bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-based reclassification of Azospirillum brasilense Az39 as the type strain of Azospirillum argentinense sp. nov.
Authors: dos Santos Ferreira Natália , Coniglio Anahí , Puente Mariana , Sant’Anna Fernando Hayashi , Maroniche Guillermo , García Julia , Molina Romina , Nievas Sofia , Volpiano Camila Gazolla , Ambrosini Adriana , Passaglia Luciane M. P. , Pedraza Raul O. , Reis Verônica Massena , Zilli Jerri Édson , Cassan Fabricio 
Published: August 2022

Strain Az39T of

Azospirillum

is a diazotrophic plant growth-promoting bacterium isolated in 1982 from the roots of wheat plants growing in Marcos Juárez, Córdoba, Argentina. It produces indole-3-acetic acid in the presence of l-tryptophan as a precursor, grows at 20–38 °C (optimal 38 °C), and the cells are curved or spiral-shaped, with diameters ranging from 0.5–0.9 to 1.8–2.2 µm. They contain C16 : 0, C18 : 0 and C18 : 1
ω7c/ω6c as the main fatty acids. Phylogenetic analysis of its 16S rRNA gene sequence confirmed that this strain belongs to the genus

Azospirillum

, showing a close relationship with

Azospirillum baldaniorum

Sp245T,

Azospirillum brasilense

Sp7T and

Azospirillum formosense

CC-Nfb-7T. Housekeeping gene analysis revealed that Az39T, together with five strains of the genus (Az19, REC3, BR 11975, MTCC4035 and MTCC4036), form a cluster apart from

A. baldaniorum

Sp245T,

A. brasilense

Sp7T and

A. formosense

CC-Nfb-7T. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) between Az39T and the aforementioned type strains revealed values below 96 %, the circumscription limit for the species delineation (ANI: 95.3, 94.1 and 94.0 %; dDDH: 62.9, 56.3 and 55.6 %). Furthermore, a phylogeny evaluation of the core proteome, including 809 common shared proteins, showed an independent grouping of Az39T, Az19, REC3, BR 11975, MTCC4035 and MTCC4036. The G+C content in the genomic DNA of these six strains varied from 68.3 to 68.5 %. Based on the combined phylogenetic, genomic and phenotypic characterization presented here, we consider that strain Az39T, along with strains Az19, REC3, BR 11975, MTCC4035 and MTCC4036, are members of a new

Azospirillum

species, for which the name Azospirillum argentinense sp. nov. is proposed. The type strain is Az39T (=LBPCV39T=BR 148428T=CCCT 22.01T).
Alizarin Red fluorescence imaging for nano calcification
Authors: Coralli Caterina Vanelli , Xue Jing , Chester Adrian H , Bertazzo Sergio 
Published: August 2022

AbstractThe formation of calcium phosphate (calcification) has been observed in a variety of healthy and diseased tissues and contributes to a wide range of pathologies. In physiological and pathological mechanisms, calcification begins at the nano scale and then develops into structures that range from a few micrometres to several centimetres. Fluorescence microscopy can be an efficient way to visualise such early calcification and its interaction with cells and proteins. The limited shelf life and high cost of commercial dyes for staining calcification, however, can be problematic when using this imaging method. Here, we aim to evaluate the effectiveness and stability of Alizarin Red (AR) as a fluorescent staining agent for nano and micro calcified structures. Our results show that AR staining for nano and micro calcified structures is a simple, reliable, effective, and quite inexpensive method to visualize calcification at the nano and micro scale in biological samples.
Eya-controlled affinity between cell lineages drives tissue self-organization during Drosophila oogenesis
Authors: Weichselberger Vanessa , Dondl Patrick , Classen Anne-Kathrin 
Published: August 2022

AbstractThe cooperative morphogenesis of cell lineages underlies the development of functional units and organs. To study mechanisms driving the coordination of lineages, we investigated soma-germline interactions during oogenesis. From invertebrates to vertebrates, oocytes develop as part of a germline cyst that consists of the oocyte itself and so-called nurse cells, which feed the oocyte and are eventually removed. The enveloping somatic cells specialize to either facilitate oocyte maturation or nurse cell removal, which makes it essential to establish the right match between germline and somatic cells. We uncover that the transcriptional regulator Eya, expressed in the somatic lineage, controls bilateral cell-cell affinity between germline and somatic cells in Drosophila oogenesis. Employing functional studies and mathematical modelling, we show that differential affinity proportional to Eya expression and the resulting forces drive somatic cell redistribution over the germline surface and control oocyte growth to match oocyte and nurse cells with their respective somatic cells. Thus, our data demonstrate that differential affinity between cell lineages is sufficient to drive the complex assembly of inter-lineage functional units and underlies tissue self-organization during Drosophila oogenesis.
Investigating manta ray collective movements via drone surveys
Authors: Perryman Robert J. Y. , Brown Culum , Pasian Nicolò , Ward Ashley J. W. , Kent M. I. A. 
Published: August 2022

AbstractDetailed observational research on free-ranging species of marine megafauna is required to understand their behavioural ecology, including how groups respond to environmental and anthropogenic pressures. New technologies are opening up potential for research on these species in the wild, especially on group-based and collective behaviours. Reef manta rays (Mobula alfredi) are socially interactive elasmobranchs that form groups in coastal reef habitats. Collective behaviours are likely important to their fitness, but may be disturbed by humans. Using small, remotely-piloted drones, we performed aerial observations of manta ray groups in Raja Ampat, West Papua. We empirically quantified patterns of collective movement including relative spatial positions, alignment, speed and leadership positions of conspecifics. We found unique patterns of spatial positioning, alignment and leadership, including differences between sexes, and high levels of local attraction, which were suggestive of distinct collective behaviour states. We suggest that ‘rules of interaction’ in manta rays vary at the individual level and can shift depending on local environmental and social conditions. Leader-follower behaviour likely has broad importance to cohesive movement and social behaviour inM. alfredi. We suggest that further studies on manta ray movement should consider utilising models of collective motion that capture group-level behavioural processes.
A Gene Expression Atlas of Lohmann White Chickens
Authors: Zhang Jiannan , Wang Xinglong , Lv Can , Wan Yiping , Zhang Xiao , Li Juan , Wang Yajun 
Published: August 2022

AbstractChicken (Gallus gallus domesticus) as one of the most economically important farm animals plays a major role in human food production and has been widely used as a key animal model that is presumed to be typical of avian and generally applicable to mammals in studies of developmental biology, virology, oncogenesis, and immunology. To get a better understanding of avian biology, global analysis of gene expression across multiple tissues is needed, which will aid genome annotation and support functional annotation of avian genes. We present a large-scale RNA-Seq dataset representing all the major organ systems from adult Lohmann White domesticus chickens. An open-access chicken tissue gene expression atlas (TGEA) (chickenatlas.avianscu.com) is presented based on the expression of 224 samples across 38 well-defined chicken tissues. Network-based cluster analysis of this dataset grouped genes according to dimensionality reduction and whole-body co-expression patterns, which were used to infer the function of uncharacterized genes from their co-expression with genes of known function. We describe the distribution and tissue specificity of 21,430 genes present in the chicken gene expression atlas and assign those signatures, where possible, to specific tissue populations or pathways. To better understand the functions of GPCRs in avian, we quantified the transcript levels of 254 nonodorant GPCRs in all tissues. Cluster analysis placed many GPCRs into expected anatomical and functional groups and predicted previously unidentified roles for less-studied receptors. We also produced this atlas to analyze male and female mRNA expression profiles in chicken somatic and gonad tissues. Our analyses uncovered numerous cases of somatic sex-biased mRNA expression, with the largest proportion found in the chicken pineal body, pituitary, and liver. This high-resolution gene expression atlas for chickens is, to our knowledge, the largest transcriptomic dataset of any avian to date. It provides a resource to improve the annotation of the current reference genome for chicken, presenting a model transcriptome for avian, and can be used as a resource for predicting roles for incompletely characterized GPCRs, exploring sex-biased specific gene expression, and for other purposes.
Physiological responses to drought stress and recovery reflect differences in leaf function and anatomy among grass lineages
Authors: Bachle Seton , Zaricor Marissa , Griffith Daniel , Qui Fan , Still Christopher J , Ungerer Mark C , Nippert Jesse B 
Published: August 2022

ABSTRACTGrasses are cosmopolitan, existing in many biome and climate types from xeric to tropical. Traits that control physiological responses to drought vary strongly among grass lineages, suggesting that tolerance strategies may differ with evolutionary history. Here, we withheld water from 12 species representing six tribes of grasses to compare how species respond to drought in different grass lineages. We measured physiological, morphological, and anatomical traits. Dominant lineages from tropical savannas, like Andropogoneae, tolerated drought due to above and belowground morphological traits (specific leaf area and root length, SLA and SRL), while temperate grasses in this study utilized conservative leaf physiology (gas exchange) and anatomy traits. Increased intrinsic water-use efficiency coincided with a larger number of stomata, resulting in greater water loss (with inherently greater carbon gain) and increased drought sensitivity. Inherent leaf and root economic strategies impacting drought response were observed in all species, resulting in either high SLA or SRL, but not both. Our results indicate that grasses subjected to severe drought were influenced by anatomical traits (e.g., number of stomata and xylem area) and similar within lineages. In addition, grasses recovered at least 50% of physiological functioning across all lineages and 92% within Andropogoneae species, illustrating how drought can influence functional responses across diverse grass lineages.
SpliceAI-10k calculator for the prediction of pseudoexonization, intron retention, and exon deletion
Authors: Canson Daffodil M. , Davidson Aimee L. , de la Hoya Miguel , Parsons Michael T. , Glubb Dylan M. , Kondrashova Olga , Spurdle Amanda B. 
Published: August 2022

ABSTRACTSummarySpliceAI is a widely used splicing prediction tool and its most common application relies on the maximum delta score to assign variant impact on splicing. We developed the SpliceAI-10k calculator (SAI-10k-calc) to extend use of this tool to predict: the splicing aberration type including pseudoexonization, intron retention, partial exon deletion, and (multi)exon skipping using a 10 kb analysis window; the size of inserted or deleted sequence; the effect on reading frame; and the altered amino acid sequence.SAI-10k-calc has 95% sensitivity and 96% specificity for predicting variants that impact splicing, computed from a control dataset of 1,212 single nucleotide variants (SNVs) with curated splicing assay results. Notably, it has high performance (≥84% accuracy) for predicting pseudoexon and partial intron retention. The automated amino acid sequence prediction allows for efficient identification of variants that are expected to result in mRNA nonsense-mediated decay or translation of truncated proteins.Availability and implementationSAI-10k-calc is implemented in R (https://github.com/adavi4/SAI-10k-calc) and also available as a Microsoft Excel spreadsheet. Users can adjust the default thresholds to suit their target performance values.Supplementary informationSupplementary data are available online.
Risk of Myocarditis after Covid-19 mRNA Vaccination: Impact of Booster Dose and Dosing Interval
Authors: Le Vu Stéphane , Bertrand Marion , Jabagi Marie-Joëlle , Botton Jérémie , Weill Alain , Dray-Spira Rosemary , Zureik Mahmoud 
Published: August 2022

AbstractCovid-19 mRNA vaccines have been shown to be associated with a short-term increased risk of myocarditis, with the highest risk observed after the second dose compared to the first. The extent of the risk associated with more distant booster doses is less clear. Here, we aimed to assess the relation between dosing interval and the risk of myocarditis, for both the two-dose primary series and the third dose (first booster). Extending our previous matched case-control study, we included 4 890 cases of myocarditis aged 12 or more and 48 900 controls up to January 31, 2022. We found that the risk of myocarditis remained elevated after the booster dose and that longer intervals between each consecutive dose (including booster doses) may decrease the occurrence of vaccine-associated myocarditis.
Hypergraph factorisation for multi-tissue gene expression imputation
Authors: Viñas Ramon , Joshi Chaitanya K. , Georgiev Dobrik , Dumitrascu Bianca , Gamazon Eric R. , Liò Pietro 
Published: August 2022

AbstractIntegrating gene expression across scales and tissues is crucial for understanding the biological mechanisms that drive disease and characterise homeostasis. However, traditional multi-tissue integration methods cannot handle uncollected tissues or rely on genotype information, which is subject to privacy concerns and often unavailable. To address these challenges, we present HYFA (HypergraphFactorisation), a novel method for joint imputation of multi-tissue and cell-type gene expression. HYFA imputes tissue-specific gene expression via a specialised graph neural network operating on a hypergraph of individuals, metagenes, and tissues. HYFA is genotype- agnostic, supports a variable number of collected tissues per individual, and imposes strong inductive biases to leverage the shared regulatory architecture of tissues. In performance comparison on data from the Genotype Tissue Expression project, HYFA achieves superior performance over existing transcriptome imputation methods, especially when multiple reference tissues are available. Through transfer learning on a paired single-nucleus RNA-seq (snRNA-seq) dataset, we further show that HYFA can accurately resolve cell-type signatures from bulk gene expression, highlighting the method’s ability to leverage gene expression programs underlying cell-type identity, even in tissues that were never observed in the training set. Using Gene Set Enrichment Analysis, we find that the metagenes learned by HYFA capture information about known biological pathways. Notably, the HYFA-imputed dataset can be used to identify regulatory genetic variations (eQTLs), with substantial gains over the original incomplete dataset. Our framework can accelerate effective and scalable integration of tissue and cell-type gene expression biorepositories.
Streptococcus suis infection on European farms is associated with an altered tonsil microbiome and resistome
Authors: Fredriksen Simen , Neila-Ibáñez Carlos , Hennig-Pauka Isabel , Guan Xiaonan , Dunkelberger Jenelle , de Oliveira Isabela Fernandes , Ferrando Maria Laura , Correa-Fiz Florencia , Aragon Virginia , Boekhorst Jos , van Baarlen Peter , Wells Jerry M. 
Published: August 2022

AbstractStreptococcus suisis a Gram-positive opportunistic pathogen causing systemic disease in piglets around weaning age. The factors predisposing to disease are not known. We hypothesised that the tonsillar microbiota might influence disease risk via colonisation resistance and/or co-infections. We conducted a cross-sectional case-control study within outbreak farms complemented by selective longitudinal sampling and comparison with control farms without disease occurrence. We found a small but significant difference in tonsil microbiota composition between case and control piglets (n=45+45). Variants of putative commensal taxa, includingRothia nasimurium, were reduced in abundance in case piglets compared to asymptomatic controls. Case piglets had higher relative abundances ofFusobacterium gastrosuis, Bacteroides heparinolyticus, and unculturedPrevotellaandAlloprevotellaspecies. Despite case-control pairs receiving equal antimicrobial treatment, case piglets had higher abundance of antimicrobial resistance genes (ARGs) conferring resistance to antimicrobial classes used to treatS. suis. This might be an adaption of disease-associated strains to frequent antimicrobial treatment.
Rapid polygenic adaptation in a wild population of ash trees under a novel fungal epidemic
Authors: Metheringham Carey L. , Plumb William J. , Flynn William R. M. , Stocks Jonathan J. , Kelly Laura J. , Gorriz Miguel Nemesio , Grieve Stuart W. D. , Moat Justin , Lines Emily R. , Buggs Richard J. A. , Nichols Richard A. 
Published: August 2022

AbstractRapid evolution via small shifts in allele frequencies at thousands of loci are a long- standing neo-Darwinian prediction but are hard to characterize in the wild. European ash tree (Fraxinus excelsior) populations have recently come under strong selection by the invasive fungal pathogenHymenoscyphus fraxineus. Using genomic prediction models based on field trial phenotypes and 7,985 loci, we show a shift in genomically estimated breeding values in an ancient woodland, between adult trees established before the epidemic started and juvenile trees established since. Using simulations, we estimate that natural selection has eliminated 31% of the juvenile population. Thus, we document a highly polygenic heritable micro-evolutionary adaptive change over a single generation in the wild.One-Sentence SummarySubtle changes at thousands of genomic locations in one generation allow woodland trees to respond to a new selective pressure
DNA Repair Strategy Sets Transposon Mobilization Rates in Caenorhabditis elegans
Authors: Chang Cindy , Pagano Daniel J. , Lowe David D. , Kennedy Scott 
Published: August 2022

AbstractTransposons are parasitic nucleic acids that threaten genome integrity in all cells. In the metazoan model organism Caenorhabditis elegans, DNA transposons are active in the soma where they are reported to exhibit mobilization rates ≅1000 fold higher than in germ cells. How and why DNA transposons might be so highly active in the C. elegans soma is a mystery. To better understand this question, we constructed reporter genes that label cells in which Tc1 has mobilized with fluorescent protein. The reporters recapitulate the known properties of DNA transposons in C. elegans and allow transposon activity to be monitored in intact, living animals. Using these reporters, we identify cytoplasmic and nuclear factors that limit transposition in the germline. Interestingly, none of these factors limit transposition in the soma. Rather, we identify a gene (nhj-1/scb-1), which we show is required for 99.9% of Tc1 mobilization events in somatic tissues, but does not influence mobilization in the germline. nhj-1/scb-1 encodes a nematode-specific component of the non-homologous end joining (NHEJ) DNA repair machinery. Mutations in the other components of the NHEJ machinery (cku-70, cku-80, and lig-4) also suppress Tc1 mobilization in the C. elegans soma by ≅1000 fold. The data show that the use of NHEJ to repair transposon-induced DNA breaks in the soma dramatically increases the rate of transposon mobilization in this tissue. And because C. elegans germ cells use homology-based repair, and not NHEJ, to fix transposon-induced breaks, we propose that the 1000-fold difference in transposon mobility reported for the C. elegans soma and germline can, in large part, be explained by tissue-specific differences in DNA repair strategy.Author SummaryTransposons are common parasitic genetic elements that threaten all genomes. For example, half of the human genome is made up of transposons. Transposon mobilization can disrupt gene function, causing disease, so transposon activity needs to be tightly regulated to prevent harm to the host. Transposons are typically less active in the soma than in the germline, because somatic transposition benefits neither host or transposon. Surprisingly, in the nematode model organism Caenorhabditis elegans, transposons are reported to be 1000-fold more active in the soma than the germline. Here, we develop a system to investigate transposon regulation in an intact live animal, and show that, in large part, tissue-specific differences in transposon activity in C. elegans is due to the use of different DNA repair pathways by these tissues, highlighting the importance of DNA repair strategy in determining outcomes of transposon excision events. Given that DNA repair factors have been linked to transposon regulation in other eukaryotes, we propose that DNA repair choice likely contributes to transposon mobilization in all eukaryotes.
ObiWan-Microbi: OMERO-based integrated workflow for annotating microbes in the cloud
Authors: Seiffarth Johannes , Scherr Tim , Wollenhaupt Bastian , Neumann Oliver , Scharr Hanno , Kohlheyer Dietrich , Mikut Ralf , Nöh Katharina 
Published: August 2022

AbstractSummaryReliable deep learning segmentation for microfluidic live-cell imaging requires comprehensive ground truth data. ObiWan-Microbi is a microservice platform combining the strength of state-of-the-art technologies into a unique integrated workflow for data management and efficient ground truth generation for instance segmentation, empowering collaborative semi-automated image annotation in the cloud.Availability and ImplementationObiWan-Microbi is open-source and available under the MIT license at https://github.com/hip-satomi/ObiWan-Microbi, along documentation and usage examples.Contactk.noeh@fz-juelich.deSupplementary informationSupplementary data are available online.