bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influences of male age, mating history and starvation on female post mating aggression and feeding inDrosophila
Authors: Bath Eleanor , Buzzoni Daisy , Ralph Toby , Wigby Stuart , Sepil Irem 
Published: September 2020

AbstractMating changes female behaviour and physiology across a wide range of taxa, with important effects for male and female fitness. These changes are often induced by components of the male ejaculate, such as sperm and seminal fluid proteins.However, males can vary significantly in their ejaculates, due to factors such as age, mating history, or nutritional status. This male variation may therefore lead to variation in the strength of responses males can stimulate in females, with alterations in fitness outcomes for both sexes.Using the fruit fly,Drosophila melanogaster, we tested whether three aspects of male condition shape an important, but understudied, post-mating response – increased female-female aggression.We found that females mated to old males fought less than females mated to young males. This effect was exacerbated in mates of old, sexually active males, but there was no effect of male starvation status on mating-induced female aggression. There was also a significant effect of age and mating history on female post-mating feeding duration.Our results add to a growing body of literature that variation in male condition can shape sexual selection through post-mating responses in females, including female-female interactions. Studying such variation may therefore be useful for understanding how the condition of sex affects the behaviour of the other.
A survey of proximal methods for monitoring leaf phenology in temperate deciduous forests
Authors: Soudani Kamel , Delpierre Nicolas , Berveiller Daniel , Hmimina Gabriel , Pontailler Jean-Yves , Seureau Lou , Vincent Gaёlle , Dufrêne Éric 
Published: September 2020

AbstractTree phenology is a major driver of forest-atmosphere mass and energy exchanges. Yet tree phenology has historically not been recorded at flux measurement sites. Here, we used seasonal time-series of ground-based NDVI (Normalized Difference Vegetation Index), RGB camera GCC (Greenness Chromatic Coordinate), broad-band NDVI, LAI (Leaf Area Index),fAPAR (fraction of Absorbed Photosynthetic Active Radiation), CC (Canopy Closure),fRvis(fraction of Reflected Radiation) and GPP (Gross Primary Productivity) to predict six phenological markers detecting the start, middle and end of budburst and of leaf senescence in a temperate deciduous forest. We compared them to observations of budburst and leaf senescence achieved by field phenologists over a 13-year period. GCC, NDVI and CC captured very well the interannual variability of spring phenology (R2> 0.80) and provided the best estimates of the observed budburst dates, with a mean absolute deviation (MAD) less than 4 days. For the CC and GCC methods, mid-amplitude (50%) threshold dates during spring phenological transition agreed well with the observed phenological dates. For the NDVI-based method, on average, the mean observed date coincides with the date when NDVI reaches 25% of its amplitude of annual variation. For the other methods, MAD ranges from 6 to 17 days. GPP provides the most biased estimates. During the leaf senescence stage, NDVI- and CC-derived dates correlated significantly with observed dates (R2=0.63 and 0.80 for NDVI and CC, respectively), with MAD less than 7 days. Our results show that proximal sensing methods can be used to derive robust phenological indexes. They can be used to retrieve long-term phenological series at flux measurement sites and help interpret the interannual variability and decadal trends of mass and energy exchanges.HighlightsWe used 8 indirect methods to predict the timing of phenological events.GCC, NDVI and CC captured very well the interannual variation of spring phenology.GCC, NDVI and CC provided the best estimates of observed budburst dates.NDVI and CC derived-dates correlated with observed leaf senescence dates.
Social networks strongly predict the gut microbiota of wild mice
Authors: Raulo Aura , Allen Bryony , Troitsky Tanya , Husby Arild , Firth Josh A , Coulson Tim , Knowles Sarah CL 
Published: September 2020

AbstractThe mammalian gut teems with beneficial microbes, yet how hosts acquire these symbionts remains poorly understood. Research in primates suggests that microbes can be picked up via social contact, but the role of social interactions in non-group-living species remains unexplored. Here, we use a passive tracking system to collect high resolution spatiotemporal activity data from wild mice (Apodemus sylvaticus). Social network analysis revealed social association strength to be the strongest predictor of microbiota similarity among individuals, controlling for factors including spatial proximity and kinship, which had far smaller or nonsignificant effects. This social effect was limited to interactions involving males (male-male and male-female), implicating sex-dependent behaviours as driving processes. Social network position also predicted microbiota richness, with well-connected hub individuals having the most diverse microbiotas. Overall, these findings suggest social contact provides a key transmission pathway for gut symbionts even in relatively asocial mammals, that strongly shapes the adult gut microbiota. This work underlines the potential for individuals to pick up beneficial symbionts as well as pathogens from social interactions.
Soundscapes predict species occurrence in tropical forests
Authors: Sethi Sarab S. , Ewers Robert M. , Jones Nick S. , Sleutel Jani , Shabrani Adi , Zulkifli Nursyamin , Picinali Lorenzo 
Published: September 2020

AbstractAccurate occurrence data is necessary for the conservation of keystone or endangered species, but acquiring it is usually slow, laborious, and costly. Automated acoustic monitoring offers a scalable alternative to manual surveys, but identifying species vocalisations requires large manually annotated training datasets, and is not always possible (e.g., for silent species). A new, intermediate approach is needed that rapidly predicts species occurrence without requiring extensive labelled data.We investigated whether local soundscapes could be used to infer the presence of 32 avifaunal and seven herpetofaunal species across a tropical forest degradation gradient in Sabah, Malaysia. We developed a machine-learning based approach to characterise species indicative soundscapes, training our models on a coarsely labelled manual point-count dataset.Soundscapes successfully predicted the occurrence of 34 out of the 39 species across the two taxonomic groups, with area under the curve (AUC) metrics of up to 0.87 (Bold-striped Tit-babblerMacronus bornensis). The highest accuracies were achieved for common species with strong temporal occurrence patterns.Soundscapes were a better predictor of species occurrence than above-ground biomass – a metric often used to quantify habitat quality across forest degradation gradients.Synthesis and applications: Our results demonstrate that soundscapes can be used to efficiently predict the occurrence of a wide variety of species. This provides a new direction for audio data to deliver large-scale, accurate assessments of habitat suitability using cheap and easily obtained field datasets.
Harnessing Ionic Selectivity In Acetyltransferase Chemoproteomic Probes
Authors: Jing Yihang , Montano Jose , Levy Michaella , Lopez Jeff , Kung Pei-Pei , Richardson Paul , Krajewski Krzysztof , Florens Laurence , Washburn Michael , Meier Jordan L. 
Published: September 2020

AbstractChemical proteomics provides a powerful strategy for the high-throughput assignment of enzyme function or inhibitor selectivity. However, identifying optimized probes for an enzyme family member of interest and differentiating signal from background remain persistent challenges in the field. To address this obstacle, here we report a physiochemical discernment strategy for optimizing chemical proteomics based on the Coenzyme A (CoA) cofactor. First, we synthesize a pair of CoA-based Sepharose pulldown resins differentiated by a single negatively charged residue, and find this change alters their capture properties in gel-based profiling experiments. Next, we integrate these probes with quantitative proteomics and benchmark analysis of ‘probe selectivity’ versus traditional ‘competitive chemical proteomics’. This reveals the former is well-suited for the identification of optimized pulldown probes for specific enzyme family members, while the latter may have advantages in discovery applications. Finally, we apply our anionic CoA pulldown probe to evaluate the selectivity of a recently reported small molecule N-terminal acetyltransferase inhibitor. These studies further validate the use of physical discriminant strategies in chemoproteomic hit identification and demonstrate how CoA-based chemoproteomic probes can be used to evaluate the selectivity of small molecule protein acetyltransferase inhibitors, an emerging class of pre-clinical therapeutic agents.
Effective control of a viral disease with a high transmission rate through selective predation
Authors: Chen Yonggui , Wang Muhua , Zhao Zhong , Weng Shaoping , Yang Jinchuan , Liu Shangyun , Liu Chang , Yuan Fenghua , Ai Bin , Zhang Haiqing , Zhang Mingyan , Lu Lirong , Yuan Kai , Yu Zhaolong , Mo Bibo , Zhong Zhiwei , Zheng Luwei , Feng Guocan , Li Shengwen Calvin , He Jianguo 
Published: September 2020

AbstractDue to the limited understanding of the characteristics of predator-pathogen-prey interactions, few attempts to use selective predation for controlling diseases in prey populations have been successful. The global pandemic of white spot syndrome (WSS), caused by white spot syndrome virus (WSSV), causes devastating economic losses in farmed shrimp production. Currently, there is no effective control for WSS. Here, we determined the transmission dynamics of WSSV and the feeding ability and selectivity of fish on healthy, infected and dead shrimp by experiments and mathematical modeling. Accordingly, we developed a novel and convenient shrimp cultural ecosystem, which that effectively prevented WSS outbreaks, by introducing aquaculture fish species. This provides a scheme for developing control strategies for viral diseases with high transmission rate.
Altered basal lipid metabolism underlies the functional impairment of naive CD8+T cells in elderly humans
Authors: Nicoli Francesco , Cabral-Piccin Mariela P. , Papagno Laura , Gallerani Eleonora , Folcher Victor , Dubois Marion , Clave Emmanuel , Vallet Hélène , Frere Justin J. , Gostick Emma , Llewellyn-Lacey Sian , Price David A. , Toubert Antoine , Boddaert Jacques , Caputo Antonella , Gavioli Riccardo , Appay Victor 
Published: September 2020

ABSTRACTBackgroundAging is associated with functional deficits in the naive T cell compartment, which compromise the generation ofde novoimmune responses against previously unencountered antigens. The mechanisms that underlie this phenomenon have nonetheless remained unclear.MethodsBiochemical and functional properties of naive CD8+T cells were characterized and compared between middle aged and older individuals.FindingsWe identified an age-related link between altered basal lipid metabolism in naive CD8+T cells and their impaired responsiveness to stimulation, characterized by low proliferative potential and susceptibility to apoptosis. Reversal of the bioenergetic anomalies with lipid-altering drugs, such as rosiglitazone, improved the functional capabilities of naive CD8+T cells in elderly subjects.InterpretationInterventions that favor lipid catabolism may find utility as adjunctive therapies in the elderly to promote vaccine-induced immunity against emerging pathogens or tumors.FundingA full list of the funding sources is detailed in the Acknowledgment section of the manuscript.RESEARCH IN CONTEXTEvidence before this studyOld subjects are highly susceptible to infections and tumors and usually present with low responses to vaccine. This is mainly due to the age-related loss of primary immune resources, i.e. a quantitative decline of naive CD8+T cells. Nonetheless, few studies have also underlined, within this cell subset, qualitative defects in elderly subjects.Added value of this studyConsidering the well-demonstrated link between nutrient usage and lymphocyte functions, we characterized the bioenergetics features of old naïve CD8+T cells. Our data show an age-dependent altered basal metabolism in this cell subset, mostly at the levels of fatty acids and mitochondrial functions. These alterations were associated with functional defects which were partially reverted through the use of lipid-lowering strategies.Implications of all the available evidenceThis study highlights the potential role of an altered cellular lipid metabolism in immunosenescence, providing clues to understand the epidemiological profile of emerging infections or tumors and to develop preventive and therapeutic strategies based on metabolic manipulation.
A Tree of Human Gut Bacterial Species and its Applications to Metagenomics and Metaproteomics Data Analysis
Authors: Stamboulian Moses , Doak Thomas G. , Ye Yuzhen 
Published: September 2020

Abstract1BackgroundRecent advances in genome and metagenome sequencing have dramatically enriched the collection of genomes of bacterial species related to human health and diseases. In metagenomic studies phylogenetic trees are commonly used to depict, describe, and compare the bacterial members of the community under study. The most accurate tree-building algorithms now use large sets of marker genes taken from across genomes. However, many of the current bacterial genomes were assembled from metagenomic datasets (i.e., metagenome assembled genomes, MAGs), and often contain missing information. It is therefore important to study how well the phylogeny approach performs on such genomes. Further, phylogeny methods are not perfect and it is important to know how reliable an inferred tree is.ResultsHere we examined the impact of incompleteness of the genomes on the tree reconstruction, and we showed that phylogeny approaches including RAxML (which handles missing data explicitly) and FastTree generally performed well on simulated collection of 400 genomes with missing information. As RAxML is computationally prohibitive for the much larger collections of gut genomes, we chose FastTree to build a unified tree of human-gut associated bacterial species (referred to as gut tree), including more than 3000 genomes, most of which are incomplete. We developed two downstream applications of the gut tree: peptide-centric analysis of metaproteomics datasets; and taxonomic characterization of metagenomic sequences. In both applications, the gut tree provided the basis for quantification of species composition at various taxonomic resolutions.ConclusionsThe gut tree presented in this study provides a useful framework for taxonomic profiling of human gut microbiome. Including MAGs in the tree provides more comprehensive representation of microbial species diversity associated with human gut, important for studying the taxonomic composition of gut microbiome.Availability and ImplementationThe tree construction pipeline and downstream applications of the gut tree are freely available athttps://github.com/mgtools/guttree.
The soybean (Glycine maxL.) cytokinin oxidase/dehydrogenase multigene family; identification of natural variations for altered cytokinin content and seed yield
Authors: Nguyen Hai Ngoc , Kambhampati Shrikaar , Kisiala Anna , Seegobin Mark , Emery RJ Neil 
Published: September 2020

AbstractCytokinins (CKs) play a fundamental role in regulating dynamics of organ source/sink relationships during plant development, including flowering and seed formation stages. As a result, CKs are key drivers of seed yield. The cytokinin oxidase/dehydrogenase (CKX) is one of the critical enzymes responsible for regulating plant CK levels by causing their irreversible degradation. Variation ofCKXgene activity is significantly correlated with seed yield in many crop species while in soybean (Glycine maxL.), the possible associations betweenCKXgene family members (GFMs) and yield parameters have not yet been assessed. In this study, seventeenGmCKXGFMs were identified, and natural variations amongGmCKXgenes were probed among soybean cultivars with varying yield characteristics. The keyCKXgenes responsible for regulating CK content during seed filling stages of reproductive development were highlighted using comparative phylogenetics, gene expression analysis and CK metabolite profiling. Five of the seventeen identifiedGmCKXGFMs, showed natural variations in the form of single nucleotide polymorphisms (SNPs). The geneGmCKX14, with high expression during critical seed filling stages, was found to have a non-synonymous mutation (H105Q), on one of the active site residues, Histidine 105, previously reported to be essential for co-factor binding to maintain structural integrity of the enzyme. Soybean lines with this mutation had higher CK content and desired yield characteristics. The potential for marker-assisted selection based on the identified natural variation withinGmCKX14, is discussed in the context of hormonal control that can result in higher soybean yield.Key MessageNatural variations in soybean cytokinin oxidase/dehydrogenase gene,GmCKX14, with high expression during seed development, were linked to increased sink strength via altered cytokinin profiles in high yielding cultivars.
Chickpea (Cicer arietinumL.) root system architecture adaptation to initial soil moisture improves seed development in dry-down conditions
Authors: Bontpart Thibaut , Robertson Ingrid , Giuffrida Valerio , Concha Cristobal , Scorza Livia C. T. , McCormick Alistair J. , Fikre Asnake , Tsaftaris Sotirios A. , Doerner Peter 
Published: September 2020

AbstractSoil water deficit (WD) impacts vascular plant phenology, morpho-physiology, and reproduction. Chickpea, which is mainly grown in semi-arid areas, is a good model plant to dissect mechanisms involved in drought resistance.We used a rhizobox-based phenotyping system to simultaneously and non-destructively characterise root system architecture (RSA) dynamics and water use (WU) patterns. We compared the drought-adaptive strategies of ‘Teketay’ to the drought-sensitive genotype ICC 1882 in high and low initial soil moisture without subsequent irrigation.WD restricted vegetative and reproductive organ biomass for both genotypes. Teketay displayed greater adaptability for RSA dynamics and WU patterns and revealed different drought adaptive strategies depending on initial soil moisture: escape when high, postponement when low. These strategies were manifested in distinct RSA dynamics: in low initial soil moisture, its reduced root growth at the end of the vegetative phase was followed by increased root growth in deeper, wetter soil strata, which facilitated timely WU for seed development and produced better-developed seeds.We demonstrate that RSA adaptation to initial soil moisture is one mechanism by which plants can tolerate WD conditions and ensure reproduction by producing well-developed seeds. Our approach will help in identifying the genetic basis for large plasticity of RSA dynamics which enhances the resilience with which crops can optimally adapt to various drought scenarios.HighlightRoot system architecture and water use patterns change dynamically for distinct drought adaptation strategies in chickpea.
The ER chaperones BiP and Grp94 regulate the formation of insulin-like growth factor 2 (IGF2) oligomers
Authors: Jin Yi , Kotler Judy L.M. , Wang Shiyu , Huang Bin , Halpin Jackson C. , Street Timothy O. 
Published: September 2020

AbstractWhile cytosolic Hsp70 and Hsp90 chaperones have been extensively studied, less is known about how the ER Hsp70 and Hsp90 paralogs (BiP and Grp94) recognize clients and influence their folding. Here, we examine how BiP and Grp94 influence the folding of insulin-like growth factor 2 (IGF2). Full-length proIGF2 is composed of an insulin-like hormone and an E-peptide that has sequence characteristics of an intrinsically disordered region. We find that the E-peptide region allows proIGF2 to form oligomers. BiP and Grp94 influence both the folding and the oligomerization of proIGF2. BiP and Grp94 exert a similar holdase function on proIGF2 folding by preferentially binding the proIGF2 unfolded state, rather than stabilizing specific folding intermediates and changing the proIGF2 folding process. In contrast, BiP and Grp94 exert counteracting effects on proIGF2 oligomerization. BiP suppresses proIGF2 oligomerization under both ADP and ATP conditions. Interestingly, Grp94 can enhance proIGF2 oligomerization when Grp94 adopts an open conformation (ADP conditions), but not when Grp94 is in the closed conformation (ATP conditions). We propose that BiP and Grp94 regulate the assembly of proIGF2 oligomers, and that regulated oligomerization may enable proIGF2 to be effectively packaged for export from the ER to the Golgi.
Super-relaxed state of myosin in human skeletal muscle is fiber-type dependent
Authors: Phung Lien A. , Foster Aurora D. , Miller Mark S. , Lowe Dawn A. , Thomas David D. 
Published: September 2020

AbstractThe myosin super-relaxed state (SRX) in skeletal muscle is hypothesized to play an important role in regulating muscle contractility and thermogenesis in humans, but has only been examined in model organisms. Here we report the first human skeletal muscle SRX measurements, using quantitative epifluorescence microscopy of fluorescent 2’/3’-O-(N-methylanthraniloyl) ATP (mantATP) single-nucleotide turnover. Myosin heavy chain (MHC) isoform expression was determined using gel electrophoresis for each permeabilized vastus lateralis fiber, to allow for novel comparisons of SRX between fiber-types. We find that the fraction of myosin in SRX is less in MHC IIA fibers than in MHC I and IIAX fibers (p = 0.008). ATP turnover of SRX is faster in MHC IIAX fibers compared to MHC I and IIA fibers (p = 0.001). We conclude that SRX biochemistry is measurable in human skeletal muscle, and our data indicate that SRX depends on fiber type as classified by MHC isoform. Extension from this preliminary work would provide further understanding regarding the role of SRX in human muscle physiology.