bluuebunny/crossref_metadata_2025_split huggingface dataset:
Testing the metabolic homeostasis hypothesis in amphibians
Authors: Kreiman Lucas E. , Solano-Iguaran Jaiber J. , Bacigalupe Leonardo D. , Naya Daniel E. 
Published: June 2019

A number of hypotheses about compensatory mechanisms that allow ectothermic animals to cope with the latitudinal decrease in ambient temperature (TA) have been proposed during the last century. One of these hypotheses, the ‘metabolic homeostasis’ hypothesis (MHH), states that species should show the highest thermal sensitivity of the metabolic rate (Q10-SMR) at the colder end of the range ofTAs they usually experience in nature. This way, species should be able to minimize maintenance costs during the colder hours of the day, but quickly take advantage of increases inTAduring the warmer parts of the day. Here, we created a dataset that includesQ10-SMRvalues for 58 amphibian species, assessed at four thermal ranges, to evaluate three predictions derived from the MHH. In line with this hypothesis, we found that: (i)Q10-SMRvalues tended to be positively correlated with latitude when measured at lowerTAs, but negative correlated with latitude when measured at higherTAs, (ii)Q10-SMRmeasured at lowerTAs were higher in temperate species, whereasQ10-SMRmeasured at higherTAs were higher in tropical species, and (iii) the experimentalTAat whichQ10-SMRwas maximal for each species decreased with latitude. This is the first study to our knowledge showing that the relationship betweenQ10-SMRand latitude in ectotherms changes with theTAat whichQ10-SMRis assessed, as predicted from an adaptive hypothesis.This article is part of the theme issue ‘Physiological diversity, biodiversity patterns and global climate change: testing key hypotheses involving temperature and oxygen’.
Physiological diversity, biodiversity patterns and global climate change: testing key hypotheses involving temperature and oxygen
Authors: Spicer John I. , Morley Simon A. , Bozinovic Francisco 
Published: June 2019

Documenting and explaining global patterns of biodiversity in time and space have fascinated and occupied biologists for centuries. Investigation of the importance of these patterns, and their underpinning mechanisms, has gained renewed vigour and importance, perhaps becoming pre-eminent, as we attempt to predict the biological impacts of global climate change. Understanding the physiological features that determine, or constrain, a species' geographical range and how they respond to a rapidly changing environment is critical. While the ecological patterns are crystallizing, explaining the role of physiology has just begun. The papers in this volume are the primary output from a Satellite Meeting of the Society of Experimental Biology Annual Meeting, held in Florence in July 2018. The involvement of two key environmental factors, temperature and oxygen, was explored through the testing of key hypotheses. The aim of the meeting was to improve our knowledge of large-scale geographical differences in physiology, e.g. metabolism, growth, size and subsequently our understanding of the role and vulnerability of those physiologies to global climate warming. While such an aim is of heuristic interest, in the midst of our current biodiversity crisis, it has an urgency that is difficult to overstate.
This article is part of the theme issue ‘Physiological diversity, biodiversity patterns and global climate change: testing key hypotheses involving temperature and oxygen’.
DNA shape complements sequence-based representations of transcription factor binding sites
Authors: DeFord Peter , Taylor James 
Published: June 2019

AbstractThe position weight matrix (PWM) has long been a useful tool for describing variation in the composition of regions of DNA such as transcription factor (TF) binding sites. It is difficult, however, to relate the sequence-based representation of a DNA motif to the biological features of the interaction of a TF with its binding site. Here we present an alternative strategy for representing DNA motifs – called Structural Motif (StruM) – that can easily represent different sets of structural features. Structural features are inferred from dinucleotide properties listed in the Dinucleotide Property Database. StruMs are able to specifically model TF binding sites, using an encoding strategy that is distinct from sequence-based models. This difference in encoding strategies makes StruMs complementary to sequence-based methods of TF binding site identification.
Construction of simplified microbial consortia to degrade recalcitrant materials based on enrichment and dilution-to-extinction cultures
Authors: Kang Dingrong , Jacquiod Samuel , Herschend Jakob , Wei Shaodong , Nesme Joseph , Sørensen Søren J. 
Published: June 2019

AbstractThe capacity of microbes degrading recalcitrant materials has been extensively explored from environmental remediation to industrial applications. Although significant achievements were obtained with single strains, focus is now going toward the use of microbial consortia because of advantages in terms of functional stability and efficiency. While consortia assembly attempts were made from several known single strains, another approach consists in obtaining consortia from complex environmental microbial communities in search for novel microbial species, genes and functions. However, assembling efficient microbial consortia from complex environmental communities is far from trivial due to large diversity and biotic interactions at play. Here we propose a strategy containing enrichment and dilution-to-extinction cultures to construct simplified microbial consortia (SMC) for keratinous waste management, from complex environmental communities. Gradual dilutions were performed from a keratinolytic microbial consortium, and dilution 10−9was selected to construct a SMC library. Further compositional analysis and keratinolytic activity assays demonstrated that microbial consortia were successfully simplified, without impacting their biodegradation capabilities. These SMC possess promising potential for efficient keratinous valorization. More importantly, this reasoning and methodology could be transferred to other topics involving screening for simplified communities for biodegradation, thus considerably broadening its application scope.ImportanceMicrobial consortia have got more and more attention and extensive applications due to their potential advantages. However, a high diversity of microbes is likely to hide uncontrollable risks in practice specific to novel strains and complicated interaction networks. Exploring a convenient and efficient way to construct simplified microbial consortia is able to broaden the applied scope of microbes. This study presents the approach based on enrichment and dilution-to-extinction cultures, which gain abundance microbial consortia including some without losing efficiency from the enriched functional microbial community. The microbial interactions at the strain level were evaluated by using compositional identification and correlation analysis, which contribute to revealing the roles of microbes in the degradation process of recalcitrant materials. Our findings provide a systematic scheme to achieve optimizing microbial consortia for biodegradation from an environmental sample, could be readily applied to a range of recalcitrant materials management from environmental remediation to industrial applications.
A framework for the development of a global standardised marine taxon reference image database (SMarTaR-ID) to support image-based analyses
Authors: Howell Kerry L. , Davies Jaime S. , Allcock A. Louise , Braga-Henriques Andreia , Buhl-Mortensen Pål , Carreiro-Silva Marina , Dominguez-Carrió Carlos , Durden Jennifer M. , Foster Nicola L. , Game Chloe A. , Hitchin Becky , Horton Tammy , Hosking Brett , Jones Daniel O. B. , Mah Christopher , Marchais Claire Laguionie , Menot Lenaick , Morato Telmo , Pearman Tabitha R. R. , Piechaud Nils , Ross Rebecca E. , Ruhl Henry A. , Saeedi Hanieh , Stefanoudis Paris V. , Taranto Gerald H. , Thompson Michael B , Taylor James R. , Tyler Paul , Vad Johanne , Victorero Lissette , Vieira Rui P. , Woodall Lucy C. , Xavier Joana R. , Wagner Daniel 
Published: June 2019

AbstractVideo and image data are regularly used in the field of benthic ecology to document biodiversity. However, their use is subject to a number of challenges, principally the identification of taxa within the images without associated physical specimens. The challenge of applying traditional taxonomic keys to the identification of fauna from images has led to the development of personal, group, or institution level reference image catalogues of operational taxonomic units (OTUs) or morphospecies. Lack of standardisation among these reference catalogues has led to problems with observer bias and the inability to combine datasets across studies. In addition, lack of a common reference standard is stifling efforts in the application of artificial intelligence to taxon identification. Using the North Atlantic deep sea as a case study, we propose a database structure to facilitate standardisation of morphospecies image catalogues between research groups and support future use in multiple front-end applications. We also propose a framework for coordination of international efforts to develop reference guides for the identification of marine species from images. The proposed structure follows the Darwin Core standard to allow integration with existing databases. We suggest a management framework where high-level taxonomic groups are curated by a regional team, consisting of both end users and taxonomic experts. We identify a mechanism by which overall quality of data within a common reference guide could be raised over the next decade. Finally, we discuss the role of a common reference standard in advancing marine ecology and supporting sustainable use of this ecosystem.
Regulation of perineuronal nets in the adult cortex by the electrical activity of parvalbumin interneurons
Authors: Devienne Gabrielle , Picaud Sandrine , Cohen Ivan , Piquet Juliette , Tricoire Ludovic , Testa Damien , Di Nardo Ariel A. , Rossier Jean , Cauli Bruno , Lambolez Bertrand 
Published: June 2019

ABSTRACTPerineuronal net (PNN) accumulation around parvalbumin-expressing (PV) inhibitory interneurons marks the closure of critical periods of high plasticity, whereas PNN removal reinstates juvenile plasticity in the adult cortex. Using targeted chemogenetic in vivo approaches in the adult mouse visual cortex, we found that transient electrical silencing of PV interneurons, directly or through inhibition of local excitatory neurons, induced PNN regression. Conversely, excitation of either neuron types did not reduce the PNN. We also observed that chemogenetically inhibited PV interneurons exhibited reduced PNN compared to their untransduced neighbors, and confirmed that single PV interneurons express multiple genes enabling cell-autonomous control of their own PNN density. Our results indicate that PNNs are dynamically regulated in the adult by PV neurons acting as sensors of their local microcircuit activities. PNN regulation provides individual PV neurons with an activity-dependent mechanism to control the local remodeling of adult cortical circuits.
Putting RFMix and ADMIXTURE to the test in a complex admixed population
Authors: Uren Caitlin , Hoal Eileen G. , Möller Marlo 
Published: June 2019

AbstractGlobal and local ancestry inference in admixed human populations can be performed using computational tools implementing distinct algorithms, such as RFMix and ADMIXTURE. The accuracy of these tools has been tested largely on populations with relatively straightforward admixture histories but little is known about how well they perform in more complex admixture scenarios. Using simulations, we show that RFMix outperforms ADMIXTURE in determining global ancestry proportions in a complex 5-way admixed population. In addition, RFMix correctly assigns local ancestry with an accuracy of 89%. The increase in reported local ancestry inference accuracy in this population (as compared to previous studies) can largely be attributed to the recent availability of large-scale genotyping data for more representative reference populations. The ability of RFMix to determine global and local ancestry to a high degree of accuracy, allows for more reliable population structure analysis, scans for natural selection, admixture mapping and case-control association studies. This study highlights the utility of the extension of computational tools to become more relevant to genetically structured populations, as seen with RFMix. This is particularly noteworthy as modern-day societies are becoming increasingly genetically complex and some genetic tools are therefore less appropriate. We therefore suggest that RFMix be used for both global and local ancestry estimation in complex admixture scenarios.
Revisiting the Fisher-KPP equation to interpret the spreading-extinction dichotomy
Authors: El-Hachem Maud , McCue Scott W. , Jin Wang , Du Yihong , Simpson Matthew J. 
Published: June 2019

AbstractThe Fisher-KPP model supports travelling wave solutions that are successfully used to model numerous invasive phenomena with applications in biology, ecology, and combustion theory. However, there are certain phenomena that the Fisher-KPP model cannot replicate, such as the extinction of invasive populations. The Fisher-Stefan model is an adaptation of the Fisher-KPP model to include a moving boundary whose evolution is governed by a Stefan condition. The Fisher-Stefan model also supports travelling wave solutions; however, a key additional feature of the Fisher-Stefan model is that it is able to simulate population extinction, giving rise to aspreading-extinction dichotomy.In this work, we revisit travelling wave solutions of the Fisher-KPP model and show that these results provide new insight into travelling wave solutions of the Fisher-Stefan model and the spreading-extinction dichotomy. Using a combination of phase plane analysis, perturbation analysis and linearisation, we establish a concrete relationship between travelling wave solutions of the Fisher-Stefan model and often-neglected travelling wave solutions of the Fisher-KPP model. Furthermore, we give closed-form approximate expressions for the shape of the travelling wave solutions of the Fisher-Stefan model in the limit of slow travelling wave speeds,c≪ 1.
Modular and efficient pre-processing of single-cell RNA-seq
Authors: Melsted Páll , Booeshaghi A. Sina , Gao Fan , Beltrame Eduardo , Lu Lambda , Hjorleifsson Kristján Eldjárn , Gehring Jase , Pachter Lior 
Published: June 2019

AbstractAnalysis of single-cell RNA-seq data begins with pre-processing of sequencing reads to generate count matrices. We investigate algorithm choices for the challenges of pre-processing, and describe a workflow that balances efficiency and accuracy. Our workflow is based on the kallisto (https://pachterlab.github.io/kallisto/) and bustools (https://bustools.github.io/) programs, and is near-optimal in speed and memory. The workflow is modular, and we demonstrate its flexibility by showing how it can be used for RNA velocity analyses. Documentation and tutorials for using the kallisto | bus workflow are available athttps://www.kallistobus.tools/.
Characterization of the virome of shallots affected by the shallot mild yellow stripe disease in France
Authors: Marais Armelle , Faure Chantal , Theil Sébastien , Candresse Thierry 
Published: June 2019

AbstractTo elucidate the etiology of a new disease on shallot in France, double-stranded RNAs from asymptomatic and symptomatic shallot plants were analyzed by high-throughput sequencing (HTS). Contigs annotation, molecular characterization and phylogenetic analyses revealed the presence in symptomatic plants of a virus complex consisting of shallot virus X (ShVX, Allexivirus), shallot latent virus (SLV, Carlavirus) and two novel viruses belonging to the genera Carlavirus and Potyvirus, for which the names of shallot virus S (ShVS) and shallot mild yellow stripe associated virus (SMYSaV), are proposed. Complete or near complete genomic sequences were obtained for all these agents, revealing divergent isolates of ShVX and SLV. Trials to fulfill Koch’s postulates were pursued but failed to reproduce the symptoms on inoculated shallots, even though the plants were proved to be infected by the four viruses detected by HTS. Replanting of bulbs from SMYSaV-inoculated shallot plants resulted in infected plants, showing that the virus can perpetuate the infection over seasons. A survey analyzing 351 shallot samples over a four years period strongly suggests an association of SMYSaV with the disease symptoms. An analysis of SMYSaV diversity indicates the existence of two clusters of isolates, one of which is largely predominant in the field over years.The sequences reported in the present manuscript have been deposited in the GenBank database under accession numbers MG571549, MH292861, MH389247 to MH389255, and MG910501 to MG910598.
Link between personality and response to THC exposure
Authors: Kardash Tetiana , Rodin Dmitry , Kirby Michael , Davis Noa , Koman Igor , Gorelick Jonathan , Michaelevski Izhak , Pinhasov Albert 
Published: June 2019

ABSTRACTThe effects of cannabis reported by users range from experiences of euphoria and anxiolytic effects to paranoia, anxiety, and increased risk of depression. Attempts to reconcile the apparent contradictions in user response have not been conclusive. Here, we utilized selectively-bred stress-resilient socially dominant (Dom) and stress-sensitive socially submissive (Sub) mice to elucidate this contradiction. Following short-term, repeated treatment with delta-9-tetrahydrocannabinol (THC) at two different doses (1.5 mg/kg and 15 mg/kg), Sub mice presented significant place-aversion in a Conditioned Place Preference paradigm at a high dose, whereas Dom mice displayed no place preference or aversion. Forced Swim test conducted after 6-week of washout period, revealed differential impact of the two THC doses depending upon behavioral pattern. Specifically, the low dose alleviated depressive-like behavior in Sub mice, while the high dose produced the opposite effect in Dom mice. Interestingly, corticosterone concentration in serum was elevated at the high dose regardless of the mice-population tested. We conclude here that differences in dominance behavior and stress vulnerability are involved in the regulation of cannabis response among users and should be considered when prescribing THC-containing medications to patients.
Proliferation genes repressed by TGF-β are downstream of Slug/Snail2 in normal bronchial epithelial progenitors and are deregulated in COPD
Authors: Brahim Chamseddine Ben , Courageux Charlotte , Jolly Ariane , Ouine Bérengère , Cartier Aurélie , de la Grange Pierre , de Koning Leanne , Leroy Pascale 
Published: June 2019

AbstractSlug/Snail2 belongs to the Epithelial-Mesenchymal Transition (EMT)-inducing transcription factors involved in development and diseases. Slug is expressed in adult stem/progenitor cells of several epithelia, making it unique among these transcription factors. To investigate Slug role in human bronchial epithelium progenitors, we studied primary bronchial basal/progenitor cells in an air-liquid interface culture system that allows regenerating a bronchial epithelium. To identify Slug downstream genes we knocked down Slug in basal/progenitor cells from normal subjects and subjects with COPD, a respiratory disease presenting anomalies in the bronchial epithelium and high levels of TGF-β in the lungs. We show that normal and COPD bronchial basal/progenitors, even when treated with TGF-β, express both epithelial and mesenchymal markers, and that the epithelial marker E-cadherin is not a target of Slug and, moreover, positively correlates with Slug. We reveal that Slug downstream genes responding to both differentiation and TGF-β are different in normal and COPD progenitors, with in particular a set of proliferation-related genes that are among the genes repressed downstream of Slug in normal but not COPD. In COPD progenitors at the onset of differentiation in presence of TGF-β, we show that there is positive correlations between the effect of differentiation and TGF-β on proliferation-related genes and on Slug protein, and that their expression levels are higher than in normal cells. As well, the expression of Smad3 and β-Catenin, two molecules from TGF-β signaling pathways, are higher in COPD progenitors, and our results indicate that proliferation-related genes and Slug protein are increased by different TGF-β-induced mechanisms.Graphical Abstract
Cell elimination strategies upon identity switch via modulation ofapterousinDrosophilawing disc
Authors: Klipa Olga , Hamaratoglu Fisun 
Published: June 2019

ABSTRACTThe ability to establish spatial organization is an essential feature of any developing tissue and is achieved through well-defined rules of cell-cell communication. Maintenance of this organization requires elimination of cells with inappropriate positional identity, a poorly understood phenomenon. Here we studied mechanisms regulating cell elimination in the context of a growing tissue, theDrosophilawing disc and its dorsal determinant Apterous. Systematic analysis ofapterousmutant clones along with their twin spots shows that they are eliminated from the dorsal compartment via three different mechanisms: sorting to the ventral compartment, basal extrusion, and death, depending on the position of the clone in the wing disc. We find that basal extrusion is the main elimination mechanism in the hinge, whereas apoptosis dominates in the pouch and in the notum. In the absence of apoptosis, extrusion takes over to ensure clearance in all regions. Notably, clones in the hinge grow larger than those in the pouch, emphasizing spatial differences. Mechanistically, we find that limiting cell division within the clones does not prevent their extrusion. Indeed, even clones of one or two cells can be extruded basally, demonstrating that the clone size is not the main determinant of the elimination mechanism to be used. Overall, we revealed three elimination mechanisms and their spatial biases for preserving pattern in a growing organ.