bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic
Authors: Nelson Chase W. , Ardern Zachary , Goldberg Tony L. , Meng Chen , Kuo Chen-Hao , Ludwig Christina , Kolokotronis Sergios-Orestis , Wei Xinzhu 
Published: May 2020

AbstractUnderstanding the emergence of novel viruses requires an accurate and comprehensive annotation of their genomes. Overlapping genes (OLGs) are common in viruses and have been associated with pandemics, but are still widely overlooked. We identify and characterizeORF3d, a novel OLG in SARS-CoV-2 that is also present in Guangxi pangolin-CoVs but not other closely related pangolin-CoVs or bat-CoVs. We then document evidence ofORF3dtranslation, characterize its protein sequence, and conduct an evolutionary analysis at three levels: between taxa (21 members ofSevere acute respiratory syndrome-related coronavirus), between human hosts (3978 SARS-CoV-2 consensus sequences), and within human hosts (401 deeply sequenced SARS-CoV-2 samples).ORF3dhas been independently identified and shown to elicit a strong antibody response in COVID-19 patients. However, it has been misclassified as the unrelated geneORF3b, leading to confusion. Our results likenORF3dto other accessory genes in emerging viruses and highlight the importance of OLGs.
A high-throughput neutralizing antibody assay for COVID-19 diagnosis and vaccine evaluation
Authors: Muruato Antonio E. , Fontes-Garfias Camila R. , Ren Ping , Garcia-Blanco Mariano A. , Menachery Vineet D. , Xie Xuping , Shi Pei-Yong 
Published: May 2020

AbstractVirus neutralization remains the gold standard for determining antibody efficacy. Therefore, a high-throughput assay to measure SARS-CoV-2 neutralizing antibodies is urgently needed for COVID-19 serodiagnosis, convalescent plasma therapy, and vaccine development. Here we report on a fluorescence-based SARS-CoV-2 neutralization assay that detects SARS-CoV-2 neutralizing antibodies in COVID-19 patient specimens and yields comparable results to plaque reduction neutralizing assay, the gold standard of serological testing. Our approach offers a rapid platform that can be scaled to screen people for antibody protection from COVID-19, a key parameter necessary to safely reopen local communities.
pH-Dependent Transcriptional Profile Changes in Iron-DeficientArabidopsisRoots
Authors: Tsai Huei-Hsuan , Schmidt Wolfgang 
Published: May 2020

ABSTRACTIron is an essential element for plants and abundantly present in most mineral soils. The mobility of iron is, however, dependent on the redox potential and hydrogen activity (pH) of the soil, factors that may limit its availability to plants in particular at alkaline pHs. Iron deficiency triggers pronounced changes in the transcriptional profile of plants, inducing processes that aid in the acquisition, uptake, and translocation of iron. How ambient pH impact the transcriptional iron deficiency response has not yet been elucidated in detail. Here, we provide an RNA-seq data set that catalogs global gene expression changes of iron-deficient plants grown at either optimal (5.5) or high (7.0) pH. A suite of 857 genes changed significantly and more than twofold in expression; only 54 genes of this suite were also differentially expressed between iron-deficient and iron-sufficient plants grown at pH 5.5. Among the high pH-responsive genes, 186 were earlier shown to be responsive to short-term transfer to low pH, 91 genes of this subset were anti-directionally regulated by high and low pH. The latter subset contained genes involved in cell wall organization, auxin homeostasis, and potential hubs of yet undefined signaling circuits. Growing iron-deficient plants at high pH also modulated the transcriptional iron deficiency response observed at pH 5.5 by compromising the enzymatic reduction of ferric chelates and favoring the production of iron-mobilizing coumarins. It is concluded that ambient pH is an important determinant of global gene expression which tunes iron acquisition to the prevailing edaphic conditions.
Psychological Impact of COVID-19 on Pakistani University Students and How They Are Coping
Authors: Salman Muhammad , Asif Noman , Mustafa Zia Ul , Khan Tahir Mehmood , Shehzadi Naureen , Hussain Khalid , Tahir Humera , Raza Muhammad Husnnain , Khan Muhammad Tanveer 
Published: May 2020

AbstractBackgroundCOVID-19 is spreading quickly, causing great deal of fear and unrest in the public. We aimed to assess the psychological impact of COVID-19 on university students and their coping strategies.MethodsThis web-based, cross-sectional study was conducted among students of four Pakistani higher education institutions. Google forms were used to disseminate the online questionnaire to assess anxiety (GAD-7), depression (PHQ-9), sources of distress (14-items) and the coping strategies (Brief-COPE).ResultsA total of 1134 responses (age 21.7 ± 3.5 years) were included. The frequency of students having moderate-severe anxiety and depression (score ≥ 10) were ≈ 34% and 45%, respectively. The respondents’ aged ≥ 31 years had significantly lower depression score than those below 30 years. Males had significantly less anxiety and depression scores than females. Additionally, those having a family member, friend or acquaintance infected with the disease had significantly higher anxiety score. The main sources of distress were the changes in daily life due to the ongoing pandemic. Regarding coping strategies, majority of respondents were found to have adopted religious/spiritual coping (6.45 ± 1.68) followed by acceptance (5.58 ± 1.65).ConclusionsCOVID-19 have significant adverse impact on students’ mental health. The most frequent coping strategy adopted by them are religious/spiritual coping, acceptance, self-distraction and active coping. It is suggested that mental health of students should not be neglected during epidemics.
Immunity after COVID-19: protection or sensitization?
Authors: Danchin Antoine , Turinici Gabriel 
Published: May 2020

AbstractMotivated by historical and present clinical observations, we discuss the possible unfavorable evolution of the immunity (similar to documented antibody-dependent enhancement scenarios) after a first infection with COVID-19. More precisely we ask the question of how the epidemic outcomes are affected if the initial infection does not provide immunity but rather sensitization to future challenges. We first provide background comparison with the 2003 SARS epidemic. Then we use a compartmental epidemic model structured by immunity level that we fit to available data; using several scenarios of the fragilization dynamics, we derive quantitative insights into the additional expected numbers of severe cases and deaths.
The role of school enjoyment in the association between externalising and depressive symptoms and academic attainment: findings from a UK prospective cohort study
Authors: Cadman Tim , Hughes Amanda , Wright Caroline , López-López José A , Morris Tim , Rice Frances , Smith George Davey , Howe Laura D 
Published: May 2020

ABSTRACTPrevious research on the relationship between children’s externalising and depressive symptoms, experience of school, and later academic attainment is inconclusive. The present study uses data from the Avon Longitudinal Study of Parents and Children (n=6,409) to investigate bidirectional associations between school experience (enjoyment and connectedness) and externalising and depressive symptoms at age 10-11 and 13-14. We also investigate the relationship between school experience and academic attainment at 16 and test whether school experience mediates associations of externalising and depressive symptoms with later attainment. A cross-lagged structural equation model was employed. Externalising and depressive symptoms at 10-11 were negatively associated with school connectedness at 13-14 (externalizing: standardised β=−0.13, CI: −0.17, −0.08; depressive: β=−0.06, CI: −0.11, 0.01), and with school enjoyment at 13-14 (externalising: β=−0.08, CI: −0.13, −0.03; depressive β=−0.04, −0.08, 0.03). School enjoyment at 13-14 was positively associated with attainment at 16 (β=0.10, CI: 0.04, 0.15), and partially mediated associations between externalising and depressive symptoms at 10-11 and attainment at 16 (externalising: proportion mediated; 4.7%, CI: 0.7, 10.1, depressive: proportion mediated 2.2%, I: −1.5, 5.9). School enjoyment is a potentially modifiable risk factor that may affect educational attainment of adolescents with depressive and externalising symptoms.
Genomic Epidemiology ofEscherichia coliIsolates from a Tertiary Referral Center in Lilongwe, Malawi
Authors: Tegha Gerald , Ciccone Emily J. , Krysiak Robert , Kaphatika James , Chikaonda Tarsizio , Ndhlovu Isaac , van Duin David , Hoffman Irving , Juliano Jonathan J. , Wang Jeremy 
Published: May 2020

ABSTRACTAntimicrobial resistance (AMR) is a global threat, including in sub-Saharan Africa. However, little is known about the genetics of resistant bacteria in the region. In Malawi, there is growing concern about increasing rates of antimicrobial resistance to most empirically used antimicrobials. The highly drug resistantEscherichia colisequence type (ST) 131, which is associated with the extended spectrum β-lactamaseblaCTX-M-15, has been increasing in prevalence globally. Previous data from isolates collected between 2006-2013 in southern Malawi have shown the presence of ST131 and theblaCTX-M-15gene in the country. We performed whole genome sequencing (WGS) of 58 clinicalE. coliisolates at Kamuzu Central Hospital, a tertiary care center in central Malawi, collected from 2012-2018. We used Oxford Nanopore Technologies (ONT) sequencing, which was performed in Malawi. We show that ST131 has become more prevalent (14.9% increasing to 32.8%) and that theblaCTX-M-15gene is occurring at a higher frequency (21.3% increasing to 44.8%). Phylogenetics show isolates are highly related between the central and southern geographic regions and confirm that ST131 isolates are contained in a single group consistent with recent expansion. All AMR genes, includingblaCTX-M-15, were widely distributed across sequence types. We also identified an increased number of ST410 isolates, which in this study tend to carry a plasmid-located copy ofblaCTX-M-15gene at a higher frequency thanblaCTX-M-15occurs in ST131. This study confirms the expanding nature of ST131 and the wide distribution of theblaCTX-M-15gene in Malawi. We also highlight the feasibility of conducting longitudinal genomic epidemiology studies of important bacteria with the sequencing done on site using a nanopore platform that requires minimal infrastructure.DATA SUMMARYThe sequencing data used for this analysis is available in public data repositories. Information on the sequences used is provided in Supplementary Table 2.
Recruitment of Archaeal DTD is a Key Event in the Emergence of Land Plants
Authors: Mazeed Mohd , Singh Raghvendra , Kumar Pradeep , Raman Bakthisaran , Kruparani Shobha P. , Sankaranarayanan Rajan 
Published: May 2020

AbstractLand plant evolution is a major leap in the history of life that took place during the Neoproterozoic Era (∼800 Mya). Charophyceae, a class of rhyzophytic green algae emerged as a land plant with innovations in biochemical, cytological and developmental adaptations and played a crucial role in establishing life on the land1,2. One such striking architectural innovation is “root” that experience harsh environmental assaults such as floods, waterlogging and therefore is the epicentre for anaerobic fermentation, which produces toxic acetaldehyde3. Here, we show that such produced acetaldehyde makes N-ethyl-adducts on a central component of translation machinery aa-tRNA. The Plant kingdom is unique among life forms in possessing two chirality-based proofreading systems represented by D-aminoacyl-tRNA deacylases (DTD1 and DTD2), derived from Bacteria and Archaea4. We identified a unique role of archaeal derived chiral proofreading module DTD2 that selectively deacylates N-ethyl-D-aminoacyl-tRNAs (NEDATs) in plants. NEDAT deacylase function is exclusive to DTD2, as no other proofreading modules with similar substrates like canonical DTD1 and peptidyl-tRNA hydrolase (PTH) can clear NEDATs. Thus, the study elucidates the cause of hypersensitivity of DTD2 knockout plants for both ethanol and acetaldehyde. We further show NEDAT elimination is rooted in Archaea which possess the biosynthesis machinery for ethanol fermentation similar to plants. While absent in other algal branches, DTD2 can be identified in plants from land plant ancestors-Charophytes onwards. DTD2 is the only gene that has only archaeal origin among the genes ascribed for architectural and genomic innovations that happened in the land plant ancestors. The work has uncovered an important gene transfer event from methanogenic archaea to the charophytes in the oldest terrestrial ecosystem bog that contains excess of D-amino acids and deprived of oxygen.
Peel-1negative selection promotes screening-free CRISPR-Cas9 genome editing inCaenorhabditis elegans
Authors: McDiarmid Troy A. , Au Vinci , Moerman Donald G. , Rankin Catharine H. 
Published: May 2020

AbstractImproved genome engineering methods that enable automation of large and precise edits are essential for systematic investigations of genome function. We adaptedpeel-1negative selection to an optimized Dual-Marker Selection (DMS) cassette protocol for CRISPR-Cas9 genome engineering inCaenorhabditis elegansand observed robust increases in multiple measures of efficiency that were consistent across injectors and four genomic loci. The use of Peel-1-DMS selection killed animals harboring transgenes as extrachromosomal arrays and spared genome edited integrants, often circumventing the need for visual screening to identify genome edited animals. To demonstrate the applicability of the approach, we created deletion alleles in the putative proteasomal subunitpbs-1and the uncharacterized geneK04F10.3and used machine vision to automatically characterize their phenotypic profiles, revealing homozygous essential and heterozygous behavioral phenotypes. These results provide a robust and scalable approach to rapidly generate and phenotype genome edited animals without the need for screening or scoring by eye.Author summaryThe ability to directly manipulate the genome and observe the resulting effects on the traits of an organism is a powerful approach to investigate gene function. CRISPR-based approaches to genome engineering have revolutionized such functional studies across model organisms but still face major challenges that limit the scope and complexity of projects that can be achieved in practice. Automating genome engineering and phenotyping would enable large-scale investigations of genome function in animals. Here, we describe the adaptation ofpeel-1negative selection to an optimized dual-marker selection cassette CRISPR-Cas9 genome engineering method inC. elegansand combine it with automated machine vision phenotyping to achieve functional studies without the need for screening or scoring by eye. To demonstrate the applicability of the approach, we generated novel deletion alleles in two understudied genes,pbs-1andK04F10.3,and used machine vision to characterize their phenotypic profiles, revealing homozygous lethal and heterozygous behavioral phenotypes. Our results open the door to systematic investigations of genome function in this model organism.
Characterization of two novel EF-hand proteins identifies a clade of putative Ca2+-binding protein specific to the Ambulacraria
Authors: Soto-Acabá Arisnel , Ortíz-Pineda Pablo A. , García-Arrarás José E. 
Published: May 2020

AbstractIn recent years, transcriptomic databases have become one of the main sources for protein discovery. In our studies of nervous system and digestive tract regeneration in echinoderms, we have identified several transcripts that have attracted our attention. One of these molecules corresponds to a previously unidentified transcript (Orpin) from the sea cucumberHolothuria glaberrimathat appeared to be upregulated during intestinal regeneration. We have now identified a second highly similar sequence and analyzed the predicted proteins using bioinformatics tools. Both sequences have EF-hand motifs characteristic of calcium-binding proteins (CaBPs) and N-terminal signal peptides. Sequence comparison analyses such as multiple sequence alignments and phylogenetic analyses only showed significant similarity to sequences from other echinoderms or from hemichordates. Semi-quantitative RT-PCR analyses revealed that transcripts from these sequences are expressed in various tissues including muscle, haemal system, gonads, and mesentery. However, contrary to previous reports, there was no significant differential expression in regenerating tissues. Nonetheless, the identification of unique features in the predicted proteins suggests that these might comprise a novel subfamily of EF-hand containing proteins specific to the Ambulacraria clade.
Influence of the artificial sodium saccharin sweetener Sucram®on the microbial community composition in the rumen content and attached to the rumen epithelium in dairy cattle: A pilot study
Authors: Koester Lucas R. , Anderson Chiron J. , Cortes Bienvenido W. , Lyte Mark , Schmitz-Esser Stephan 
Published: May 2020

AbstractThe products of rumen microbial fermentations are considered essential for animal growth and performance. Changes in these microbial communities can have major effects on animal growth and performance. Saccharin-based artificial sweeteners can be included in livestock diets to increase palatability and encourage feed intake. Despite the importance of the rumen microbial fermentation, little or no research is available regarding how saccharin-based artificial sweeteners affect rumen content and rumen epithelial microbial communities. The aim of this study was to identify changes in both the rumen content and rumen epithelial microbial communities in response to the supplementation of Sucram®, a sodium-saccharin-based sweetener (Pancosma S.A./ADM Groups, Rolle, Switzerland) during standard, non-stress conditions using 16SrRNA gene amplicon sequencing.The rumen epithelial and rumen content microbiota of five Holstein-Friesian milking dairy cattle were compared before (baseline, BL) and after a 28-day supplementation of Sucram®. Illumina MiSeq-based 16S rRNA gene sequencing was conducted, and community analysis revealed significant changes in the abundance of specific phylotypes when comparing BL to Sucram®experimental groups. Sucram®did not have a significant effect on overall rumen microbial community structure between experimental groups. Statistically significant changes in microbial community composition following Sucram®supplementation were observed most consistently across a number of bacterial taxa in the rumen epithelium, while fewer changes were seen in the rumen content. Predicted genomic potentials of several significantly different OTUs were mined for genes related to feed efficiency and saccharin degradation. Operational taxonomic units (OTUs) classified asPrevotellaandSharpeawere significantly (p<0.05) increased in samples supplemented with Sucram®, whereas a reduction in abundance was seen for OTUs classified asTreponema,Leptospiraceae,Ruminococcusand methanogenic archaea. This is the first study to report an effect of Sucram®on ruminant microbial communities, suggesting possible beneficial impacts of Sucram®on animal health and performance that may extend beyond increasing feed palatability.
Identification of French Guiana anopheline mosquitoes by MALDI-TOF MS profiling using protein signatures from two body parts
Authors: Briolant Sébastien , de Melo Costa Monique , Nguyen Christophe , Dusfour Isabelle , de Santi Vincent Pommier , Girod Romain , Almeras Lionel 
Published: May 2020

AbstractIn French Guiana, the malaria, a parasitic infection transmitted byAnophelinemosquitoes, remains a disease of public health importance. To prevent malaria transmission, the main effective way remainsAnophelescontrol. For an effective control, accurateAnophelesspecies identification is indispensable to distinguish malaria vectors from non-vectors. Although, morphological and molecular methods are largely used, an innovative tool, based on protein pattern comparisons, the Matrix Assisted Laser Desorption / Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) profiling, emerged this last decade for arthropod identification. However, the limited mosquito fauna diversity of reference MS spectra remains one of the main drawback for it large usage. The aim of the present study was then to create and to share reference MS spectra for the identification of French GuianaAnophelinespecies. A total of eight distinctAnophelesspecies, among which four are malaria vectors, were collected in 6 areas. To improveAnophelesidentification, two body parts, legs and thoraxes, were independently submitted to MS for the creation of respective reference MS spectra database (DB). This study underlined that double checking by MS enhanced theAnophelesidentification confidence and rate of reliable classification. The sharing of this reference MS spectra DB should made easierAnophelesspecies monitoring in endemic malaria area to help malaria vector control or elimination programs.
Plant Co-expression Annotation Resource: a webserver for identifying targets for genetically modified crop breeding pipelines
Authors: Viana Marcos José Andrade , Zerlotini Adhemar , de Alvarenga Mudadu Mauricio 
Published: May 2020

ABSTRACTBackgroundThe development of genetically modified crops (GM) includes the discovery of candidate genes through bioinformatics analysis using genomics data, gene expression, and others. Proteins of unknown function (PUFs) are interesting targets for GM crops breeding pipelines for the novelty associated to such targets and also to avoid copyright protections. One method of inferring the putative function of PUFs is by relating them to factors of interest such as abiotic stresses using orthology and co-expression networks, in a guilt-by-association manner.ResultsIn this regard, we have downloaded, analyzed, and processed genomics data of 53 angiosperms, totaling 1,862,010 genes and 2,332,974 RNA. Diamond and InterproScan were used to discover 72,266 PUFs for all organisms. RNA-seq datasets related to abiotic stresses were downloaded from NCBI/GEO. The RNA-seq data was used as input to the LSTrAP software to construct co-expression networks. LSTrAP also created clusters of transcripts with correlated expression, whose members are more probably related to the molecular mechanisms associated to abiotic stresses in the plants. Orthologous groups were created (OrhtoMCL) using all 2,332,974 proteins in order to associate PUFs to abiotic stress related clusters of co-expression and therefore infer their function in a guilt-by-association manner.ConclusionA freely available web resource named “Plant Co-expression Annotation Resource” (https://www.machado.cnptia.embrapa.br/plantannot),Plantannot, was created to provide indexed queries to search for PUF putatively associated to abiotic stresses. The web interface also allows browsing, querying and retrieving of public genomics data from 53 plants. We hopePlantannotto be useful for researchers trying to obtain novel GM crops resistant to climate change hazards.