bluuebunny/crossref_metadata_2025_split huggingface dataset:
DegeneratingDrosophilaLarval Epidermal Cells Drive Thorax Closure
Authors: Athilingam Thamarailingam , Parihar Saurabh Singh , Bhattacharya Rachita , Rizvi Mohd. Suhail , Kumar Amit , Sinha Pradip 
Published: September 2020

AbstractAdult thorax formation inDrosophilabegins during pre-pupal development by fusion of its two contralateral progenitor halves, the heminotal epithelia (HE). HEs migrate and replace an underlying cell layer of thoracic larval epidermal cells (LECs) during a morphogenetic process called thorax closure. The LEC layer has so far been proposed to be a passive substrate over which HEs migrate before their zipping. By contrast, here we show that the pull forces generated within the LEC layer drive HE migration. During thorax closure, the LECs display actomyosin-mediated contraction, via enrichment of non-muscle myosin-II and actin, besides squamous-to-pseudostratified columnar epithelial transition and tissue shrinkage. This shrinkage of the LEC layer is further accompanied by cell extrusion and death, that prevent overcrowding of LECs, thereby promoting further shrinkage. The pull forces thus generated by the shrinking LEC layer are then relayed to the HEs by their mutual adhesions via βPS1 (Mys) and αPS3 (Scb) integrins. Suppression of cell death in the LEC layer by a gain of p35 leads to cell overcrowding, which impedes HE migration and zipping. Further, knockdown ofsqh, the light chain of non-muscle myosin II, in LECs or integrins (mysorscb) in either the LEC layer or in the HEs, or both abrogate thorax closure. Mathematical modeling also reveals the biophysical underpinnings of the forces that drive this tissue closure process wherein a degenerating LEC layer mediates its succession by the future adult primodia. These essential principles of thorax closure appear ancient in origin and recur in multiple morphogenetic contexts and tissue repair.
A comprehensive, FAIR file format for neuroanatomical structure modeling
Authors: Sullivan A. E. , Tappan S. J. , Angstman P. J. , Rodriguez A. , Thomas G. C. , Hoppes D. M. , Abdul-Karim M. A. , Heal M. L. , Glaser J. R. 
Published: September 2020

AbstractWith advances in microscopy and computer science, the technique of digitally reconstructing, modeling, and quantifying microscopic anatomies has become central to many fields of biological research. MBF Bioscience has chosen to openly document their digital reconstruction file format, Neuromorphological File Specification (4.0), available atwww.mbfbioscience.com/filespecification(Angstman et al. 2020). One of such technologies, the format created and maintained by MBF Bioscience is broadly utilized by the neuroscience community. The data format’s structure and capabilities have evolved since its inception, with modifications made to keep pace with advancements in microscopy and the scientific questions raised by worldwide experts in the field. More recent modifications to the neuromorphological data format ensure it abides by the Findable, Accessible, Interoperable, and Reusable (FAIR) data standards promoted by the International Neuroinformatics Coordinating Facility (INCF; Wilkinson et al. 2016). The incorporated metadata make it easy to identify and repurpose these data types for downstream application and investigation. This publication describes key elements of the file format and details their relevant structural advantages in an effort to encourage the reuse of these rich data files for alternative analysis or reproduction of derived conclusions.
Chronic stress induces sex-specific functional and morphological alterations in cortico-accumbal and cortico-tegmental pathways
Authors: Bittar Thibault P. , Pelaez Mari Carmen , Silva Jose Cesar Hernandez , Quessy Francis , Lavigne Andrée-Anne , Morency Daphnée , Blanchette Léa-Jeanne , Arsenault Eric , Cherasse Yoan , Seigneur Josée , Timofeev Igor , Sephton Chantelle F. , Proulx Christophe D. , Labonté Benoit 
Published: September 2020

AbstractBackgroundThe medial prefrontal cortex (mPFC) is part of a complex circuit controlling stress responses by sending projections to different limbic structures including the nucleus accumbens (NAc) and ventral tegmental area (VTA). However, the impact of chronic stress on NAc- and VTA-projecting mPFC neurons is still unknown and the distinct contribution of these pathways to stress responses in males and females is unclear.MethodsBehavioral stress responses were induced by 21 days of chronic variable stress (CVS) in male and female C57BL6 mice. An inter-sectional viral approach was used to label both pathways and assess the functional, morphological, and transcriptional adaptations in NAc- and VTA-projecting mPFC neurons in stressed males and females. Using chemogenetic approaches, we modified neuronal activity of NAc-projecting mPFC neurons to decipher their contribution to stress phenotypes.ResultsCVS induced depressive-like behaviors in males and females. NAc- and VTA-projecting mPFC neurons exhibited sex-specific functional, morphological, and transcriptional alterations. The functional changes were more severe in females in NAc-projecting mPFC neurons while males exhibited more drastic reductions in dendritic complexity in VTA-projecting mPFC neurons after CVS. Finally, chemogenetic overactivation of the cortico-accumbal pathway triggered anxiety and behavioral despair in both sexes while its inhibition rescued the phenotype only in females.ConclusionsOur results suggest that by changing the activity of transcriptional programs controlling neuronal plasticity, CVS interferes with the morphological and synaptic properties of the cortico-accumbal and tegmental pathways differently in males and females contributing to the expression of anxiety and depressive-like behaviors distinctly in a sex-specific fashion.
Quantification of extracellular vesicles with unaltered surface membranes using an internalized oligonucleotide tracer and droplet digital PCR applied to modeling ofin vivokinetics
Authors: De Luca Thomas , Stratford Robert E. , Edwards Madison E. , Ferreira Christina R. , Benson Eric A. 
Published: September 2020

AbstractExtracellular vesicles (EVs) continue to attract interest for their potential role in targeted therapeutics and as biomarkers of disease and drug response. In order to achieve clinical utility, it is important to determine the pharmacokinetic parameters of candidate EVs during preclinical development usingin vivoanimal models. To date, no methods exist for studying EV kinetics without modification to surface ligands that may affect normal behavior. Here we introduce an accessible method for labeling and quantifying EVs administered to conscious animals, without disrupting endogenous ligands. Our method relies upon established laboratory techniques and can be tailored to a variety of biological questions. Digital PCR is leveraged to detect a non-homologous oligonucleotide tracer introduced into the vesicles, allowing for quantification over a wide dynamic range. Using an application of this method, we found differences in thein vivokinetics of EVs from three different cell types using non-linear mixed effects modeling. We propose that this method will provide a complementary approach for the of study EV ligand-receptor interactions in the context of EV uptake and targeted therapeutics.
Enrichment of novelVerrucomicrobia, BacteroidetesandKrumholzibacteriain an oxygen-limited, methane- and iron-fed bioreactor inoculated with Bothnian Sea sediments
Authors: Martins Paula Dalcin , de Jong Anniek , Lenstra Wytze K. , van Helmond Niels A. G. M. , Slomp Caroline P. , Jetten Mike S. M. , Welte Cornelia U. , Rasigraf Olivia 
Published: September 2020

AbstractMicrobial methane oxidation is a major biofilter preventing larger emissions of this powerful greenhouse gas from marine coastal areas into the atmosphere. In these zones, various electron acceptors such as sulfate, metal oxides, nitrate or oxygen can be utilized. However, the key microbial players and mechanisms of methane oxidation are poorly understood. In this study, we inoculated a bioreactor with methane- and iron-rich sediments from the Bothnian Sea in order to investigate microbial methane and iron cycling under low oxygen concentrations. Using metagenomics, we observed shifts in the microbial community over approximately 2.5 years of bioreactor operation. Marker genes for methane and iron cycling, as well as respiratory and fermentative metabolism, were investigated. Metagenome-assembled genomes representing novelVerrucomicrobia, BacteroidetesandKrumholzibacteriawere recovered and revealed potential for methane oxidation, organic matter degradation, and iron cycling, respectively. This work brings new insights into the identity and metabolic versatility of microorganisms that may be members of such functional guilds in coastal marine sediments and highlights that the methane biofilter in these sediments may be more diverse than previously appreciated.ImportanceDespite the essential role of microorganisms in preventing most methane in the ocean floor to reach the atmosphere, comprehensive knowledge on the identity and the mechanisms employed by these microorganisms is still lacking. This is problematic because such information is needed to understand how the ecosystem functions in the present and how microorganisms may respond to climate change in the future. Here, we enriched and identified novel taxa potentially involved in methane and iron cycling in an oxygen-limited bioreactor inoculated with methane- and iron-rich coastal sediments. Metagenomic analyses provided hypotheses about the mechanisms they may employ, such as the use of oxygen at very low concentrations. The implication of our results is that in more shallow sediments, where oxygen-limited conditions are present, the methane biofilter is potentially composed of novel, metabolically versatileVerrucomicrobiathat could contribute to mitigating methane emissions from coastal marine zones.
Basolateral amygdala parvalbumin neurons report aversive prediction error to constrain fear learning
Authors: Yau Joanna Oi-Yue , Chaichim Chanchanok , Power John M. , McNally Gavan P. 
Published: September 2020

AbstractAnimals, including humans, use prediction error to guide learning about danger in the environment. The basolateral amygdala (BLA) is obligatory for this learning and BLA excitatory projection neurons are instructed by aversive prediction error to form fear associations. Complex networks of inhibitory interneurons, dominated by parvalbumin (PV) expressing GABAergic neurons, form the intrinsic microcircuitry of the BLA to control projection neuron activity. Whether BLA PV interneurons are also sensitive to prediction error and how they use this error to control fear learning remains unknown. We used PV cell-type specific recording and manipulation approaches in male transgenic PV-Cre rats to address these issues. We show that BLA PV neurons control fear learning about aversive events but not learning about their omission. Furthermore, during fear learning BLA PV neurons express the activity signatures of aversive prediction error: greater activity to unexpected than expected aversive events and greater activity to better rather than poorer predictors of these events. Crucially, we show that BLA PV neurons act to limit fear learning across these variations in prediction error. Together, this demonstrates that prediction error instructs and regulates BLA fear association formation in a cell-type specific manner. Whereas BLA projection neurons use prediction error signals to form and store fear associations, BLA PV interneurons use prediction error signals to constrain fear association formation.Significance StatementThe capacity to predict sources of danger in the environment is essential for survival. This capacity is supported by associative learning mechanisms that are triggered when the danger experienced is greater than the danger expected. Here we show that the activity of parvalbumin positive GABAergic interneurons in the rat basolateral amygdala neurons report this difference between the danger expected and the danger experienced and that they use this difference to limit the amount of fear which is learned.
A bacterial effector uncovers a metabolic pathway involved in resistance to bacterial wilt disease
Authors: Wang Yaru , Morcillo Rafael J. L. , Yu Gang , Zhao Achen , Xue Hao , Rufian Jose S. , Sang Yuying , Macho Alberto P. 
Published: September 2020

AbstractBacterial wilt caused by the soil-borne pathogenRalstonia solanacearumis a devastating disease worldwide. Upon plant colonization,R. solanacearumreplicates massively, causing plant wilting and death; collapsed infected tissues then serve as a source of inoculum. In this work, we show that the metabolic pathway mediated by pyruvate decarboxylases (PDCs), activated in response to low oxygen and involved in drought stress tolerance, contributes to resistance against bacterial wilt disease. Arabidopsis and tomato plants with deficient PDC activity are more susceptible to bacterial wilt, and treatment with either pyruvic acid or acetic acid (substrate and product of the PDC pathway, respectively) enhances resistance. An effector protein secreted byR. solanacearum, RipAK, interacts with PDCs and inhibits their oligomerisation and enzymatic activity. This work reveals a metabolic pathway involved in resistance to biotic and abiotic stresses, and a bacterial virulence strategy to promote disease and the completion of the pathogenic life cycle.
Why the COVID-19 pandemic is a traumatic stressor
Authors: Bridgland Victoria M. E. , Moeck Ella K. , Green Deanne M. , Swain Taylor L. , Nayda Diane , Matson Lucy A. , Hutchison Nadine P. , Takarangi Melanie K.T. 
Published: September 2020

AbstractThe COVID-19 pandemic does not fit into prevailing Post-traumatic Stress Disorder (PTSD) models, or diagnostic criteria, yet emerging research shows traumatic stress symptoms as a result of this ongoing global stressor. Current pathogenic event models focus on past, and largely direct, trauma exposure to certain kinds of life-threatening events. Nevertheless, among a sample of online participants (N= 1,040) in five western countries, we found participants had PTSD-like symptoms for events that had not happened and when participants had been directly (e.g., contact with virus)orindirectly exposed to COVID-19 (e.g., via media). Moreover, 13.2% of our sample were likely PTSD-positive, despite types of COVID-19 “exposure” (e.g., lockdown) not fitting DSM-5 criteria. The emotional impact of “worst” experienced/anticipated events best predicted PTSD-like symptoms. Our findings add to existing literature supporting apathogenic event memorymodel of traumatic stress.
Steady state evoked potential (SSEP) responses in the primary and secondary somatosensory cortices of anesthetized cats: nonlinearity characterized by harmonic and intermodulation frequencies
Authors: Kawashima Yota , Li Rannee , Chen Spencer Chin-Yu , Vickery Richard Martin , Morley John W. , Tsuchiya Naotsugu 
Published: September 2020

AbstractWhen presented with an oscillatory sensory input at a particular frequency,F[Hz], neural systems respond with the corresponding frequency,f[Hz], and its multiples. When the input includes two frequencies (F1andF2) and they are nonlinearly integrated in the system, responses at intermodulation frequencies (i.e.,n1*f1+n2*f2[Hz], wheren1andn2are non-zero integers) emerge. Utilizing these properties, the steady state evoked potential (SSEP) paradigm allows us to characterize linear and nonlinear neural computation performed in cortical neurocircuitry. Here, we analyzed the steady state evoked local field potentials (LFPs) recorded from the primary (S1) and secondary (S2) somatosensory cortex of anesthetized (ketamine-xylazine) cats while we presented slow (F1=23Hz) and fast (F2=200Hz) somatosensory vibration to the contralateral paw pads and digits. Over 9 experimental sessions, we recorded LFPs fromN=1620 andN=1008 bipolar-referenced sites in S1 and S2 using electrode arrays. Power spectral analyses revealed strong responses at 1) the fundamental (f1,f2), 2) its harmonic, 3) the intermodulation frequencies, and 4) broadband frequencies (50-150Hz). To compare the computational architecture in S1 and S2, we employed simple computational modeling. Our modeling results necessitate nonlinear computation to explain SSEP in S2 more than S1. Combined with our current analysis of LFPs, our paradigm offers a rare opportunity to constrain the computational architecture of hierarchical organization of S1 and S2 and to reveal how a large-scale SSEP can emerge from local neural population activities.
Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genusEmbletonia
Authors: Karmeinski Dario , Meusemann Karen , Goodheart Jessica A. , Schroedl Michael , Martynov Alexander , Korshunova Tatiana , Wägele Heike , Donath Alexander 
Published: September 2020

AbstractBackgroundCladobranch sea slugs represent roughly half of the biodiversity of soft-bodied, marine gastropod molluscs (Nudibranchia) on the planet. Despite their global distribution from shallow waters to the deep sea, from tropical into polar seas, and their important role in marine ecosystems and for humans (as bioindicators and providers of medical drug leads), the evolutionary history of cladobranch sea slugs is not yet fully understood. Here, we amplify the current knowledge on the phylogenetic relationships by extending the cladobranch and outgroup taxon sampling using transcriptome data.ResultsWe generated new transcriptome data for 19 species of cladobranch sea slugs and two additional outgroup taxa. We complemented our taxon sampling with previously published transcriptome data, resulting in a final supermatrix covering 56 species from all but one accepted cladobranch superfamilies. Transcriptome assembly using six different assemblers, selection of those assemblies providing the largest amount of potentially phylogenetically informative sites, and quality-driven compilation of data sets resulted in three different supermatrices: one with a full coverage of genes per species (446 single-copy protein-coding genes) and two with a less stringent coverage (667 genes with 98.9% partition coverage and 1,767 genes with 86% partition coverage, respectively). We used these supermatrices to infer statistically robust maximum-likelihood trees. All analyses, irrespective of the data set, indicate maximum statistical support for all major splits and phylogenetic relationships on family level. The only discordance between the inferred trees is the position ofEmbletonia pulchra. Extensive testing using Four-cluster Likelihood Mapping, Approximately Unbiased tests, and Quartet Scores revealed that its position is not due to any informative phylogenetic signal, but caused by confounding signal.ConclusionsOur data matrices and the inferred trees inferred can serve as a solid foundation for future work on the taxonomy and evolutionary history of Cladobranchia. The correct placement ofE. pulchra, however, proves challenging, even with large data sets. Moreover, quartet mapping shows that confounding signal present in the data is sufficient to explain the inferred position ofE. pulchra, again leaving its phylogenetic position as an enigma.
Mining the potential ofVRS1-5gene to raise barley grain yield
Authors: Shen Liping , Liu Yangyang , Sun Zhiwen , Wang Ziying , Zhang Lili , Cai Yu , Jiao Yuannian , Wu He , Shen Kuocheng , Yang Ping , Guo Zifeng 
Published: September 2020

AbstractVRS1-5genes determine spike row types during the early stages of spike development in barley (Hordeum vulgare), yet their functions for the determination of grain yield during the late stages of spike development are largely unknown. To assess the role ofVRS1-5genes in determining grain yield components, we sequencedVRS1-5genes from 894 worldwide barley accessions and measured 19 spike morphology traits in four environments. Single nucleotide polymorphism SNP markers and gene marker-based haplotypes forVRS1-5displayed close associations with spike morphology traits. We further developed a spatiote-temporal transcriptome atlas (255 samples) at 17 stages and five positions along the spike, that linked spike morphology to spikelet development and expression patterns ofVRS1-5genes. Phenotypic measurements demonstrated that mutations inVRS1-5suppress the initiation of spikelet primordia and, trigger spikelet abortion by increasing cytokinin content and improving sensitivity of spikelet primordia to cytokinin. Our integrated results illustrate how breeding can globally alter spike morphology through diversity at theVRS1-5genes, which show great potential in increasing barley grain yield.
Membrane binding controls ordered self-assembly of animal septins
Authors: Szuba Agata , Bano Fouzia , Iv François , Mavrakis Manos , Richter Ralf P. , Bertin Aurelie , Koenderink Gijsje H. 
Published: September 2020

AbstractSeptins are conserved cytoskeletal proteins that regulate cell cortex mechanics. The mechanisms of their interactions with the plasma membrane remain poorly understood. Here we show by cell-free reconstitution that membrane binding requires electrostatic interactions of septins with anionic lipids and promotes the ordered self-assembly of fly septins into filamentous meshworks. Transmission electron microscopy reveals that both fly and mammalian septins form arrays of single and paired filaments. Atomic force microscopy and quartz crystal microbalance demonstrate that the fly filaments form mechanically rigid, 12 to 18 nm thick, double layers of septins. By contrast, C-terminally truncated septin mutants form 4 nm thin monolayers, indicating that stacking requires the C-terminal coiled coils on DSep2 and Pnut subunits. Our work shows that membrane binding is required for fly septins to form ordered arrays of single and paired filaments and provides new insights into the mechanisms by which septins may regulate cell surface mechanics.
Humoral response to SARS-CoV-2 by healthy and sick dogs during COVID-19 pandemic in Spain
Authors: Perisé-Barrios Ana Judith , Tomeo-Martín Beatriz Davinia , Gómez-Ochoa Pablo , Delgado-Bonet Pablo , Plaza Pedro , Palau-Concejo Paula , González Jorge , Ortiz-Diez Gustavo , Meléndez-Lazo Antonio , Gentil Michaela , García-Castro Javier , Barbero-Fernández Alicia 
Published: September 2020

SummaryCOVID-19 is a zoonotic disease originated by SARS-CoV-2. Infection of animals with SARS-CoV-2 are being reported during last months, and also an increase of severe lung pathologies in domestic dogs has been detected by veterinarians in Spain. Therefore it is necessary to describe the pathological processes in those animals that show symptoms similar to those described in humans affected by COVID-19. The potential for companion animals contributing to the continued human-to-human disease, infectivity, and community spread is an urgent issue to be considered.Forty animals with pulmonary pathologies were studied by chest X-ray, ultrasound study, and computed tomography. Nasopharyngeal and rectal swab were analyzed to detect canine pathogens, including SARS-CoV-2. Twenty healthy dogs living in SARS-CoV-2 positive households were included. Immunoglobulin detection by different immunoassays was performed. Our findings show that sick dogs presented severe alveolar or interstitial pattern, with pulmonary opacity, parenchymal abnormalities, and bilateral lesions. Forty dogs were negative for SARS-CoV-2 butMycoplasmaspp. was detected in 26 of 33 dogs. Five healthy and one pathological dog presented IgG against SARS-CoV-2.Here we report that despite detecting dogs with IgG α-SARS-CoV-2, we never obtained a positive RT-qPCR, not even in dogs with severe pulmonary disease; suggesting that even in the case of a canine infection transmission would be unlikely. Moreover, dogs living in COVID-19 positive households could have been more exposed to be infected during outbreaks.