Etnobotânica e divergência genética de variedades de mandioca, Poconé, Mato Grosso.

A região denominada Baixada Cuiabana fica ao norte do Pantanal Mato-Grossense. É uma das poucas regiões do Mato Grosso que preserva as antigas características de comunidades de agricultores de subsistência que mantêm expressiva diversidade de mandioca (Manihot esculenta Crantz) e outros cultivos, visto a região ser centro de diversidade do gênero. Este estudo teve por objetivo caracterizar a diversidade genética de mandiocas mediante o conhecimento etnobotânico das variedades e marcadores microssatélites para compreender a dinâmica de conservação e manejo do acervo usado pelos agricultores da Comunidade São Benedito, Poconé, Mato Grosso. O presente trabalho foi autorizado pelo Conselho de Gestão do Patrimônio Genético (processo n. 02000.003025/2013-13-MMA deliberado em 28 de abril de 2015 e publicado no D.O.U em 13 de julho de 2015). Para o inventário etnobotânico foram aplicadas entrevistas semiestruturadas em 10 unidades domésticas para obter informações sobre as mandiocas cultivadas. Das 11 variedades locais cultivadas foi realizada análise por microssatélites (12 locus). Apesar da baixa diversidade etnobotânica encontrada (H?=2,05), foi encontrada alta heterozigosidade observada (Ho = 0,92) e diversidade gênica (He = 0,75). Os agricultores que sobrevivem basicamente do cultivo da mandioca e produção de farinha para comercialização, direcionam suas escolhas de variedades para as mais produtivas e menos suscetíveis ao ataque de pragas. A variedade brava foi a mais frequente (80% das roças) e é apontada como a mais rentável para a produção de farinha, sendo uma importante fonte de recurso genético para programas de melhoramento. Através da análise de rede pode-se observar que a rede de circulação de propágulos e informações ocorre entre os moradores e também com outras comunidades da região, importantes fontes de novas variedades. Dois agricultores foram identificados como os mais atuantes nas trocas. De acordo com o agrupamento e análise de coordenadas principais feitos utilizando os dados genéticos, as variedades introduzidas mais recentemente separam-se das introduzidas há mais tempo. As variedades apontadas como com alto teor de ácido cianídrico pelos agricultores também ficaram agrupadas. Notou-se que as variedades locais apresentam genes úteis para características importantes como, resistência a estresses bióticos e abióticos.Edição Especial dos Anais do 3 Simpósio da Rede de Recursos Genéticos Vegetais do Nordeste, Aracaju, out. 2017

Influence of the use of manioc on its genetic diversity conservation in a quilombo community in Mato Grosso, Brazil.

Local cassava varieties play an important role in food security and the autonomy of subsistence farmers. They can be important resources for breeding and conservation programs. We examined the genetic diversity of cassava through ethnobotanical knowledge and microsatellite markers to understand the dynamics of conservation and management of the varieties used local small-scale farmers of a rural quilombo (a slave-descendant community) in Mato Grosso, Brazil. To obtain ethnobotanical information, semi-structured interviews were applied to 10 family units who cultivated cassava. Each family cultivated from one to five varieties, with 2.3 ± 1.16 varieties/farmer, on average. Genetic analysis was was made of the 11 local varieties with microsatellite markers (12 loci). Despite low ethnobotanical diversity (H' = 2.05), high genetic diversity was found (Na = 6.75, HO = 0.92, HE = 0.75, on average) in these local varieties. These farmers, who derive their income mainly from cassava cultivation and flour production for the market, direct their variety choices to those that are most productive. Brava variety was the most frequent (found in eight family units) and was considered the most profitable for the production of flour Network analysis showed that propagule circulation and information occurs between the residents and also with other communities of the region, which are important sources of new varieties. Two farmers were identified as the most active in this network, showing potential as key elements for the circulation of propagating material. According to the cluster analysis using the genetic data, the most recently introduced varieties (Baixinha, Liberatona, Broto roxo, Mansa, Ramo branco, Carneiro and Cuiabana) are separated from those introduced a long time ago. The varieties pointed out as bitter by the farmers were also grouped together. The results showed the importance of traditional farmers in maintaining a high genetic diversity of manioc varieties, despite the directing of the choice of varieties to meet market needs

Third Report on Chicken Genes and Chromosomes 2015

Following on from the First Report on Chicken Genes and Chromosomes [Schmid et al., 2000] and the Second Report in 2005 [Schmid et al., 2005], we are pleased to publish this long-awaited Third Report on the latest developments in chicken genomics. The First Report highlighted the availability of genetic and physical maps, while the Second Report was published as the chicken genome sequence was released. This report comes at a time of huge technological advances (particularly in sequencing methodologies) which have allowed us to examine the chicken genome in detail not possible until now. This has also heralded an explosion in avian genomics, with the current availability of more than 48 bird genomes [Zhang G et al., 2014b; Eöry et al., 2015], with many more planned

Inborn errors of type I IFN immunity in patients with life-threatening COVID-19.

Clinical outcome upon infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ranges from silent infection to lethal coronavirus disease 2019 (COVID-19). We have found an enrichment in rare variants predicted to be loss-of-function (LOF) at the 13 human loci known to govern Toll-like receptor 3 (TLR3)- and interferon regulatory factor 7 (IRF7)-dependent type I interferon (IFN) immunity to influenza virus in 659 patients with life-threatening COVID-19 pneumonia relative to 534 subjects with asymptomatic or benign infection. By testing these and other rare variants at these 13 loci, we experimentally defined LOF variants underlying autosomal-recessive or autosomal-dominant deficiencies in 23 patients (3.5%) 17 to 77 years of age. We show that human fibroblasts with mutations affecting this circuit are vulnerable to SARS-CoV-2. Inborn errors of TLR3- and IRF7-dependent type I IFN immunity can underlie life-threatening COVID-19 pneumonia in patients with no prior severe infection

HMDB 5.0: the Human Metabolome Database for 2022

The Human Metabolome Database or HMDB (https://hmdb.ca) has been providing comprehensive reference information about human metabolites and their associated biological, physiological and chemical properties since 2007. Over the past 15 years, the HMDB has grown and evolved significantly to meet the needs of the metabolomics community and respond to continuing changes in internet and computing technology. This year's update, HMDB 5.0, brings a number of important improvements and upgrades to the database. These should make the HMDB more useful and more appealing to a larger cross-section of users. In particular, these improvements include: (i) a significant increase in the number of metabolite entries (from 114 100 to 217 920 compounds); (ii) enhancements to the quality and depth of metabolite descriptions; (iii) the addition of new structure, spectral and pathway visualization tools; (iv) the inclusion of many new and much more accurately predicted spectral data sets, including predicted NMR spectra, more accurately predicted MS spectra, predicted retention indices and predicted collision cross section data and (v) enhancements to the HMDB's search functions to facilitate better compound identification. Many other minor improvements and updates to the content, the interface, and general performance of the HMDB website have also been made. Overall, we believe these upgrades and updates should greatly enhance the HMDB's ease of use and its potential applications not only in human metabolomics but also in exposomics, lipidomics, nutritional science, biochemistry and clinical chemistry.Analytical BioScience

Novel Primate Model of Serotonin Transporter Genetic Polymorphisms Associated with Gene Expression, Anxiety and Sensitivity to Antidepressants

This is the final version of the article. It first appeared from Nature Publishing Group via https://dx.doi.org/10.1038/npp.2016.41Genetic polymorphisms in the repeat upstream region of the serotonin transporter gene (SLC6A4) are associated with individual differences in stress reactivity, vulnerability to affective disorders and response to pharmacotherapy. However, the molecular, neurodevelopmental and psychopharmacological mechanisms underlying the link between SLC6A4 polymorphisms and the emotionally vulnerable phenotype are not fully understood. Thus, using the marmoset monkey Callithrix jacchus we characterize here a new neurobiological model to help to address these questions. We first sequenced the marmoset SLC6A4 promoter and identified a double nucleotide polymorphism (−2053AC/CT) and two single nucleotide polymorphisms (−2022C/T and −1592G/C) within the repeat upstream region. We showed their association with gene expression using in vivo quantitative PCR and with affective behavior using a primate test of anxiety (human intruder test). The low-expressing haplotype (AC/C/G) was linked with high anxiety whilst the high-expressing one (CT/T/C) was associated with an active coping strategy in response to threat. Pharmacological challenge with an acute dose of the selective serotonin reuptake inhibitor (SSRI), citalopram, revealed a genotype-dependent behavioral response. Whilst individuals homozygous for the high anxiety-related haplotype AC/C/G exhibited a dose-dependent, anxiogenic response, individuals homozygous for the low anxiety-related haplotype CT/T/C showed an opposing, dose-dependent anxiolytic effect. These findings provide a novel genetic and behavioral primate model to study the molecular, neurodevelopmental and psychopharmacological mechanisms that underlie genetic variation-associated complex behaviors, with specific implications for the understanding of normal and abnormal serotonin actions and the development of personalized pharmacological treatments for psychiatric disorders.Work was supported by an MRC Programme (ACR; G0901884) and performed within the Behavioural and Clinical Neuroscience Institute, University of Cambridge, funded jointly by the Wellcome Trust and MRC. AMS was supported by a McDonnell Foundation grant (PI’s: E. Phelps, T.W. Robbins; Co-Investigators: ACR and J. LeDoux; 22002015501) and currently supported by MRC; YS supported by the Long Term Student Support Program provided by Osaka University and the Ministry of Education, Culture, Sports, Science and Technology of Japan; HC supported by MRC Career Development Award and ACFS/MI supported by grants from the MRC and Wellcome Trust. GC supported by the Behavioural and Clinical Neuroscience Institute, Cambridge, United Kingdom. EHSS was self-funded

Diverse Roles and Interactions of the SWI/SNF Chromatin Remodeling Complex Revealed Using Global Approaches

A systems understanding of nuclear organization and events is critical for determining how cells divide, differentiate, and respond to stimuli and for identifying the causes of diseases. Chromatin remodeling complexes such as SWI/SNF have been implicated in a wide variety of cellular processes including gene expression, nuclear organization, centromere function, and chromosomal stability, and mutations in SWI/SNF components have been linked to several types of cancer. To better understand the biological processes in which chromatin remodeling proteins participate, we globally mapped binding regions for several components of the SWI/SNF complex throughout the human genome using ChIP-Seq. SWI/SNF components were found to lie near regulatory elements integral to transcription (e.g. 5′ ends, RNA Polymerases II and III, and enhancers) as well as regions critical for chromosome organization (e.g. CTCF, lamins, and DNA replication origins). Interestingly we also find that certain configurations of SWI/SNF subunits are associated with transcripts that have higher levels of expression, whereas other configurations of SWI/SNF factors are associated with transcripts that have lower levels of expression. To further elucidate the association of SWI/SNF subunits with each other as well as with other nuclear proteins, we also analyzed SWI/SNF immunoprecipitated complexes by mass spectrometry. Individual SWI/SNF factors are associated with their own family members, as well as with cellular constituents such as nuclear matrix proteins, key transcription factors, and centromere components, implying a ubiquitous role in gene regulation and nuclear function. We find an overrepresentation of both SWI/SNF-associated regions and proteins in cell cycle and chromosome organization. Taken together the results from our ChIP and immunoprecipitation experiments suggest that SWI/SNF facilitates gene regulation and genome function more broadly and through a greater diversity of interactions than previously appreciated