bluuebunny/crossref_metadata_2025_split huggingface dataset:
eDNA metabarcoding reveals a core and secondary diets of the greater horseshoe bat with strong spatio-temporal plasticity
Authors: Tournayre Orianne , Leuchtmann Maxime , Galan Maxime , Trillat Marine , Piry Sylvain , Pinaud David , Filippi-Codaccioni Ondine , Pontier Dominique , Charbonnel Nathalie 
Published: June 2020

AbstractDietary plasticity is an important issue for conservation biology as it may be essential for species to cope with environmental changes. However, this process still remains scarcely addressed in the literature, potentially because diet studies have long been constrained by methodological limits. The advent of molecular approaches now makes it possible to get a precise picture of diet and its plasticity, even for endangered and elusive species. Here we focused on the greater horseshoe bat (Rhinolophus ferrumequinum) in Western France, where this insectivorous species has been classified as ‘Vulnerable’ on the Regional Red List in 2016. We applied an eDNA metabarcoding approach on 1986 fecal samples collected in six maternity colonies at three sampling dates. We described its diet and investigated whether the landscape surrounding colonies and the different phases of the maternity cycle influenced the diversity and the composition of this diet. We showed thatR. ferrumequinumfeed on a highly more diverse spectrum of prey than expected from previous studies, therefore highlighting how eDNA metabarcoding can help improving diet knowledge of a flying elusive endangered species. Our approach also revealed thatR. ferrumequinumdiet is composed of two distinct features: the core diet consisting in a few preferred taxa shared by all the colonies (25% of the occurrences) and the secondary diet consisting in numerous rare prey that were highly different between colonies and sampling dates (75% of the occurrences). Energetic needs and constraints associated with the greater horseshoe bat life-cycle, as well as insect phenology and landscape features, strongly influenced the diversity and composition of both the core and whole diets. Further research should now explore the relationships betweenR. ferrumequinumdietary plasticity and fitness, to better assess the impact of core prey decline onR. ferrumequinumpopulations viability.
Transduction catalysis: doxorubicin accelerates and enhances rAAV-mediated gene expression in the cortex of mouse, cat and monkey
Authors: Gong Hongliang , Yuan Nini , Shen Zhiming , Tang Cheng , Shipp Stewart , Qian Liling , Lu Yiliang , Andolina Ian Max , Zhang Shenghai , Wu Jihong , Yang Hui , Wang Wei 
Published: June 2020

SUMMARYRapid and efficient gene transduction via recombinant adeno-associated viruses (rAAVs) is highly desirable across many basic and clinical research domains. Here we report vector co-infusion with doxorubicin, a clinical anti-cancer drug, markedly enhanced rAAV-mediated gene expression in the cerebral cortex across mammalian species (cat, mouse, and macaque), acting throughout the time-period examined and detectable at just three days post-transfection. This enhancement showed serotype generality, being common to rAAV serotypes 2, 8, 9 and PHP.eB tested, and was observed both locally, and at remote locations consistent with doxorubicin undergoing retrograde axonal transport. All these effects were observed at doses matching human blood plasma levels in clinical therapy, and lacked detectable cytotoxicity as assessed by cell morphology, activity, apoptosis and behavioral testing. Altogether, this study identifies an effective means to improve the capability and scope ofin vivorAAV applications, accelerating and augmenting gene transduction at doxorubicin concentrations paralleling medical practice.HighlightsAnti-cancer drug doxorubicin doubles the rate of rAAV-mediated transgene expressionDoxorubicin enhancement generalizes across rAAV serotypes and animal speciesThe effect is observed in both locally and retrogradely infected cortical neuronsThe effective dosage is free from appreciable cytotoxicity and matches clinical settings
A genomic amplification affecting a carboxylesterase gene cluster confers organophosphate resistance in the mosquitoAedes aegypti: from genomic characterization to high-throughput field detection
Authors: Cattel Julien , Haberkorn Chloé , Laporte Fréderic , Gaude Thierry , Cumer Tristan , Renaud Julien , Sutherland Ian W. , Hertz Jeffrey C. , Bonneville Jean-Marc , Arnaud Victor , Noûs Camille , Fustec Bénédicte , Boyer Sébastien , Marcombe Sébastien , David Jean-Philippe 
Published: June 2020

ABSTRACTBy altering gene expression and creating paralogs, genomic amplifications represent a key component of short-term adaptive processes. In insects, the use of insecticides can select gene amplifications causing an increased expression of detoxification enzymes, supporting the usefulness of these DNA markers for monitoring the dynamics of resistance alleles in the field. In this context, the present study aims to characterise a genomic amplification event associated with resistance to organophosphate insecticides in the mosquitoAedes aegyptiand to develop a molecular assay to monitor the associated resistance alleles in the field. An experimental evolution experiment using a composite population from Laos supported the association between the over-transcription of multiple contiguous carboxylesterase genes on chromosome 2 and resistance to multiple organophosphate insecticides. Combining whole genome sequencing and qPCR on specific genes confirmed the presence of a ~100 Kb amplification spanning at least five carboxylesterase genes at this locus with the co-existence of multiple structural duplication haplotypes. Field data confirmed their circulation in South-East Asia and revealed high copy number polymorphism among and within populations suggesting a trade-off between this resistance mechanism and associated fitness costs. A dual-colour multiplex TaqMan assay allowing the rapid detection and copy number quantification of this amplification event inAe. aegyptiwas developed and validated on field populations. The routine use of this novel assay will improve the tracking of resistance alleles in this major arbovirus vector.
IGD: high-performance search for large-scale genomic interval datasets
Authors: Feng Jianglin , Sheffield Nathan C. 
Published: June 2020

SummaryDatabases of large-scale genome projects now contain thousands of genomic interval datasets. These data are a critical resource for understanding the function of DNA. However, our ability to examine and integrate interval data of this scale is limited. Here, we introduce the integrated genome database (IGD), a method and tool for searching genome interval datasets more than three orders of magnitude faster than existing approaches, while using only one hundredth of the memory. IGD uses a novel linear binning method that allows us to scale analysis to billions of genomic regions.Availabilityhttps://github.com/databio/IGD
Mms19promotes spindle microtubule assembly in neural stem cells through two distinct pathways
Authors: Chippalkatti Rohan , Egger Boris , Suter Beat 
Published: June 2020

AbstractMitotic divisions depend on the timely assembly and proper orientation of the mitotic spindle. Malfunctioning of these processes can considerably delay mitosis, thereby compromising tissue growth and homeostasis, and leading to chromosomal instability. Here we identified Mms19 as an important player in these processes as it promotes spindle and astral microtubule (MT) growth and consequently regulates spindle orientation and mitosis duration inDrosophilaneural stem cells. Loss of functionalMms19drastically affects the growth and development of mitotic tissues inDrosophilalarvae. We found thatMms19performs its mitotic activities through two different pathways. By stimulating the mitotic kinase cascade, it triggers the localization of the MT regulatory complex TACC/Msps (Transforming Acidic Coiled Coil/Minispindles, the homolog of human ch-TOG) to the centrosome. In addition, we present evidence that Mms19 stimulates MT stability and bundling by binding directly to MTs.
Bacterivorous nematodes correlate with soil fertility and improved crop production in an organic minimum tillage system
Authors: Schmidt Jan H. , Hallmann Johannes , Finckh Maria R. 
Published: June 2020

AbstractOrganic farming systems are generally based on intensive soil tillage for seed bed preparation and weed control, which in the long-term often leads to reduced soil fertility. To avoid this, organic farming systems need to adopt conservation agriculture practices, such as minimum tillage and diligent crop rotations. However, minimum tillage generally delays soil warming in spring causing reduced nitrogen mineralization and thus poor plant growth. This negative effect needs to be compensated. We hypothesize that, in a diverse crop rotation, organic minimum tillage based on frequent cover cropping and application of dead mulch will improve soil fertility and thus crop production as confirmed by a number of chemical and biological soil indicators.We made use of two long-term field experiments that compare typical organic plough-based systems (25 cm) with minimum tillage systems (<15 cm) including application of transfer mulch to potatoes. Both tillage systems were either fertilized with compost or equivalent amounts of mineral potassium and phosphate. In 2019, soil samples from both fields were collected and analyzed for soil pH, organic carbon, macro-, micronutrients, microbial biomass, microbial activity and total nematode abundance. In addition, performance of pea in the same soils was determined under greenhouse conditions.Results from the field experiments showed an increase of macronutrients (+52%), micronutrients (+11%), microbial biomass (+51%), microbial activity (+86%), and bacterivorous nematodes (+112%) in minimum tillage compared with the plough-based system. In the accompanying greenhouse bioassay, pea biomass was 45% higher under minimum than under plough tillage. In conclusion, the study showed that under organic conditions, soil fertility can be improved in minimum tillage systems by intensive cover cropping and application of dead mulch to levels higher than in a plough-based system. Furthermore, the abundance of bacterivorous nematodes can be used as a reliable indicator for the soil fertility status.
Long-distance dispersal of oilseed rape seeds: The role of grain trailers
Authors: Bailleul Diane , Ollier Sébastien , Lecomte Jane 
Published: June 2020

AbstractIn agroecosystems, anthropogenic activities can modify the natural dispersal capacity of crops and their capacity to establish feral populations. In the case of oilseed rape (OSR), seed spillage from grain trailers during harvest was first quantified by anin situscientific study (Selommes, Loir-et-Cher, France). Demographic analysis of seeds collected from 85 traps set on road verges suggested that OSR dispersal distance due to seed spillage from grain trailers can be up to 400m. In the present study, we used SSR markers to genotype seeds collected from trap-sites and from surrounding OSR fields to precisely estimate the distances between traps and fields. Trailer directions on each road were also considered. Few seeds (5.8%) were not linked to a field in the studied area, while most of the seeds (59.2%) were linked to a field situated over 400 m away. The overall mean dispersal distance was 1250 m. It ranged from 308 m to 1392 m for one-lane roads, and from 1048 m to 1404 m for two-lane roads. Events of seed dispersal at greater distances (> 5 km) were rare but still possible. It thus follows that OSR seed dispersal due to spillage from grain trailers should be carefully considered in the context of genetically modified plant cultivation.
The role of dermis resident macrophages and their interaction with neutrophils in the early establishment ofLeishmania majorinfection transmitted by sand fly bite
Authors: Chaves Mariana M. , Lee Sang Hun , Kamenyeva Olena , Ghosh Kashinath , Sacks David 
Published: June 2020

AbstractThere is substantial experimental evidence to indicate thatLeishmaniainfections that are transmitted naturally by the bites of infected sand flies differ in fundamental ways from the inflammatory and immune reactions initiated by needle inocula. We have used flow cytometry and intravital microscopy (IVM) to reveal the heterogeneity of sand fly transmission sites with respect to the subsets of phagocytes in the skin that harborL. majorwithin the first hours and days after infection. By flow cytometry analysis, dermis resident macrophages (TRMs) were on average the predominant infected cell type at 1 hr and 24 hr. By confocal IVM, the co-localization ofL. majorand neutrophils varied depending on the proximity of deposited parasites to the presumed site of vascular damage, defined by the highly localized swarming of neutrophils. Some of the dermal TRMs could be visualized acquiring their infections via transfer from or efferocytosis of parasitized neutrophils, providing direct evidence for the “Trojan Horse” model. The role of neutrophil engulfment by dermal TRMs and the involvement of the Tyro3/Axl/Mertk family of receptor tyrosine kinases in these interactions and in sustaining the anti-inflammatory program of dermal TRMs was supported by the effects observed in neutrophil depleted and inAxl-/-Mertk-/-mice. TheAxl-/-Mertk-/-mice also displayed reduced parasite burdens but more severe pathology followingL. majorinfection transmitted by sand fly bite.SummarySand flies transmitLeishmania majorwhich causes cutaneous leishmaniasis in humans and in non-human hosts. Our analyses of sand fly transmission sites ofL. majorin the mouse skin revealed that dermis resident macrophages (TRM) were the predominant phagocytes to take up the parasite within the first 24 hr post-bite. The early involvement of neutrophils varied depending on the proximity of deposited parasites to the site of tissue damage around which the neutrophils coalesced. By intra-vital microscopy, some of the dermal TRMs could be visualized acquiring their infections by direct transfer from or phagocytosis of parasitized neutrophils. The involvement of the Tyro3/Axl/Mertk family of receptor tyrosine kinases in these cellular interactions and in sustaining the anti-inflammatory functions of dermal TRMs was supported by the reduced parasite burdens but more severe pathology observed inAxl-/-Mertk-/-mice. The heterogeneity of sand fly transmission sites with respect to the dose of parasites and the early cellular interactions described here likely contribute to the wide range of infection outcomes that are associated with natural transmission ofL. majorobserved in mouse models and possibly humans.
A ChIP-exo screen of 887 PCRP transcription factor antibodies in human cells
Authors: Lai William K. M. , Mariani Luca , Rothschild Gerson , Smith Edwin R. , Venters Bryan J. , Blanda Thomas R. , Kuntala Prashant K. , Bocklund Kylie , Mairose Joshua , Dweikat Sarah N , Mistretta Katelyn , Rossi Matthew J. , James Daniela , Anderson James T. , Phanor Sabrina K. , Zhang Wanwei , Zhao Zibo , Shah Avani P. , Novitzky Katherine , McAnarney Eileen , Keogh Michael-C. , Shilatifard Ali , Basu Uttiya , Bulyk Martha L. , Pugh B. Franklin 
Published: June 2020

AbstractAntibodies offer a powerful means to interrogate specific proteins in a complex milieu. However, antibody availability and reliability are problematic and epitope tagging can be impractical in many cases. In an effort to improve this situation, the Protein Capture Reagents Program (PCRP) generated over a thousand renewable monoclonal antibodies (mAbs) against human-presumptive chromatin proteins. However, these reagents have not been widely field-tested. We therefore performed a screen to test their ability to enrich genomic regions via chromatin immunoprecipitation (ChIP) and a variety of orthogonal assays. 887 unique antibodies against 681 unique human transcription factors (TFs), were assayed by ultra-high resolution ChIP-exo/seq, primarily in a single pass in one cell type (K562). Deep systematic analyses of the resulting ∼1,200 ChIP-exo datasets can be found atwww.PCRPvalidation.org. Subsets of PCRP mAbs were further tested in ChIP-seq, CUT&RUN, STORM super-resolution microscopy, immunoblots, and protein binding microarray (PBM) experiments. About 5% of the tested antibodies displayed target (i.e., cognate antigen) enrichment across at least one assay and are strong candidates for additional validation. An additional 34% produced ChIP-exo data that was distinct from background and thus warrant further testing. The remaining 61% were not substantially different from background, and likely require consideration of a much broader survey of cell types and/or assay optimizations. We demonstrate and discuss the metrics and challenges to antibody validation in chromatin-based assays.
D936Y and Other Mutations in the Fusion Core of the SARS-Cov-2 Spike Protein Heptad Repeat 1 Undermine the Post-Fusion Assembly
Authors: Cavallo Luigi , Oliva Romina 
Published: June 2020

AbstractThe iconic “red crown” of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is made of its spike (S) glycoprotein. The S protein is the Trojan horse of coronaviruses, mediating their entry into the host cells. While SARS-CoV-2 was becoming a global threat, scientists have been accumulating data on the virus at an impressive pace, both in terms of genomic sequences and of three-dimensional structures. On April 21st, the GISAID resource had collected 10,823 SARS-CoV-2 genomic sequences. We extracted from them all the complete S protein sequences and identified point mutations thereof. Six mutations were located on a 14-residue segment (929-943) in the “fusion core” of the heptad repeat 1 (HR1). Our modeling in the pre- and post-fusion S protein conformations revealed, for three of them, the loss of interactions stabilizing the post-fusion assembly. On May 29th, the SARS-CoV-2 genomic sequences in GISAID were 34,805. An analysis of the occurrences of the HR1 mutations in this updated dataset revealed a significant increase for the S929I and S939F mutations and a dramatic increase for the D936Y mutation, which was particularly widespread in Sweden and Wales/England. We notice that this is also the mutation causing the loss of a strong inter-monomer interaction, the D936-R1185 salt bridge, thus clearly weakening the post-fusion assembly.
An optogenetic method for interrogating YAP1 and TAZ nuclear-cytoplasmic shuttling
Authors: Dowbaj Anna M. , Jenkins Robert P. , Heddleston John M. , Ciccarelli Alessandro , Fallesen Todd , Hahn Klaus , Montagner Marco , Sahai Erik 
Published: June 2020

AbstractThe shuttling of transcription factors and transcriptional regulators in and out of the nucleus is central to the regulation of many biological processes. Here we describe a new method for studying the rates of nuclear entry and exit of transcriptional regulators. A photo-responsive AsLOV (Avena sativaLight Oxygen Voltage) domain is used to sequester fluorescently-labelled transcriptional regulators YAP1 and TAZ/WWTR1 on the surface of mitochondria and reversibly release them upon blue light illumination. After dissociation, fluorescent signals from mitochondria, cytoplasm and nucleus are extracted with a bespoke app and used to generate rates of nuclear entry and exit. Using this method, we demonstrate that phosphorylation of YAP1 on canonical sites enhances its rate of nuclear export. Moreover, we provide evidences that, despite high intercellular variability, YAP1 import and export rates correlated within the same cell. By simultaneously releasing YAP1 and TAZ from sequestration, we show that their rates of entry and exit are correlated. Furthermore, tracking of light-sensitive YAP1 with lattice lightsheet microscopy revealed high heterogeneity of YAP1 dynamics within different subcellular regions, suggesting that implementing high resolution volumetric 3D data could shed light on new mechanisms of nuclear-cytoplasmic shuttling of proteins.
Slow oscillation-spindle coupling is negatively associated with emotional memory formation following stress
Authors: Denis Dan , Kim Sara Y. , Kark Sarah M. , Daley Ryan T. , Kensinger Elizabeth A. , Payne Jessica D. 
Published: June 2020

AbstractBoth stress and sleep enhance emotional memory. They also interact, with the largest effect of sleep on emotional memory being seen when stress occurs shortly before or after encoding. Slow wave sleep (SWS) is critical for long-term episodic memory, facilitated by the temporal coupling of slow oscillations and sleep spindles. Prior work in humans has shown these associations for neutral information in non-stressed participants. Whether coupling interacts with stress to facilitate emotional memory formation is unknown. Here, we addressed this question by reanalyzing an existing dataset of 64 individuals. Participants underwent a psychosocial stressor (32) or comparable control (32) prior to the encoding of 150-line drawings of neutral, positive, and negative images. All participants slept overnight with polysomnography, before being given a surprise memory test the following day. In the stress group, time spent in SWS was positively correlated with memory for images of all valences. Results were driven by those who showed a high cortisol response to the stressor, compared to low responders. The amount of slow oscillation-spindle coupling during SWS was negatively associated with neutral and emotional memory in the stress group only. The association with emotional memory was significantly stronger than for neutral memory within the stress group. These results suggest that stress around the time of initial memory formation impacts the relationship between slow wave sleep and memory.
Feature Extraction Approaches for Biological Sequences: A Comparative Study of Mathematical Models
Authors: Bonidia Robson Parmezan , Sampaio Lucas Dias Hiera , Domingues Douglas Silva , Paschoal Alexandre Rossi , Lopes Fabrício Martins , de Leon Ferreira de Carvalho André Carlos Ponce , Sanches Danilo Sipoli 
Published: June 2020

AbstractThe number of available biological sequences has increased significantly in recent years due to various genomic sequencing projects, creating a huge volume of data. Consequently, new computational methods are needed to analyze and extract information from these sequences. Machine learning methods have shown broad applicability in computational biology and bioinformatics. The utilization of machine learning methods has helped to extract relevant information from various biological datasets. However, there are still several obstacles that motivate new algorithms and pipeline proposals, mainly involving feature extraction problems, in which extracting significant discriminatory information from a biological set is challenging. Considering this, our work proposes to study and analyze a feature extraction pipeline based on mathematical models (Numerical Mapping, Fourier, Entropy, and Complex Networks). As a case study, we analyze Long Non-Coding RNA sequences. Moreover, we divided this work into two studies, e.g., (I) we assessed our proposal with the most addressed problem in our review, e.g., lncRNA vs. mRNA; (II) we tested its generalization on different classification problems, e.g., circRNA vs. lncRNA. The experimental results demonstrated three main contributions: (1) An in-depth study of several mathematical models; (2) a new feature extraction pipeline and (3) its generalization and robustness for distinct biological sequence classification.