bluuebunny/crossref_metadata_2025_split huggingface dataset:
Why do people vary in disgust?
Authors: Tybur Joshua M. , Çınar Çağla , Karinen Annika K. , Perone Paola 
Published: June 2018

People vary in the degree to which they experience disgust toward—and, consequently, avoid—cues to pathogens. Prodigious work has measured this variation and observed that it relates to, among other things, personality, psychopathological tendencies, and moral and political sentiments. Less work has sought to generate hypotheses aimed at explaining why this variation exists in the first place, and even less work has evaluated how well data support these hypotheses. In this paper, we present and review the evidence supporting three such proposals. First, researchers have suggested that variability reflects a general tendency to experience anxiety or emotional distress. Second, researchers have suggested that variability arises from parental modelling, with offspring calibrating their pathogen avoidance based on their parents' reactions to pathogen cues. Third, researchers have suggested that individuals calibrate their disgust sensitivity to the parasite stress of the ecology in which they develop. We conclude that none of these hypotheses is supported by existing data, and we propose directions for future research aimed at better understanding this variation.This article is part of the Theo Murphy meeting issue ‘Evolution of pathogen and parasite avoidance behaviours’.
The role of social cognition in parasite and pathogen avoidance
Authors: Kavaliers Martin , Choleris Elena 
Published: June 2018

The acquisition and use of social information are integral to social behaviour and parasite/pathogen avoidance. This involves social cognition which encompasses mechanisms for acquiring, processing, retaining and acting on social information. Social cognition entails the acquisition of social information about others (i.e. social recognition) and from others (i.e. social learning). Social cognition involves assessing other individuals and their infection status and the pathogen and parasite threat they pose and deciding about when and how to interact with them. Social cognition provides a framework for examining pathogen and parasite avoidance behaviours and their associated neurobiological mechanisms. Here, we briefly consider the relationships between social cognition and olfactory-mediated pathogen and parasite avoidance behaviours. We briefly discuss aspects of (i) social recognition of actual and potentially infected individuals and the impact of parasite/pathogen threat on mate and social partner choice; (ii) the roles of ‘out-groups’ (strangers, unfamiliar individuals) and ‘in-groups’ (familiar individuals) in the expression of parasite/pathogen avoidance behaviours; (iii) individual and social learning, i.e. the utilization of the pathogen recognition and avoidance responses of others; and (iv) the neurobiological mechanisms, in particular the roles of the nonapeptide, oxytocin and steroid hormones (oestrogens) associated with social cognition and parasite/pathogen avoidance.This article is part of the Theo Murphy meeting issue ‘Evolution of pathogen and parasite avoidance behaviours'.
The structure and function of pathogen disgust
Authors: Curtis Val , de Barra Mícheál 
Published: June 2018

Researchers have long noted that many of the multiple elicitors of disgust have some relation to infectious disease. There is an emerging consensus that disgust evolved in Animalia to direct the behaviours that reduce risk of infection, so-called ‘parasite avoidance theory’. If this is correct, then the disgust motive should be structured in a manner that reflects the ways in which infectious disease can be avoided. In this study, we generated a set of items based on the epidemiology of disease transmission. These were then rated for their capacity to elicit disgust by a large, predominantly North American/UK sample and subjected to factor analysis to identify latent variables. While a number of plausible factor solutions emerged, Velicer's MAP (minimum average partial) test suggested six domains: atypical appearance, lesions, sex, hygiene, food and animals. This structure did not exactly mirror the transmission routes of infections, as we initially predicted, but it may rather reflect distinct kinds of behavioural tasks involved in avoiding disease. This finding makes sense from the perspective of a cognitive system that evolved under selection for a behavioural response to threats from the social and biological environment. We suggest that regularly occurring types of infectious disease problems have produced regularities in the domain structure ofpathogen disgustand discuss the implications of these results for understanding the structure, function and measurement of motives such as disgust in humans and other animals.This article is part of the Theo Murphy meeting issue ‘Evolution of pathogen and parasite avoidance behaviours’.
Chromomycin A2potently inhibits glucose-stimulated insulin secretion from pancreatic β cells
Authors: Kalwat Michael A , Hwang In Hyun , Macho Jocelyn , Grzemska Magdalena G , Yang Jonathan Z , McGlynn Kathleen , MacMillan John B , Cobb Melanie H 
Published: June 2018

ABSTRACTEnhancers or inhibitors of insulin secretion could become therapeutics as well as lead to the identification of requisite β-cell regulatory pathways and increase our understanding of pancreatic islet function. Toward this goal, we previously used an insulin-linked luciferase that is co-secreted with insulin in MIN6 β-cells to perform a high-throughput natural product screen for chronic effects on glucose-stimulated insulin secretion. Using multiple phenotypic analyses, we identified that one of the top natural product hits, chromomycin A2 (CMA2), potently inhibited insulin secretion through at least three mechanisms: disruption of Wnt signaling, interfering with β-cell gene expression, and suppression of triggering calcium (Ca2+) influx. Chronic treatment with CMA2 largely ablated glucose-stimulated insulin secretion even post-washout, but did not inhibit glucose-stimulated generation of ATP or Ca2+influx. However, by using the KATPchannel-opener diazoxide, we uncovered defects in depolarization-induced Ca2+influx which may contribute to the suppressed secretory response. Glucose-responsive ERK1/2 and S6 phosphorylation were also disrupted by chronic CMA2 treatment. The FUSION bioinformatic database indicated that the phenotypic effects of CMA2 clustered with a number of Wnt/GSK3 pathway-related genes. Consistently, CMA2 decreased GSK3 phosphorylation and suppressed activation of a β-catenin activity reporter. CMA2 and a related compound mithramycin are described to have DNA-interaction properties, possibly abrogating transcription factor binding to critical β-cell gene promoters. We observed that CMA2, but not mithramycin, suppressed expression of PDX1 and UCN3. However, neither expression of INSI/II nor insulin content was affected by chronic CMA2. The mechanisms of CMA2-induced insulin secretion defects may involve components both proximal and distal to Ca2+influx. Therefore, CMA2 is an example of a chemical that can simultaneously disrupt β-cell function through both non-cytotoxic and cytotoxic mechanisms. Future applications of CMA2 and similar aureolic acid analogs for disease therapies should consider the potential impacts on pancreatic islet function.
Microbiome interaction networks and community structure from lab-reared and field-collected Aedes aegypti, Aedes albopictus, and Culex quinquefasciatus mosquito vectors
Authors: Hegde Shivanand , Khanipov Kamil , Albayrak Levent , Golovko George , Pimenova Maria , Saldaña Miguel A. , Rojas Mark M , Hornett Emily A. , Motl Greg C. , Fredregill Chris L. , Dennett James A. , Debboun Mustapha , Fofanov Yuriy , Hughes Grant L. 
Published: June 2018

AbstractMicrobial interactions are an underappreciated force in shaping insect microbiome communities. Although pairwise patterns of symbiont interactions have been identified, we have a poor understanding regarding the scale and the nature of co-occurrence and co-exclusion interactions within the microbiome. To characterize these patterns in mosquitoes, we sequenced the bacterial microbiome of Aedes aegypti, Ae. albopictus, and Culex quinquefasciatus caught in the field or reared in the laboratory and used these data to generate interaction networks. For collections, we used traps that attracted host-seeking or ovipositing female mosquitoes to determine how physiological state affects the microbiome under field conditions. Interestingly, we saw few differences in species richness or microbiome community structure in mosquitoes caught in either trap. Co-occurrence and co-exclusion analysis identified 116 pairwise interactions substantially increasing the list of bacterial interactions observed in mosquitoes. Networks generated from the microbiome of Ae. aegypti often included highly interconnected hub bacteria. There were several instances where co-occurring bacteria co-excluded a third taxa, suggesting the existence of tripartite relationships. Several associations were observed in multiple species or in field and laboratory-reared mosquitoes indicating these associations are robust and not influenced by environmental or host factors. To demonstrate that microbial interactions can influence colonization of the host, we administered symbionts to Ae. aegypti larvae that either possessed or lacked their resident microbiota. We found that the presence of resident microbiota can inhibit colonization of particular bacterial taxa. Our results highlight that microbial interactions in mosquitoes are complex and influence microbiome composition.
Modified protocol for quick and large-scale transformation ofPichia pastoris
Authors: Kumar Ravinder 
Published: June 2018

AbstractOver the last couple of decades, methylotrophic yeast,Pichia pastorisemerges as an important yeast species owing to its increasing application in industry and basic biological research. Transformation ofPichia pastoriscells for the introduction of the gene of interest is common practice for expression and purification of a heterologous protein(s). Presently available protocol ofPichia pastoristransformation involves preparation of competent cells and followed by their transformation. Preparation of competent cells requires growth of cells to certain cell density which requires lots of resource, space, time and efforts. This limits the number of transformations that can be performed by an individual at a time. In the present paper, I will describe a modification in the available protocol which makesP. pastoristransformation hassle free. The present procedure does not require growth of pre-culture or growth of cells to certain cell density rather cells are grown in a patch on YPD plate(s) and rest procedure is performed in small eppendrof tubes which allow a large number of transformations in quickest possible time with minimal resource and efforts. In the end, I also compare various protocols in tabular form which allows the user to choose best suitable procedure depending on the available resource, time, number of transformations, requirement, and efforts. The present modified protocol does not require big centrifuge and shaker which further makes this procedure more useful. I believe that present protocol of transformation with its many unique features will be really helpful to those working withP. pastoris.
ASTN2 modulates synaptic strength by trafficking and degradation of surface proteins
Authors: Behesti Hourinaz , Fore Taylor , Wu Peter , Horn Zachi , Leppert Mary , Hull Court , Hatten Mary E 
Published: June 2018

AbstractSurface protein dynamics dictate synaptic connectivity and function in neuronal circuits.ASTN2, a gene disrupted by copy number variations (CNVs) in neurodevelopmental disorders, including autism spectrum, was previously shown to regulate the surface expression of ASTN1 in glial-guided neuronal migration. Here, we demonstrate that ASTN2 binds to and regulates the surface expression of multiple synaptic proteins in post-migratory neurons by endocytosis, resulting in modulation of synaptic activity. In cerebellar Purkinje cells (PCs), by immuno-gold electron microscopy, ASTN2 localizes primarily to endocytic and autophagocytic vesicles in the cell soma and in subsets of dendritic spines. Overexpression of ASTN2 in PCs, but not of ASTN2 lacking the FNIII-domain commonly disrupted by CNVs in patients including in a family presented here, increases inhibitory and excitatory postsynaptic activity and reduces levels of ASTN2 binding partners. Our data suggest a fundamental role for ASTN2 in dynamic regulation of surface proteins by endocytic trafficking and protein degradation.
ARGs-OSP: online searching platform for antibiotic resistance genes distribution in metagenomic database and bacterial whole genome database
Authors: Zhang An Ni , Hou Chen-Ju , Li Li-Guan , Zhang Tong 
Published: June 2018

AbstractBackgroundThe antibiotic resistant genes (ARGs) have been emerging as one of the top global issue s in both medical and environmental fields. The metagenomic analysis has been widely adopted in ARG-related studies, revealing a universal presence of ARGs in diverse environments from medical settings to natural habitats, even in drinking water and ancient permafrost. With the tremendous resources of accessible metagenomic datasets, it would be feasible and beneficial to construct a global profile of antibiotic resistome as a guidance of its phylogenetic and ecological distribution. And such information should be shared by an open webpage to avoid the unnecessary repeat of data processing and the bias caused by incompatible search method.ResultsTwo dataset collections, the Whole Genome Database (WGD, 54,718 complete and draft bacterial genomes) and the Metagenomic Database (MGD, 854 metagenomic datasets of 7 eco-types), were downloaded and analyzed using a standard method of ARG online analysis platform (ARGs-OAP v1.0). The representativeness of WGD and MGD was evaluated to have a comprehensive coverage of ARGs in bacterial genomes and metagenomes. Besides, an ARGs online searching platform (ARGs-OSP, http://args-osp.herokuapp.com/) was developed in this study to make the data accessible to other researchers via the search and download functionality. Finally, flexible usage of the ARGs-OAP was demonstrated by evaluating the co-occurrence of class 1 integrases and total ARGs across different environments.ConclusionsThe ARGs-OSP is presented in this study as the valuable sources and references for future studies with versatile research interests, meanwhile avoiding unnecessary re-computations and re-analysis.
What can computational modeling tell us about the diversity of odor-capture structures in the Pancrustacea?
Authors: Waldrop Lindsay D. , He Yanyan , Khatri Shilpa 
Published: June 2018

AbstractA major transition in the history of the Pancrustacea was the invasion of several lineages of these animals onto land. We investigated the functional performance of odor-capture organs, antennae with olfactory sensilla arrays, through the use of a computational model of advection and diffusion of odorants to olfactory sensilla while varying three parameters thought to be important to odor capture (Reynolds number, gap-width-to-sensillum-dameter ratio, and angle of the sensilla array with respect to oncoming flow). We also performed a sensitivity analysis on these parameters using uncertainty quantification to analyze their relative contributions to odor-capture performance. The results of this analysis indicate that odor capture in water and in air are fundamentally different. Odor capture in water and leakiness of the array are highly sensitive to Reynolds number and moderately sensitive to angle, whereas odor capture in air is highly sensitive to gap widths between sensilla and moderately sensitive to angle. Leakiness is not a good predictor of odor capture in air, likely due to the relative importance of diffusion to odor transport in air compared to water. We also used the sensitivity analysis to make predictions about morphological and kinematic diversity in extant groups of aquatic and terrestrial crustaceans. Aquatic crustaceans will likely exhibit denser arrays and induce flow within the arrays, whereas terrestrial crustaceans will rely on more sparse arrays with wider gaps and little-to-no animal-induced currents.
Planktonic Protist Biodiversity and Biogeography in Lakes From Four Brazilian River-Floodplain Systems
Authors: Lentendu Guillaume , Buosi Paulo Roberto Bressan , Cabral Adalgisa Fernada , Segóvia Bianca Trevisan , de Meira Bianca Ramos , Lansac-Tôha Fernando Miranda , Velho Luiz Felipe Machado , Ritter Camila , Dunthorn Micah 
Published: June 2018

ABSTRACTWhile the biodiversity and biogeography of protists inhabiting many ecosystems have been intensely studied using different sequencing approaches, tropical ecosystems are relatively under-studied. Here we sampled planktonic waters from 32 lakes associated with four different river-floodplains systems in Brazil, and sequenced the DNA using a metabarcoding approach with general eukaryotic primers. The lakes were dominated by the largely free-living Discoba (mostly the Euglenida) and Ciliophora unlike previously sampled Neotropical environments, bu the community similarities between samples were likewise low. These protists inhabiting these floodplains potentially form part of the large diversity of unknown diversity in the tropics.
O-GlcNAc Homeostasis Controls Cell Fate Decisions During Hematopoiesis
Authors: Zhang Zhen , Parker Matt P. , Graw Stefan , Novikova Lesya V. , Fedosyuk Halyna , Fontes Joseph D. , Koestler Devin C. , Peterson Kenneth R. , Slawson Chad 
Published: June 2018

AbstractThe addition of O-GlcNAc (a single β-D-N-acetylglucosamine sugar at serine and threonine residues) by O-GlcNAc transferase (OGT) and removal by O-GlcNAcase (OGA) maintains homeostatic levels of O-GlcNAc. We investigated the role of O-GlcNAc homeostasis in hematopoiesis utilizing G1E-ER4 cells carrying a GATA-1 transcription factor fused to the estrogen receptor (GATA-1ER) that undergo erythropoiesis following the addition of β-estradiol (E2) and myeloid leukemia cells that differentiate into neutrophils in the presence of all-trans retinoic acid. During G1E-ER4 differentiation, a decrease in overall O-GlcNAc levels and an increase in GATA-1 interactions with OGT and OGA were observed. Transcriptome analysis on G1E-ER4 cells differentiated in the presence of Thiamet-G (TMG), an OGA inhibitor, identified expression changes in 433 GATA-1 target genes. Chromatin immunoprecipitation demonstrated that the occupancy of GATA-1, OGT, and OGA atLaptm5gene GATA site was decreased with TMG. Myeloid leukemia cells showed a decline in O-GlcNAc levels during differentiation and TMG reduced the expression of genes involved in differentiation. Sustained treatment with TMG in G1E-ER4 cells prior to differentiation caused a reduction of hemoglobin positive cells during differentiation. Our results show that alterations in O-GlcNAc homeostasis disrupt transcriptional programs causing differentiation errors suggesting a vital role of O-GlcNAcylation in control of cell fate.
Practical Model Selection for Prospective Virtual Screening
Authors: Liu Shengchao , Alnammi Moayad , Ericksen Spencer S. , Voter Andrew F. , Ananiev Gene E. , Keck James L. , Hoffmann F. Michael , Wildman Scott A. , Gitter Anthony 
Published: June 2018

AbstractVirtual (computational) high-throughput screening provides a strategy for prioritizing compounds for experimental screens, but the choice of virtual screening algorithm depends on the dataset and evaluation strategy. We consider a wide range of ligand-based machine learning and docking-based approaches for virtual screening on two protein-protein interactions, PriA-SSB and RMI-FANCM, and present a strategy for choosing which algorithm is best for prospective compound prioritization. Our workflow identifies a random forest as the best algorithm for these targets over more sophisticated neural network-based models. The top 250 predictions from our selected random forest recover 37 of the 54 active compounds from a library of 22,434 new molecules assayed on PriA-SSB. We show that virtual screening methods that perform well in public datasets and synthetic benchmarks, like multi-task neural networks, may not always translate to prospective screening performance on a specific assay of interest.
Habitat heterogeneity drives scale-dependent biodiversity loss in a temperate marine ecosystem
Authors: Starko Samuel , Bailey Lauren , Creviston Elandra , James Katelyn , Warren Alison , Neufeld Christopher J. 
Published: June 2018

AbstractBiodiversity loss is driven by interacting factors operating at different spatial scales. Yet, there remains uncertainty as to how fine-scale environmental conditions mediate biological responses to broad-scale stressors. We surveyed mid-latitude kelp bed habitats to determine whether local habitat heterogeneity has mediated changes in community diversity after more than two decades of extreme temperature events, most notably the 2013-2016 heat wave. Local wave exposure conditions were key in determining responses, with some habitats remaining stable and others experiencing near complete diversity loss, leading to local declines without regional extinctions. Wave-sheltered shores, which saw the largest declines, are a very common habitat type in the Northeast Pacific and may be especially sensitive to climate-related losses in kelp diversity and abundance. Our findings highlight how local gradients can interact with global drivers to facilitate diversity loss and demonstrate how incorporating differences between habitat patches can be essential to capturing scale-dependent biodiversity loss across the landscape.
FADS1and the timing of human adaptation to agriculture
Authors: Mathieson Sara , Mathieson Iain 
Published: June 2018

AbstractVariation at theFADS1/FADS2gene cluster is functionally associated with differences in lipid metabolism and is often hypothesized to reflect adaptation to an agricultural diet. Here, we test the evidence for this relationship using both modern and ancient DNA data. We show that almost all the inhabitants of Europe carried the ancestral allele until the derived allele was introduced approximately 8,500 years ago by Early Neolithic farming populations. However, we also show that it was not under strong selection in these populations. We find that this allele, and other proposed agricultural adaptations atLCT/MCM6andSLC22A4, were not strongly selected until much later, perhaps as late as the Bronze Age. Similarly, increased copy number variation at the salivary amylase geneAMY1is not linked to the development of agriculture although, in this case, the putative adaptation precedes the agricultural transition. Our analysis shows that selection at theFADSlocus was not tightly linked to the initial introduction of agriculture and the Neolithic transition. Further, it suggests that the strongest signals of recent human adaptation in Europe did not coincide with the Neolithic transition but with more recent changes in environment, diet or efficiency of selection due to increases in effective population size.