bluuebunny/crossref_metadata_2025_split huggingface dataset:
A collection ofSerratia marcescensdiffering in their insect pathogenicity towardsManduca sextalarvae
Authors: Jensen Ellen C. , Katz Amburn Diana Sue , Schlegel Aimee Hultine , Nickerson Kenneth W. 
Published: July 2020

AbstractWe investigated the ability ofSerratia marcescensto killManduca sexta(tobacco/tomato hornworm) larvae following injection of ca. 5 × 105bacteria into the insect hemolymph. Fifteen bacterial strains were examined, including 12 non-pigmented clinical isolates from humans. They fell into 6 groups depending on the timing and rate at which they caused larval death. Relative insect toxicity was not correlated with pigmentation, colony morphology, biotype, motility, capsule formation, iron availability, surfactant production, swarming ability, antibiotic resistance, bacteriophage susceptibility, salt tolerance, nitrogen utilitization patterns, or the production of 4 exoenzymes: proteases, DNase, lipase, or phospholipase. There were marked differences in chitinase production, the types of homoserine lactone (HSL) quorum sensing molecules produced, and the blood agar hemolysis patterns observed. However, none of these differences correlated with the six insect larval virulence groups. Thus, the actual offensive or defensive virulence factors possessed by these strains remain unidentified. The availability of this set ofS. marcescensstrains, covering the full range from highly virulent to non-virulent, should permit future genomic comparisons to identify the precise mechanisms of larval toxicity.
Livestock grazing is associated with seasonal reduction in pollinator biodiversity and functional dispersion but cheatgrass invasion is not: variation in bee assemblages in a multi-use shortgrass prairie
Authors: Thapa-Magar Khum Bahadur , Davis Thomas Seth , Kondratieff Boris C. 
Published: July 2020

AbstractLivestock grazing and non-native plant species affect rangeland habitats globally. These factors may have important effects on ecosystem services including pollination, yet, interactions between pollinators, grazing, and invasive plants are poorly understood. To address this, we tested the hypothesis that cattle grazing and site colonization by cheatgrass (Bromus tectorum) impact bee foraging and nesting habitats, and the biodiversity of wild bee communities, in a shortgrass prairie system. Bee nesting habitats (litter and wood cover) were marginally improved in non-grazed sites, though foraging habitat (floral cover and richness) did not differ among grazed, non-grazed, or cheatgrass colonized sites. However, floral cover was a good predictor of bee abundance and functional dispersion. Mean bee abundance, richness, diversity and functional diversity were significantly lower in cattle-grazed habitats than in cheatgrass-colonized or non-grazed habitats. Differences in bee diversity among habitats were pronounced early in the growing season (May) but by late-season (August) these differences eroded. Fourth-corner analysis revealed that sites with high floral cover tended to support large, social, polylectic bees; sites with high grass cover tended to support oligolectic solitary bees. Both cattle-grazed and cheatgrass-colonized sites were associated with lower abundances of above-ground nesting bees but higher abundance of below-ground nesters. We conclude that cheatgrass-invaded sites are not associated with reduced bee biodiversity or abundance, but cattle grazing was negatively associated with bee abundances and altered species composition. Although floral cover is an important predictor of bee assemblages, this was not impacted by grazing and our suggests that cattle likely impact bee communities through effects other than those mediated by forbs, including soil disturbance or nest destruction. Efforts aimed at pollinator conservation in prairie habitats should focus on managing cattle impacts early in the growing season to benefit sensitive bee species.
Enhanced BCR signalling inflicts early plasmablast and germinal centre B cell death
Authors: Yam-Puc JC , Zhang L , Maqueda-Alfaro RA , Garcia-Ibanez L , Zhang Y , Davies J , Senis YA , Snaith M , Toellner KM 
Published: July 2020

AbstractIt is still not clear how B-cell receptor (BCR) signalling intensity affects plasma cell and germinal centre (GC) B cell differentiation. We generated Cγ1Cre/+Ptpn6fl/flmice where SHP-1, a negative regulator of BCR signalling, is deleted rapidly after B cell activation. Although immunisation with T-dependent antigens increased BCR signalling, it led to plasma cells reduction and increased apoptosis. Dependent on the antigen, the early GC B cell response was equally reduced and apoptosis increased. At the same time, a higher proportion of GC B cells expressed cMYC, indicating increased GC B cell – Tfh cell interactions. While GC B cell numbers returned to normal at later stages, affinity maturation was suppressed in the long term. This confirms that BCR signalling not only directs affinity dependent B cell selection but also, without adequate Tfh cell help, can inflict cell death, which may be important for the maintenance of B cell tolerance.
A pilot study of the effect of deployment on the gut microbiome and traveler’s diarrhea susceptibility
Authors: Stamps Blake W. , Lyon Wanda J. , Irvin Adam P. , Kelley-Loughnane Nancy , Goodson Michael S. 
Published: July 2020

AbstractTraveler’s diarrhea (TD) is a recurrent and significant issue for many travelers including the military. While many known enteric pathogens exist that are causative agents of diarrhea, our gut microbiome may also play a role in travelers’ diarrhea susceptibility. To this end we conducted a pilot study of the microbiome of warfighters prior to- and after deployment overseas to identify marker taxa relevant to traveler’s diarrhea. This initial study utilized full-length 16S rRNA gene sequencing to provide additional taxonomic resolution towards identifying predictive taxa.16S rRNA analyses of pre- and post-deployment fecal samples identified multiple marker taxa as significantly differentially abundant in subjects that reported diarrhea, including Weissella, Butyrivibrio, Corynebacterium, uncultivated Erysipelotrichaceae, Jeotgallibaca, unclassified Ktedonobacteriaceae, Leptolinea, and uncultivated Ruminiococcaceae. The ability to identify TD risk prior to travel will inform prevention and mitigation strategies to influence diarrhea susceptibility while traveling.
Proteolytic cleavage ofArabidopsis thalianaphosphoenolpyruvate carboxykinase-1 modifies its allosteric regulation
Authors: Rojas Bruno E. , Hartman Matías D. , Figueroa Carlos M. , Iglesias Alberto A. 
Published: July 2020

AbstractPhosphoenolpyruvate carboxykinase (PEPCK) plays a crucial role in gluconeogenesis. In this work, we analyze the proteolysis ofArabidopsis thalianaPEPCK1 (AthPEPCK1) in germinating seedlings. We found that expression ofAthPEPCK1 peaks at 24-48 hours post-imbibition. Concomitantly, we observed shorter versions ofAthPEPCK1, putatively generated by metacaspase-9 (AthMC9). To study the impact ofAthMC9 cleavage on the kinetic and regulatory properties ofAthPEPCK1, we produced truncated mutants based on the reportedAthMC9 cleavage sites. The Δ19 and Δ101 truncated mutants ofAthPEPCK1 showed similar kinetic parameters and the same quaternary structure than the WT. However, activation by malate and inhibition by glucose 6-phosphate were abolished in the Δ101 mutant. We propose that proteolysis ofAthPEPCK1 in germinating seedlings operates as a mechanism to adapt the sensitivity to allosteric regulation during the sink-to-source transition.HighlightThis paper describes the effects of the N-terminal proteolytic cleavage on the kinetic and regulatory properties ofArabidopsis thalianaphosphoenolpyruvate carboxykinase-1.
The molecular taxonomy of primate amygdala via single-nucleus RNA-sequencing analysis
Authors: Zhang Lei , Cheng Yanyong , Wu Shihao , Lu Yufeng , Xue Zhenyu , Chen Dai , Zhang Bo , Qiu Zilong , Jiang Hong 
Published: July 2020

ABSTRACTAmygdala is the central brain region governing emotional responses of mammals. However, the detailed molecular taxonomy of amygdala in higher mammals such as primates is still absent. Here we present the molecular taxonomy of amygdala in rhesus monkeys by single-cell RNA sequencing analysis. We found that there are five major cell types in primate amygdala, glutamatergic neurons, GABAergic neurons, astroglia, oligodendrocytes and oligodendrocyte progenitor cells (OPCs). Glutamatergic neurons in the primate amygdala exhibits a great diversity comparing to them in the rodent amygdala. In particular, GABAergic neurons in primate amygdala appeared to be quite unique and contain different cellular composition as them in rodent amygdala. The astroglia in primate amygdala contains two more subtypes comparing to astroglia in rodent amygdala. Taken together, although the evolutionary conservation, the molecular taxonomy study of primate amygdala provides critical insights for understanding the cellular architecture of the primate brain.
How does an ectodomain of membrane-associated proteins stand upright and exert robust signal?
Authors: Lankipalli Swetha , Ramagopal Udupi A. 
Published: July 2020

AbstractEven after decades of research, a comprehensive mechanism that elucidates the underpinnings of signaling through the cell membrane is still elusive. Here, we address a simple question- “how does the ectodomain of a membrane-associated protein consisting of multiple domains and connected by flexible linkers stand ‘upright’ on the membrane?”. Our analysis based on large amount of available structural and functional data, looking for a pattern of association of these molecules in the crystal structures and with the concept that ‘random things seldom repeat’ lead to a surprisingly interesting and consistent observation that (1) the weakcis-interaction mediated symmetric oligomerization of signaling molecules not only support their ‘upright’ orientation but often bury their ligand-binding surface to avoid spurious signaling (2) the linkers connecting the domains are probably not flexible as presumed. This analysis provides a model for pre-liganded receptor supramolecular organization that resolves some of the mysteries unanswered by hypothesis such as ‘lipid-rafts’ and ‘fence and pickets. With CD4, pMHCII, CD2 and TNFR1 as examples, we show that the observedcis-association of molecules also correlate well with their functional role. Further, our analysis reconciles the long-standing controversies related to these molecules and appear to be generic enough to be applied to other signaling molecules.
Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds
Authors: Di Muri C. , Handley L.L. , Bean C.W. , Li J. , Peirson G. , Sellers G.S. , Walsh K. , Watson H.V. , Winfield I.J. , Hänfling B. 
Published: July 2020

AbstractThe sampling of environmental DNA (eDNA) coupled with cost-efficient and ever-advancing sequencing technology is propelling changes in biodiversity monitoring within aquatic ecosystems. Despite the growth of DNA metabarcoding approaches, the ability to quantify species biomass and abundance in natural systems remains a major challenge. Few studies have examined the association between eDNA metabarcoding data and biomass inferred by whole-organism sampling, mesocosms or mock communities, and the interpretation of sequencing reads as a measure of biomass or number of organisms is largely disputed.Here we tested whether read counts from eDNA metabarcoding provide accurate quantitative estimates of fish abundance in holding ponds with known fish biomass and number of individuals.eDNA samples were collected from two fishery ponds with high fish density and broad species diversity. In one pond, two different DNA capture strategies (on-site filtration with enclosed filters and three different preservation buffers versus lab filtration using open filters) were used to evaluate their performance in relation to fish community composition and biomass/abundance estimates. Fish species read counts were significantly correlated with both biomass and abundance, and this result, together with information on fish diversity, was repeatable when open or enclosed filters with different preservation buffers were used.This research demonstrates that eDNA metabarcoding provides accurate qualitative and quantitative information on fish communities in small ponds, and results are consistent between different methods of DNA capture. This method flexibility will be beneficial for future eDNA-based fish monitoring and their integration into fisheries management.
Halophytic bacterial endophytome: a potential source of beneficial microbes for a sustainable agriculture
Authors: Christakis Christos A. , Daskalogiannis Georgia , Chatzakis Anastasia , Markakis Emmanouil A. , Sagia Angeliki , Rizzo Giulio Flavio , Catara Vittoria , Lagkouvardos Ilias , Studholme David J. , Sarris Panagiotis F. 
Published: July 2020

AbstractHalophytes have evolved several strategies to survive in saline environments; however, additional support from their associated microbiota could help combat adverse conditions. Endophytic communities of halophytes may be different than those in other plants because salinity acts as an environmental filter. At the same time, they may contribute to the host’s adaptation to adverse environmental conditions and can improve host tolerance against various biotic and abiotic stresses, which may be of importance in modern and sustainable agriculture.In this study the culturable endophytic bacteria of three halophytic speciesCakile maritima,Matthiola tricuspidataandCrithmum maritimumwere isolated and identified. Endophytic bacteria were isolated from roots and leaves of the sampled plants. Significant differences were observed in bacterial species abundance among different plant species and tissue from which the isolates were obtained. In total, 115 strains were identified by analysis of complete 16S rDNA sequences, while the majority of these isolates were derived from the root samples.The strains were evaluated for their ability to: 1) growin-vitroin high levels of NaCl; 2) inhibit the growth of the economically important plant pathogenic fungusVerticillium dahliae in vitroandin planta, the human pathogenic fungusAspergillus fumigatus in vitro, as well as, the economically important plant bacterial pathogensRalstonia solanacearumandClavibacter michiganensis in vitro; 3) provide salt tolerancein planta; 4) provide growth promoting effectin planta.Additionally, the genomes of twelve selected isolates, exhibiting interesting features, were sequenced and analysed. Three novel bacterial species were identified that belong to the genusPseudomonas(two strains) andArthrobacter(one strain).The outcome of our study is the proof-of-concept that the crop wild relatives (CWR) halophytic microbiome could potentially serve as a source of beneficial microorganisms that could be used (as unique species or as artificial communities) as Bio-Inoculants, for the enhancement of plant growth and stress tolerance in crops, including the high-salinity stress.This is very important in the era of ecosystem degradation and climate change, where the maximizing microbial functions in agroecosystems could be a prerequisite for the future of global sustainable agriculture. Globally, there is a strong need for the identification and bio-banking of novel beneficial endophytic microbes with as many desirable characters, for the development of a new environmentally friendly global strategy in food production that will be based in the sustainable agriculture with low chemical inputs and a low environmental impact.
Heterodimeric insecticidal peptide provides new insights into the molecular and functional diversity of ant venoms
Authors: Touchard Axel , Mendel Helen C. , Boulogne Isabelle , Herzig Volker , Emidio Nayara Braga , King Glenn F. , Triquigneaux Mathilde , Jaquillard Lucie , Béroud Rémy , De Waard Michel , Delalande Olivier , Dejean Alain , Muttenthaler Markus , Duplais Christophe 
Published: July 2020

AbstractAnts use venom for predation, defence and communication, however, the molecular diversity, function and potential applications of ant venom remains understudied compared to other venomous lineages such as arachnids, snakes and cone snails. In this work, we used a multidisciplinary approach that encompassed field work, proteomics, sequencing, chemical synthesis, structural analysis, molecular modelling, stability studies, and a series ofin vitroandin vivobioassays to investigate the molecular diversity of the venom of the AmazonianPseudomyrmex penetratorants. We isolated a potent insecticidal heterodimeric peptide Δ-pseudomyrmecitoxin-Pp1a (Δ-PSDTX-Pp1a) composed of a 27-residue long A-chain and a 33-residue long B-chain crosslinked by two disulfide bonds in an antiparallel orientation. We chemically synthesised Δ-PSDTX-Pp1a, its corresponding parallel AA and BB homodimers, and its monomeric chains and demonstrated that Δ-PSDTX-Pp1a had the most potent insecticidal effects in blow fly assays (LD50= 3 nM). Molecular modelling and circular dichroism studies revealed strong alpha-helical features, indicating its cytotoxic effects could derive from membrane disruption, which was further supported by insect cell calcium assays. The native heterodimer was also substantially more stable against proteolytic degradation (t1/2=13 h) than its homodimers or monomers (t1/2<20 min), indicating an evolutionary advantage of the more complex structure. The proteomic analysis ofPseudomyrmex penetratorvenom and in-depth characterisation of Δ-PSDTX-Pp1a provide novel insights in the structural complexity of ant venom, and further exemplifies how nature exploits disulfide-bond formation and dimerization to gain an evolutionary advantageviaimproved stability; a concept that is also highly relevant for the design and development of peptide therapeutics, molecular probes and bioinsecticides.
Functional dispersion of wetland birds, invertebrates and plants more strongly influenced by hydroperiod than each other
Authors: Daniel Jody , Rooney Rebecca C 
Published: July 2020

AbstractThe relative role of biological and abiotic filters on the assembly of co-occurring taxa is widely debated. While some authors point to biological interactions (e.g., competition) as the stronger driver of ecological selection, others assert that abiotic conditions are more important because they filter species at the regional level. Because communities influenced by a dominant abiotic filter, (e.g., Prairie Pothole Region (PPR) wetlands, each varying in ponded water permanence), often have strong cross-taxon relationships, we can study these communities to better understand the relative influence of abiotic vs biotic filters on community structure. Using functional dispersion as our measure of communities, we test six alternate hypotheses about the relative importance of various pathways representing influence of biological and permanence filters on birds, aquatic macroinvertebrates and wetland plants in the northwest PPR using structural equation modeling. We aimed to understand whether: 1) ponded water permanence alone explained functional dispersion; 2) the influence of permanence on functional dispersion was direct or mediated; and 3) abiotic filtering by permanence was stronger than biotic filtering by co-occurring taxa. The best model suggests that there is a direct influence of permanence on the functional dispersion of each taxonomic group and that both bird and macroinvertebrate functional dispersion are causally related to plant functional dispersion, though for invertebrates the influence of plants is much less than that of permanence. Thus, the relative importance of wetland permanence and the functional dispersion of co-occurring taxa depends on which taxon is considered in PPR wetlands.
The influence of liver fluke infection on production in sheep and cattle: a meta-analysis
Authors: Hayward Adam D. , Skuce Philip J. , McNeilly Tom N. 
Published: July 2020

ABSTRACTLiver flukes (Fasciolaspp) are important parasites of sheep and cattle across the world, causing significant damage to animal health and productivity due to both acute and chronic infection. Many comprehensive reviews have discussed the results of decades of research into the impact of fluke infection on livestock performance traits such as weight gain and milk production. While fluke are considered to be important, there have been no attempts to collate previous research in a quantitative manner, and nor has there been an attempt to determine why some studies find substantial effects of fluke while others conclude that effects of fluke on animal performance are negligible. In this study, we used meta-analysis to provide quantitative estimates of the impact of liver fluke on animal performance, and to identify elements of study design that influence the conclusions of such studies. A literature search provided 233 comparisons of performance in “fluke-infected” and “uninfected” animals. We standardized these data as log response ratios and calculated effect size variances in order to weight studies by their sample size and accuracy of their estimates. We performed multi-level meta-analysis to estimate effects of fluke infection in five traits: daily weight gain (N = 77); live weight (N = 47); carcass weight (N = 84); total weight gain (N = 18) and milk production (N = 6). There were significant negative effects of fluke infection on daily weight gain, live weight and carcass weight (9%, 6% and 0.6% reductions in performance, respectively), but not total weight gain or milk production. We then used mixed-effects meta-analysis to estimate the impact of moderator variables, including host, fluke, and study design factors, on study outcomes. We found that, in general, studies that gave experimental infections found generally larger effects of fluke than observational or drug studies; younger animals were more likely to suffer the effects of fluke infection on daily weight gain; and that effects on live weight increased across the course of an experiment. Our results provide the first quantitative estimate of the importance of liver fluke on performance across studies and highlight the elements of study design that can influence conclusions. Furthermore, our literature search revealed areas of research into liver fluke that could be the subject of greater effort, and types of study that could form the basis of future meta-analyses.