2020

AbstractOxford Nanopore sequencing is fastly becoming an active field in genomics, and it’s critical to basecall nucleotide sequences from the complex electrical signals. Many efforts have been devoted to developing new basecalling tools over the years. However, the basecalled reads still suffer from a high error rate and slow speed. Here, we developed an open-source basecalling method, CATCaller, by simultaneously capturing global context through Attention and modeling local dependencies through dynamic convolution. The method was shown to consistently outper-form the ONT default basecaller Albacore, Guppy, and a recently developed attention-based method SACall in read accuracy. More importantly, our method is fast through a heterogeneously computational model to integrate both CPUs and GPUs. When compared to SACall, the method is nearly 4 times faster on a single GPU, and is highly scalable in parallelization with a further speedup of 3.3 on a four-GPU node.
Evidence of genetic overlap between circadian preference and brain white matter microstructure
Authors: García-Marín Luis M. , Alcauter Sarael , Campos Adrian I. , Mulcahy Aoibhe , Kho Pik-Fang , Cuéllar-Partida Gabriel , Rentería Miguel E. 
Published: November 2020

AbstractStudy objectivePrevious neuroimaging studies have highlighted differences in white matter microstructure among individuals with different chronotypes, but it is unclear whether those differences are due to genetic or environmental factors.MethodsHere we leverage summary statistics from recent large-scale genome-wide association studies (GWAS) of chronotype and diffusion tensor imaging (DTI) measures to examine the genetic overlap and infer causal relationships between these traits.ResultsWe identified 29 significant pairwise genetic correlations, of which 13 also had evidence for a causal association. Negative genetic correlations were identified between chronotype and brain-wide mean, axial and radial diffusivities. When exploring individual tracts, ten negative genetic correlations were observed with mean diffusivities, 10 with axial diffusivities, 4 with radial diffusivities and 2 with mode of anisotropy. We found evidence for a possible causal association of chronotype with white matter microstructure in individual tracts including the posterior limb and retrolenticular part of the internal capsule; the genu and splenium of the corpus callosum and the posterior, superior and anterior regions of the corona radiata.ConclusionsOur results suggest thateveningnessis associated with variation in tract-specific white matter microstructure and, for an evening person, increases in axial and / or radial diffusivities may influence a higher mean diffusivity. These findings add to our understanding of circadian preference and its relationship with the brain, providing new perspectives on the genetic neurological underpinnings of chronotype’s role in health and disease.Statement of SignificanceSleep is essential for a healthy brain function, particularly for neural organization and brain structure development. Individual chronotype differences have been associated with depression, schizophrenia, diabetes and obesity, among other conditions. Investigating the shared genetic aetiology between chronotype and white matter microstructure is essential to understand the neurological basis of individual variation in chronotype. In the present study, we show that tract-specific white matter microstructure is genetically correlated and causally associated with chronotype.
Single cell transcriptomic re-analysis of immune cells in bronchoalveolar lavage fluids reveals the correlation of B cell characteristics and disease severity of patients with SARS-CoV-2 infection
Authors: Kim Chae Won , Oh Ji Eun , Lee Heung Kyu 
Published: November 2020

AbstractThe COVID-19 pandemic (SARS-CoV-2) is a global infectious disease with rapid spread. Some patients have severe symptoms and clinical signs caused by an excessive inflammatory response, which increases the risk of mortality. In this study, we reanalyzed scRNA-seq data of cells from bronchoalveolar lavage fluids of patients with COVID-19 with mild and severe symptoms, focusing on antibody-producing cells. In patients with severe disease, B cells seemed to be more activated and expressed more immunoglobulin genes compared with cells from patients with mild disease, and macrophages expressed higher levels of the TNF superfamily member B-cell activating factor but not of APRIL (a proliferation-inducing ligand). In addition, macrophages from patients with severe disease had increased pro-inflammatory features and pathways associated with Fc receptor-mediated signaling, compared with patients with mild disease. CCR2-positive plasma cells accumulated in patients with severe disease, probably because of increased CCL2 expression on macrophages from patients with severe disease. Together, these results support that different characteristics of B cells might affect the severity of COVID-19 infection.
Modelling the impact of the macroalgaeAsparagopsis taxiformison rumen microbial fermentation and methane production
Authors: Muñoz-Tamayo Rafael , Chagas Juana C. , Ramin Mohammad , Krizsan Sophie J. 
Published: November 2020

AbstractBackgroundThe red macroalgae Asparagopsis taxiformis is a potent natural supplement for reducing methane production from cattle. A. taxiformis contains several anti-methanogenic compounds including bromoform that inhibits directly methanogenesis. The positive and adverse effects of A. taxiformis on the rumen microbiota are dose-dependent and operate in a dynamic fashion. It is therefore key to characterize the dynamic response of the rumen microbial fermentation for identifying optimal conditions on the use of A. taxiformis as a dietary supplement for methane mitigation. Accordingly, the objective of this work was to model the effect of A. taxiformis supplementation on the rumen microbial fermentation under in vitro conditions. We adapted a published mathematical model of rumen microbial fermentation to account for A. taxiformis supplementation. We modelled the impact of A. taxiformis on the fermentation and methane production by two mechanisms, namely (i) direct inhibition of the growth rate of methanogens by bromoform and (ii) hydrogen control on sugars utilization and on the flux allocation towards volatile fatty acids production. We calibrated our model using a multi-experiment estimation approach that integrated experimental data with six macroalgae supplementation levels from a published in vitro study assessing the dose-response impact of A. taxiformis on rumen fermentation.Resultsour model captured satisfactorily the effect of A. taxiformis on the dynamic profile of rumen microbial fermentation for the six supplementation levels of A. taxiformis with an average determination coefficient of 0.88 and an average coefficient of variation of the root mean squared error of 15.2% for acetate, butyrate, propionate, ammonia and methane.Conclusionsour results indicated the potential of our model as prediction tool for assessing the impact of additives such as seaweeds on the rumen microbial fermentation and methane production in vitro. Additional dynamic data on hydrogen and bromoform are required to validate our model structure and look for model structure improvements. We expect this model development can be useful to help the design of sustainable nutritional strategies promoting healthy rumen function and low environmental footprint.
A tractable bottom-up model of the yeast polarity genotype-phenotype map for evolutionary relevant predictions
Authors: Daalman Werner Karl-Gustav , Sweep Els , Laan Liedewij 
Published: November 2020

AbstractAccurate phenotype prediction based on genetic information has numerous societal applications, such as crop design or cellular factories. Epistasis, when biological components interact, complicates modelling phenotypes from genotypes. Here we show an approach to mitigate this complication for polarity establishment in budding yeast, where mechanistic information is abundant. We coarse-grain molecular interactions into a so-called mesotype, which we combine with gene expression noise into a physical cell cycle model. Firstly, we show with computer simulations that the mesotype allows validation of the most current biochemical polarity models by quantitatively matching doubling times. Secondly, the mesotype elucidates epistasis emergence as exemplified by evaluating the predicted mutational effect of key polarity protein Bem1p when combined with known interactors or under different growth conditions. This example also illustrates how unlikely evolutionary trajectories can become more accessible. The tractability of our biophysically justifiable approach inspires a road-map towards bottom-up phenotype modelling beyond statistical inferences.
Small Animal Jet Injection Technique Results in Enhanced Immunogenicity of Hantavirus DNA Vaccines
Authors: Brocato Rebecca L. , Kwilas Steven A. , Josleyn Matthew D. , Long Simon , Zeng Xiankun , Perley Casey C. , Principe Lucia M. , Somerville Brandon , Cohen Melanie V. , Hooper Jay W. 
Published: November 2020

AbstractDNA vaccine evaluation in small animals is hampered by low immunogenicity when the vaccines are delivered using a needle and syringe. To overcome this technical hurdle we tested the possibility that a device developed for human intradermal medicine delivery might be adapted to successfully deliver a DNA vaccine to small animals. The PharmaJet®Tropis device is a FDA 510(k)-cleared disposable syringe, needle-free jet injection device designed to administer medicines to the human dermis in a 0.1 mL volume. Here, we found that hantavirus DNA vaccines administered to Syrian hamsters using Tropis were substantially more immunogenic than the same vaccines delivered by needle/syringe or particle mediated epidermal delivery (gene gun) vaccination. By adjusting how the device was used we could deliver vaccine to either subcutaneous tissues, or through the skin into the muscle. RNA and/or antigen expression was detected in epidermal, subepidermal and fibroblast cells. We directly compared six optimized and non-optimized hantavirus DNA vaccines in hamsters. Optimization, including codon-usage and mRNA stability, did not necessarily result in increased immunogenicity for all vaccines tested; however, optimization of the Andes virus (ANDV) DNA vaccine protected vaccinated hamsters from lethal disease. This is the first time active vaccination with an ANDV DNA vaccine has shown protective efficacy in the hamster model. The adaptation of a human intradermal jet injection device for use as a method of subcutaneous and intramuscular jet injection of DNA vaccines will advance the development of nucleic acid based medical countermeasures for diseases modeled in hamsters.
Impact of the pear psyllidCacopsylla pyrihost instar on the behavior and fitness of the parasitoidTrechnites insidious
Authors: Le Goff Guillaume Jean , Berthe Jeremy , Tougeron Kévin , Dochy Benoit , Lebbe Olivier , Renoz François , Hance Thierry 
Published: November 2020

AbstractPear is one of the most important fruit crops of temperate regions. The control of its mains pest,Cacopsylla pyri, is still largely based on the use of chemical pesticides, with all that this implies in terms of negative effects on the environment and health.Within the context of integrated pest management, innovative and ecologically sustainable strategies must be developed for. AlthoughTrechnites insidiosusis the most abundant parasitoid ofC. pyri, its biology and its potential as a control agent have been little studied.In this paper, we conducted experiments to evaluate the behavior of the specialist parasitoidT. insidiosuswhen exposed to different larval instars of the pear psyllidC. pyri, and to assess the quality of the next generation of parasitoids.We found that althoughT. insidiosusaccepts all host instars for oviposition, the third and fourth instars were the most suitable host in terms of behavioral acceptance and progeny development.Our study is a first step for further studies on the interaction between psyllids and parasitoids and provides evidence that the specialist parasitoidT. insidiosusis a promising candidate for biological control strategies of the pear psyllidC. pyri.
Astrocytes drive divergent metabolic gene expression in humans and chimpanzees
Authors: Zintel Trisha M. , Pizzollo Jason , Claypool Christopher G. , Babbitt Courtney C. 
Published: November 2020

ABSTRACTThe human brain utilizes ∼ 20% of all of the body’s metabolic resources, while chimpanzee brains use less than 10%. Although previous work shows significant differences in metabolic gene expression between the brains of primates, we have yet to fully resolve the contribution of distinct brain cell types. To investigate cell-type specific interspecies differences in brain gene expression, we conducted RNA-Seq on neural progenitor cells (NPCs), neurons, and astrocytes generated from induced pluripotent stem cells (iPSCs) from humans and chimpanzees. Interspecies differential expression (DE) analyses revealed that twice as many genes exhibit DE in astrocytes (12.2% of all genes expressed) than neurons (5.8%). Pathway enrichment analyses determined that astrocytes, rather than neurons, diverged in expression of glucose and lactate transmembrane transport, as well as pyruvate processing and oxidative phosphorylation. These findings suggest that astrocytes may have contributed significantly to the evolution of greater brain glucose metabolism with proximity to humans.