The Microbiome in Light of Host Evolution

Recent advances in sequencing technologies have provided an unprecedented window in the unseen biological world. Accompanying this revolution is a growing appreciation for the ubiquity and diversity of beneficial interactions between animals and the microbes they carry. Given the symbiotic roles of microbes in host nutrition, immunity, behavior, development, and nearly every other facet of host biology, it is becoming increasingly clear that any understanding of hosts and their evolution would be incomplete without also considering the microbial dimension. Yet despite the growing body of evidence that many of these partnerships are rooted deep in evolutionary time, the majority of studies have tended to focus on how the composition of the present-day microbiome is shaped by present-day factors. In order to place the microbiome in the larger context of host biology, a more complete understanding of the evolutionary interplay between hosts and their microbial associates is needed. Here, I use Odontotaenius disjunctus, a large xylophagous beetle found throughout eastern North America, to explore how its present-day gut microbiome has both shaped and been shaped by evolutionary processes that have acted on the host. First, I show that recent evolution in O. disjunctus reflects the influence of Pleistocene glaciation on the host’s demographic history. Next, I show that the present-day gut microbiome of O. disjunctus reflects both the influence of this recent host evolution and the more ancient influence of natural selection that has acted on the host to maintain these beneficial partnerships over a much longer timescale. Finally, I show that the persistence of certain members of the gut microbiome over evolutionary time may be explained by their role in host lignocellulose digestion. My findings demonstrate that, much like host genomes, the microbiome has been, is being, and will continue to be shaped simultaneously by forces of selection and neutrality along the arc of evolutionary history shared by these intimate partners

Linked CSF reduction of phosphorylated tau and IL-8 in HIV associated neurocognitive disorder.

HIV-associated neurocognitive disorder (HAND) is a common condition in both developed and developing nations, but its cause is largely unknown. Previous research has inconsistently linked Alzheimer's disease (AD), viral burden, and inflammation to the onset of HAND in HIV-infected individuals. Here we simultaneously measured cerebrospinal fluid (CSF) levels of established amyloid and tau biomarkers for AD, viral copy numbers, and six key cytokines in 41 HIV-infected individuals off combination anti-retroviral therapy (14 with HAND) who underwent detailed clinical and neuropsychological characterization, and compared their CSF patterns with those from young healthy subjects, older healthy subjects with normal cognition, and older people with AD. HAND was associated with the lowest CSF levels of phosphorylated tau (p-Tau181) after accounting for age and race. We also found very high CSF levels of the pro-inflammatory interferon gamma-induced protein 10 (IP-10/CXCL10) in HIV regardless of cognition, but elevated CSF interleukin 8 (IL-8/CXCL8) only in HIV-NC but not HAND. Eleven HIV-infected subjects underwent repeat CSF collection six months later and showed strongly correlated longitudinal changes in p-Tau181 and IL-8 levels (R = 0.841). These data suggest reduced IL-8 relative to IP-10 and reduced p-Tau181 to characterize HAND

Dug: a semantic search engine leveraging peer-reviewed knowledge to query biomedical data repositories

MOTIVATION: As the number of public data resources continues to proliferate, identifying relevant datasets across heterogenous repositories is becoming critical to answering scientific questions. To help researchers navigate this data landscape, we developed Dug: a semantic search tool for biomedical datasets utilizing evidence-based relationships from curated knowledge graphs to find relevant datasets and explain why those results are returned. RESULTS: Developed through the National Heart, Lung and Blood Institute's (NHLBI) BioData Catalyst ecosystem, Dug has indexed more than 15 911 study variables from public datasets. On a manually curated search dataset, Dug's total recall (total relevant results/total results) of 0.79 outperformed default Elasticsearch's total recall of 0.76. When using synonyms or related concepts as search queries, Dug (0.36) far outperformed Elasticsearch (0.14) in terms of total recall with no significant loss in the precision of its top results. AVAILABILITY AND IMPLEMENTATION: Dug is freely available at https://github.com/helxplatform/dug. An example Dug deployment is also available for use at https://search.biodatacatalyst.renci.org/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Minor Physical Anomalies in Patients with Schizophrenia, Unaffected First-Degree Relatives, and Healthy Controls: A Meta-Analysis

Background: Minor physical anomalies (MPAs) have been found to be more prevalent in schizophrenia than control participants in numerous studies and may index a potential endophenotype for schizophrenia.</p

Variation in carbon and nitrogen concentrations among peatland categories at the global scale

Publisher Copyright: © 2022 This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.Peatlands account for 15 to 30% of the world's soil carbon (C) stock and are important controls over global nitrogen (N) cycles. However, C and N concentrations are known to vary among peatlands contributing to the uncertainty of global C inventories, but there are few global studies that relate peatland classification to peat chemistry. We analyzed 436 peat cores sampled in 24 countries across six continents and measured C, N, and organic matter (OM) content at three depths down to 70 cm. Sites were distinguished between northern (387) and tropical (49) peatlands and assigned to one of six distinct broadly recognized peatland categories that vary primarily along a pH gradient. Peat C and N concentrations, OM content, and C:N ratios differed significantly among peatland categories, but few differences in chemistry with depth were found within each category. Across all peatlands C and N concentrations in the 10-20 cm layer, were 440 ± 85.1 g kg-1 and 13.9 ± 7.4 g kg-1, with an average C:N ratio of 30.1 ± 20.8. Among peatland categories, median C concentrations were highest in bogs, poor fens and tropical swamps (446-532 g kg-1) and lowest in intermediate and extremely rich fens (375-414 g kg-1). The C:OM ratio in peat was similar across most peatland categories, except in deeper samples from ombrotrophic tropical peat swamps that were higher than other peatlands categories. Peat N concentrations and C:N ratios varied approximately two-fold among peatland categories and N concentrations tended to be higher (and C:N lower) in intermediate fens compared with other peatland types. This study reports on a unique data set and demonstrates that differences in peat C and OM concentrations among broadly classified peatland categories are predictable, which can aid future studies that use land cover assessments to refine global peatland C and N stocks.Peer reviewe

DarkSide-50 532-day dark matter search with low-radioactivity argon

FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOThe DarkSide-50 direct-detection dark matter experiment is a dual-phase argon time projection chamber operating at Laboratori Nazionali del Gran Sasso. This paper reports on the blind analysis of a (16 660 +/- 270) kg d exposure using a target of low-radioactivity argon extracted from underground sources. We find no events in the dark matter selection box and set a 90% C. L. upper limit on the dark matter-nucleon spin-independent cross section of 1.14 x 10(-44) cm(2) (3.78 x 10(-44) cm(2), 3.43 x 10(-43) cm(2)) for a WIMP mass of 100 GeV/c(2) (1 TeV/c(2), 10 TeV/c(2)).9810117FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOFAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO2016/09084-0Agências de fomento estrangeiras apoiaram essa pesquisa, mais informações acesse artig

DarkSide status and prospects

Sem informaçãoDarkSide uses a dual-phase Liquid Argon Time Projection Chamber to search for WIMP dark matter. The current detector, DarkSide-50, is running since mid 2015 with a target of 50 kg of Argon from an underground source. Here it is presented the latest results of searches of WIMP-nucleus interactions, with WIMP masses in the GeV-TeV range, and of WIMP-electron interactions, in the sub-GeV mass range. The future of DarkSide with a new generation experiment, involving a global collaboration from all the current Argon based experiments, is presented.422-315Sem informaçãoSem informaçãoSem informaçã