bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biogeographical patterns and diversity in the diet of the culpeo (Lycalopex culpaeus) in South America
Authors: Lozano Jorge , Guntiñas Marta , Cisneros Rodrigo , Llorente Esther , Malo Aurelio F. 
Published: September 2021

ABSTRACTHere we describe the dietary patterns of the culpeo (or Andean fox) at a biogeographical scale. We also analyze the influence of exotic lagomorphs on its diet and explore differences between culpeo subspecies. We selected 17 mutually comparable diet studies, which include 19 independent diet assessments. Then, we extracted and standardized the values of the different diet components from these studies and calculated the relative frequency of occurrence (RF) of the ten main trophic groups that we found. Further, we calculated the Shannon-Wienner H’ trophic diversity index.The results showed that small mammals (41%), lagomorphs (21%), invertebrates (12.4%) and large herbivores (7.3%) were the most consumed groups. A factorial analysis of all trophic groups rendered four orthogonal factors that were used as response variables in relation to a set of environmental predictors. Altitude correlated with most factors (i.e. trophic groups). Exotic lagomorphs were consumed in lowlands, in higher latitudes and in regions showing high values of the human footprint index, replacing in these areas native fauna as the main prey. There were no differences in diet between the two main culpeo subspecies analysed, L.c. culpaeus and L.c. andinus.Finally, the best explanatory models (GLM) of trophic diversity selected, using the Akaike’s information criterion (AIC), showed that the most diverse diets were those composed of large herbivores, edentates, carnivorous species, birds and herptiles (i.e. amphibians and reptils), in areas of high rainfall located in protected areas. Neither latitude nor altitude seemed to have an effect on the trophic diversity of the culpeos, as they were not retained by the final models.
A faithful in vivo model of human macrophages in metastatic melanoma
Authors: Voillet Valentin , Berger Trisha R. , McKenna Kelly M. , Paulson Kelly G. , Smythe Kimberly S. , Hunter Daniel S. , Valente William J. , Weaver Stephanie , Campbell Jean S. , Kim Teresa S. , Byrd David R. , Bielas Jason H. , Pierce Robert H. , Chapuis Aude G. , Gottardo Raphaël , Rongvaux Anthony 
Published: September 2021

AbstractDespite recent therapeutic progress, advanced melanoma remains lethal for many patients. The composition of the immune tumor microenvironment (TME) has decisive impacts on therapy response and disease outcome. High dimensional analyses of patient samples can reveal the composition and heterogeneity of the immune TME. In particular, macrophages are known for their cancer-supportive role, but the underlying mechanisms are incompletely understood, and experimental in vivo systems are needed to test the functional properties of these cells. We characterized a humanized mouse model, reconstituted with a human immune system and a human melanoma, in which: (1) human macrophages support metastatic spread of the tumor; and (2) tumor-infiltrating macrophages have a specific transcriptional signature that faithfully represents the transcriptome of macrophages from patient melanoma samples and is associated with shorter survival. This model complements patient sample analyses, enabling the elucidation of fundamental principles in melanoma biology, and the development and evaluation of candidate therapies.
Lateralized phenotypic differences after intrahippocampal kainic acid injection in female mice
Authors: Cutia Cathryn A. , Leverton Leanna K. , Ge Xiyu , Youssef Rana , Raetzman Lori T. , Christian-Hinman Catherine A. 
Published: September 2021

AbstractClinical evidence indicates that patients with temporal lobe epilepsy (TLE) often show differential outcomes of comorbid conditions in relation to the lateralization of the seizure focus. A particularly strong relationship exists between the side of seizure focus and the propensity for distinct reproductive endocrine comorbidities in women with TLE. Therefore, here we evaluated whether targeting of left or right dorsal hippocampus for intrahippocampal kainic acid (IHKA) injection, a model of TLE, produces different outcomes in hippocampal granule cell dispersion, body weight gain, and multiple measures of reproductive endocrine dysfunction in female mice. One, two, and four months after IHKA or saline injection, in vivo measurements of estrous cycles and weight were followed by ex vivo examination of hippocampal dentate granule cell dispersion, circulating ovarian hormone and corticosterone levels, ovarian morphology, and pituitary gene expression. IHKA mice with right-targeted injection (IHKA-R) showed greater granule cell dispersion and pituitary Fshb expression compared to mice with left-targeted injection (IHKA-L). By contrast, pituitary expression of Lhb and Gnrhr were higher in IHKA-L mice compared to IHKA-R, but these values were not different from respective saline-injected controls. IHKA-L mice also showed an increased rate of weight gain compared to IHKA-R mice. Increases in estrous cycle length, however, were similar in both IHKA-L and IHKA-R mice. These findings indicate that although major reproductive endocrine dysfunction phenotypes present similarly after targeting left or right dorsal hippocampus for IHKA injection, distinct underlying mechanisms based on lateralization of epileptogenic insult may contribute to produce similar emergent reproductive endocrine outcomes.HighlightsGreater granule cell dispersion with right-sided IHKA injectionChanges in pituitary gene expression vary with side of injectionIncreased weight gain after left-sided injectionSimilar estrous cycle disruption after injection of left or right hippocampus
Extending the CWM approach to intraspecific trait variation: how to deal with overly optimistic standard tests?
Authors: Zelený David , Helsen Kenny , Lee Yi-Nuo 
Published: September 2021

AbstractCommunity weighted means (CWMs) are widely used to study the relationship between community-level functional traits and environment. For certain null hypotheses, CWM-environment relationships assessed by linear regression or ANOVA and tested by standard parametric tests are prone to inflated Type I error rates. Previous research has found that this problem can be solved by permutation tests (i.e. the max test). A recent extension of the CWM approach allows the inclusion of intraspecific trait variation (ITV) by the separate calculation of fixed, site-specific, and intraspecific CWMs. The question is whether the same Type I error rate inflation exists for the relationship between environment and site-specific or intraspecific CWM. Using simulated and real-world community datasets, we show that site-specific CWM-environment relationships have also inflated Type I error rate, and this rate is negatively related to the relative ITV magnitude. In contrast, for intraspecific CWM-environment relationships, standard parametric tests have the correct Type I error rate, although somewhat reduced statistical power. We introduce an ITV-extended version of the max test, which can solve the inflation problem for site-specific CWM-environment relationships and, without considering ITV, becomes equivalent to the "original" max test used for the CWM approach. We show that this new ITV-extended max test works well across the full possible magnitude of ITV on both simulated and real-world data. Most real datasets probably do not have intraspecific trait variation large enough to alleviate the problem of inflated Type I error rate, and published studies possibly report overly optimistic significance results.
Evaluating the power and limitations of genome-wide association mapping in C. elegans
Authors: Widmayer Samuel J. , Evans Kathryn , Zdraljevic Stefan , Andersen Erik C. 
Published: September 2021

ABSTRACTA central goal of evolutionary genetics in Caenorhabditis elegans is to understand the genetic basis of traits that contribute to adaptation and fitness. Genome-wide association (GWA) mappings scan the genome for individual genetic variants that are significantly correlated with phenotypic variation in a population, or quantitative trait loci (QTL). GWA mappings are a popular choice for quantitative genetic analyses because the QTL that are discovered segregate in natural populations. Despite numerous successful mapping experiments, the empirical performance of GWA mappings has not, to date, been formally evaluated for this species. We developed an open-source GWA mapping pipeline called NemaScan and used a simulation-based approach to provide benchmarks of mapping performance among wild C. elegans strains. Simulated trait heritability and complexity determined the spectrum of QTL detected by GWA mappings. Power to detect smaller-effect QTL increased with the number of strains sampled from the C. elegans Natural Diversity Resource (CeNDR). Population structure was a major driver of variation in GWA mapping performance, with populations shaped by recent selection exhibiting significantly lower false discovery rates than populations composed of more divergent strains. We also recapitulated previous GWA mappings of experimentally validated quantitative trait variants. Our simulation-based evaluation of GWA performance provides the community with critical context for pursuing quantitative genetic studies using CeNDR to elucidate the genetic basis of complex traits in C. elegans natural populations.
HypVW is an HOCl-Sensing Two Component System in Escherichia coli
Authors: El Hajj Sara , Henry Camille , Vergnes Alexandra , Loiseau Laurent , Brasseur Gaël , Barré Romain , Aussel Laurent , Ezraty Benjamin 
Published: September 2021

ABSTRACTTwo component systems (TCS) are signalling pathways that allow bacterial cells to sense, respond and adapt to fluctuating environments. Among the classical TCS of Escherichia coli, YedVW has been recently showed to be involved in the regulation of msrPQ, encoding for the periplasmic methionine sulfoxide reductase system. In this study, we demonstrate that hypochlorous acid (HOCl) induces the expression of msrPQ in a YedVW dependant manner, whereas H2O2, NO and paraquat (a superoxide generator) do not. Therefore, YedV appears to be an HOCl-sensing histidine kinase. Based on this finding, we proposed to rename this system HypVW. Moreover, using a directed mutagenesis approach, we show that Met residues located in the periplasmic loop of HypV (formerly YedV) are important for its activity. Given that HOCl oxidizes preferentially Met residues, we bring evidences that HypV could be activated via the reversible oxidation of its methionine residues, thus conferring to MsrPQ a role in switching HypVW off. Based on these results, we propose that the activation of HypV by HOCl could occur through a Met redox switch. HypVW appears to be the first characterized TCS able to detect HOCl in E. coli. This study represents an important step in understanding the mechanisms of reactive chlorine species resistance in prokaryotes.IMPORTANCEUnderstanding molecularly how bacteria respond to oxidative stress is crucial to fight pathogens. HOCl is one of the most potent industrial and physiological microbiocidal oxidant. Therefore, bacteria have developed counterstrategies to survive HOCl-induced stress. Over the last decade, important insights into these bacterial protection factors have been obtained. Our work establishes HypVW as an HOCl-sensing two component system in Escherichia coli MG1655 which regulates the expression of the periplasmic HOCl-oxidized proteins repair system MsrPQ. Moreover we bring evidences suggesting that HOCl could activate HypV through a methionine redox switch.
Stimulation related artifacts and a multipurpose template-based offline removal solution for a novel sensing-enabled deep brain stimulation device
Authors: Hammer Lauren H , Kochanski Ryan B , Starr Philip A , Little Simon 
Published: September 2021

AbstractBackgroundThe Medtronic “Percept” is the first FDA approved deep brain stimulation (DBS) device with sensing capabilities during active stimulation. Its real-world signal recording properties have yet to be fully described.ObjectiveThis study details sources of artifact (and potential mitigations) in local field potential (LFP) signals collected by the Percept, and assesses the potential impact of artifact on the future development of adaptive DBS (aDBS) using this device.MethodsLFP signals were collected from seven subjects in both experimental and clinical settings. The presence of artifacts and their effect on the spectral content of neural signals were evaluated in both the stimulation ON and OFF states using three distinct offline artifact removal techniques.ResultsTemplate subtraction successfully removed multiple sources of artifact, including 1) electrocardiogram (ECG), 2) non-physiologic polyphasic artifacts, and 3) ramping related artifacts seen when changing stimulation amplitudes. ECG removal from stimulation ON (at 0 mA) signals recovered the spectral shape seen when OFF stimulation (averaged difference in normalized power in theta, alpha, and beta bands ≤ 3.5%). ECG removal using singular value decomposition was similarly successful, though required subjective researcher input. QRS interpolation produced similar recovery of beta-band signal, but resulted in residual low-frequency artifact.ConclusionsArtifacts present when stimulation is enabled notably affected the spectral properties of sensed signals using the Percept. Multiple discrete artifacts could be successfully removed offline using an automated template subtraction method. The presence of unrejected artifact likely influences online power estimates, with the potential to affect aDBS algorithm performance.
Genome Assembly of the Roundjaw Bonefish (Albula glossodonta), a Vulnerable Circumtropical Sportfish
Authors: Pickett Brandon D. , Talma Sheena , Glass Jessica R. , Ence Daniel , Cowley Paul D. , Ridge Perry G. , Kauwe John S. K. 
Published: September 2021

ABSTRACTBackgroundBonefishes are cryptic species indiscriminately targeted by subsistence and recreational fisheries worldwide. The roundjaw bonefish,Albula glossodontais the most widespread bonefish species in the Indo-Pacific and is listed as vulnerable to extinction by the IUCN’s Red List due to anthropogenic activities. Whole-genome datasets allow for improved population and species delimitation, which – prior to this study – were lacking forAlbulaspecies.ResultsWe generated a high-quality genome assembly of anA. glossodontaindividual from Hawai‘i, USA. The assembled contigs had an NG50 of 4.75 Mbp and a maximum length of 28.2 Mbp. Scaffolding yielded an NG50 of 14.49 Mbp, with the longest scaffold reaching 42.29 Mbp. Half the genome was contained in 20 scaffolds. The genome was annotated with 28.3 K protein-coding genes. We then analyzed 66A. glossodontaindividuals and 38,355 SNP loci to evaluate population genetic connectivity between six atolls in Seychelles and Mauritius in the Western Indian Ocean. We observed genetic homogeneity between atolls in Seychelles and evidence of reduced gene flow between Seychelles and Mauritius. The South Equatorial Current could be one mechanism limiting gene flow ofA. glossodontapopulations between Seychelles and Mauritius.ConclusionsQuantifying the spatial population structure of widespread fishery species such as bonefishes is necessary for effective transboundary management and conservation. This population genomic dataset mapped to a high-quality genome assembly allowed us to discern shallow population structure in a widespread species in the Western Indian Ocean. The genome assembly will be useful for addressing the taxonomic uncertainties of bonefishes globally.
CuBi-MeAn Customized Pipeline for Metagenomic Data Analysis
Authors: Keshani-Langroodi Saeed , Sales Christopher M. 
Published: September 2021

1.AbstractWhole genome shotgun sequencing is a powerful to study microbial community is a given environment. Metagenomic binning offers a genome centric approach to study microbiomes. There are several tools available to process metagenomic data from raw reads to the interpretation there is still lack of standard approach that can be used to process the metagenomic data step by step. In this study CuBi-MeAn (Customizable Binning and Metagenomic Analysis) create a customizable and flexible processing pipeline, to process the metagenomic data and generate results for further interpretation.This study aims to perform metagenomic binning to enhance taxonomical classification, functional potentials, and interactions among microbial populations in environmental systems. This customized pipeline which is comprised of a series of genomic/metagenomic tools designed to recover better quality results and reliable interpretation of the system dynamics for the given systems. For this reason, a metagenomic data processing pipeline is developed to evaluate metagenomic data from three environmental engineering projects.The use of our pipeline was demonstrated and compared on three different datasets that were of different sizes, from different sequencing platforms, and generated from three different environmental sources. By designing and developing a flexible and customized pipeline, this study has showed how to process large metagenomic data sets with limited resources. This result not only would help to uncover new information from environmental samples, but also, could be applicable to any other metagenomic studies across various disciplines.
Transplantation of bacteriophages from ulcerative colitis patients shifts the gut bacteriome and exacerbates severity of DSS-colitis
Authors: Sinha Anshul , Li Yue , Mirzaei Mohammadali Khan , Shamash Michael , Samadfam Rana , King Irah L. , Maurice Corinne F. 
Published: September 2021

ABSTRACTInflammatory bowel diseases (IBDs) including Crohn’s disease (CD) and ulcerative colitis (UC) are characterized by chronic and debilitating gut inflammation. Altered bacterial communities of the intestine are strongly associated with IBD initiation and progression. The gut virome, which is primarily composed of bacterial viruses (bacteriophages, phages) is thought to be an important factor regulating and shaping microbial communities in the gut. While alterations in the gut virome have been observed in IBD patients, the contribution of these viruses to alterations in the bacterial community and heightened inflammatory responses associated with IBD patients remains largely unknown. Here, we performed in vivo microbial cross-infection experiments to follow the effects of fecal virus-like particles (VLPs) isolated from UC patients and healthy controls on bacterial diversity and severity of experimental colitis in human microbiota-associated (HMA) mice. Shotgun metagenomics confirmed that several phages were transferred to HMA mice, resulting in treatment-specific alterations in the gut virome. VLPs from healthy and UC patients also shifted gut bacterial diversity of these mice, an effect that was amplified during experimental colitis. VLPs isolated from UC patients specifically altered the relative abundance of several bacterial taxa previously implicated in IBD progression. Additionally, UC VLP administration heightened colitis severity in HMA mice, as indicated by shortened colon length and increased pro-inflammatory cytokine production. Importantly, this effect was dependent on intact VLPs. Our findings build on recent literature indicating that phages are dynamic regulators of bacterial communities in the gut and implicate the intestinal virome in modulating intestinal inflammation and disease.
Cyclic mechanical stresses alter erythrocyte membrane composition and microstructure and trigger macrophage phagocytosis
Authors: Garcia-Herreros Antoni , Yeh Yi-Ting , Peng Zhangli , del Álamo Juan C. 
Published: September 2021

AbstractRed blood cells (RBCs) are cleared from the circulation when they become damaged or display aging signals targeted by macrophages. This process occurs mainly in the spleen, where blood flows through submicrometric constrictions called inter-endothelial slits (IES), subjecting RBCs to large-amplitude deformations. In this work, we circulated RBCs through microfluidic devices containing microchannels that replicate the IES. The cyclic mechanical stresses experienced by the cells affected their biophysical properties and molecular composition, accelerating cell aging. Specifically, RBCs quickly transitioned to a more spherical, less deformable phenotype that hindered microchannel passage, causing hemolysis. This transition was associated with the release of membrane vesicles, which self-extinguished as the spacing between membrane-cytoskeleton linkers became tighter. Proteomics analysis of the mechanically aged RBCs revealed significant losses of essential proteins involved in antioxidant protection, gas transport, and cell metabolism. Finally, we show that these changes made mechanically aged RBCs more susceptible to macrophage phagocytosis. These results provide a comprehensive model to explain how physical stress induces RBC clearance in the spleen.
Environmental stress determines the colonization and impact of an endophytic fungus on invasive knotweed
Authors: Garnica Sigisfredo , Liao Zhiyong , Hamard Samuel , Waller Frank , Parepa Madalin , Bossdorf Oliver 
Published: September 2021

AbstractThere is increasing evidence that microbes play a key role in some plant invasions. A diverse and widespread but little understood group of plant-associated microbes are the fungal root endophytes of the order Sebacinales. They are associated with exotic populations of invasive knotweed (Reynoutria ssp.) in Europe, but their effects on the invaders are unknown.We used the recently isolated Sebacinales root endophyte Serendipita herbamans to experimentally inoculate invasive knotweed and study root colonisation and effects on knotweed growth under different environmental conditions. We verified the inoculation success and fungal colonisation through immunofluorescence microscopy and qPCR.We found that S. herbamans strongly colonized invasive knotweed in low-nutrient and shade environments, but much less under drought or benign conditions. At low nutrients, the endophyte had a positive effect on plant growth, whereas the opposite was true under shaded conditions.Synthesis. Our study demonstrates that the root endophyte S. herbamans has the potential to colonize invasive knotweed fine roots and impact its growth, and it could thus also play a role in natural populations. Our results also show that effects of fungal endophytes on plants can be strongly environment-dependent, and may only be visible under stressful environmental conditions.