Genomic instability at the 13q31 locus and somatic mtDNA mutation in the D-loop site correlate with tumor aggressiveness in sporadic Brazilian breast cancer cases

OBJECTIVE: Genomic instability is a hallmark of malignant tissues. In this work, we aimed to characterize nuclear and mitochondrial instabilities by determining short tandem repeats and somatic mitochondrial mutations, respectively, in a cohort of Brazilian sporadic breast cancer cases. Furthermore, we performed an association analysis of the molecular findings and the clinical pathological data. METHODS: We analyzed 64 matched pairs of breast cancer and adjacent non-cancerous breast samples by genotyping 13 nuclear short tandem repeat loci (namely, D2S123, TPOX, D3S1358, D3S1611, FGA, D7S820, TH01, D13S317, D13S790, D16S539, D17S796, intron 12 BRCA1 and intron 1 TP53) that were amplified with the fluorescent AmpFlSTR Identifiler Genotyping system (Applied Biosystems, USA) and by silver nitrate staining following 6% denaturing polyacrylamide gel electrophoresis. Somatic mtDNA mutations in the D-loop site were assessed with direct sequencing of the hypervariable HVI and HVII mitochondrial regions. RESULTS: Half of the cancer tissues presented some nuclear instability. Interestingly, the D13S790 locus was the most frequently affected (36%), while the D2S123 locus presented no alterations. Forty-two percent of the cases showed somatic mitochondrial mutations, the majority at region 303-315 poly-C. We identified associations between Elston grade III, instabilities at 13q31 region (p = 0.0264) and mtDNA mutations (p = 0.0041). Furthermore, instabilities at 13q31 region were also associated with TP53 mutations in the invasive ductal carcinoma cases (p= 0.0207). CONCLUSION: Instabilities at 13q31 region and the presence of somatic mtDNA mutations in a D-loop site correlated with tumor aggressiveness

Quantitative proteomic profiling of bovine follicular fluid during follicle development

Bovine follicular fluid (FF) constitutes the microenvironment of follicles and includes various biologically active proteins. We performed a study involving 18 healthy non-lactating Holstein cows to determine the protein expression profile of FF at key-stages of follicular development. Follicles were individually aspirated in vivo at pre-deviation (F1∼7.0mm); deviation (F1∼8.5mm); post-deviation (F1∼12.0mm); and pre-ovulatory stages of follicle development, which were confirmed by measurement of follicular estradiol and progesterone concentrations. The FF from nine cows were selected for proteomic analysis. After albumin depletion, triplicates of pooled FF were reduced, alkylated, and digested with trypsin. The resulting peptides were labelled with TMTsixplex and quantified using LC-MS/MS. A total of 143 proteins was identified and assigned to a variety of biological processes, including response to stimulus and metabolic processes. Twenty-two differentially (P < 0.05) expressed proteins were found between stages indicating intrafollicular changes over development, with expected deviation time critical to modulate the protein expression. For instance, high concentrations of follistatin, inhibin, serglycin, spondin-1, fibrinogen, and anti-testosterone antibody were found during early stages of follicular development. In contrast, apolipoprotein H, alpha-2-macroglobulin, plasminogen, antithrombin-III, and immunoglobulins were increased after deviation. Amongst the differentially abundant proteins, 19 were found to be associated with steroidogenesis. Pathway analysis identified proteins that were mainly associated with the acute phase response signaling, coagulation system, complement system, liver/retinoid X receptor activation, and biosynthesis of nitric oxide and reactive oxygen. The differentially expressed proteins provide insights into the size-dependent protein changes in the ovarian follicle microenvironment that could influence follicular function

Genetic Diversity and Virulence Potential of Shiga Toxin-Producing Escherichia coli O113:H21 Strains Isolated from Clinical, Environmental, and Food Sources

Shiga toxin-producing Escherichia coli strains of serotype O113:H21 have caused severe human diseases, but they are unusual in that they do not produce adherence factors coded by the locus of enterocyte effacement. Here, a PCR microarray was used to characterize 65 O113:H21 strains isolated from the environment, food, and clinical infections from various countries. in comparison to the pathogenic strains that were implicated in hemolytic-uremic syndrome in Australia, there were no clear differences between the pathogens and the environmental strains with respect to the 41 genetic markers tested. Furthermore, all of the strains carried only Shiga toxin subtypes associated with human infections, suggesting that the environmental strains have the potential to cause disease. Most of the O113:H21 strains were closely related and belonged in the same clonal group (ST-223), but CRISPR analysis showed a great degree of genetic diversity among the O113:H21 strains.French Joint Ministerial Program of R&D against CBRNE RisksFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Food & Drug Adm, Div Microbiol, College Pk, MD 20740 USAFrench Agcy Food Environm & Occupat Hlth & Safety, Lab Food Safety, Maisons Alfort, FranceFood & Drug Adm, Div Mol Biol, Laurel, MD USAUniversidade Federal de São Paulo, Dept Microbiol Immunol & Parasitol, São Paulo, BrazilFed Inst Risk Assessment, Natl Reference Lab Escherichia coli, Berlin, GermanyInst Nacl Enfermedades Infecciosas ANLIS Dr Carlo, Serv Fisiopatogenia, Buenos Aires, DF, ArgentinaUniv Melbourne, Peter Doherty Inst Infect & Immun, Dept Microbiol & Immunol, Melbourne, Vic, AustraliaUniv Adelaide, Res Ctr Infect Dis, Sch Mol & Biomed Sci, Adelaide, SA, AustraliaUniversidade Federal de São Paulo, Dept Microbiol Immunol & Parasitol, São Paulo, BrazilFrench Joint Ministerial Program of R&D against CBRNE Risks: C17609-2Web of Scienc

Cryptococcus gattii in North American Pacific Northwest: whole-population genome analysis provides insights into species evolution and dispersal

The emergence of distinct populations of Cryptococcus gattii in the temperate North American Pacific Northwest (PNW) was surprising, as this species was previously thought to be confined to tropical and semitropical regions. Beyond a new habitat niche, the dominant emergent population displayed increased virulence and caused primary pulmonary disease, as opposed to the predominantly neurologic disease seen previously elsewhere. Whole-genome sequencing was performed on 118 C. gattii isolates, including the PNW subtypes and the global diversity of molecular type VGII, to better ascertain the natural source and genomic adaptations leading to the emergence of infection in the PNW. Overall, the VGII population was highly diverse, demonstrating large numbers of mutational and recombinational events; however, the three dominant subtypes from the PNW were of low diversity and were completely clonal. Although strains of VGII were found on at least five continents, all genetic subpopulations were represented or were most closely related to strains from South America. The phylogenetic data are consistent with multiple dispersal events from South America to North America and elsewhere. Numerous gene content differences were identified between the emergent clones and other VGII lineages, including genes potentially related to habitat adaptation, virulence, and pathology. Evidence was also found for possible gene introgression from Cryptococcus neoformans var. grubii that is rarely seen in global C. gattii but that was present in all PNW populations. These findings provide greater understanding of C. gattii evolution in North America and support extensive evolution in, and dispersal from, South America. Importance: Cryptococcus gattii emerged in the temperate North American Pacific Northwest (PNW) in the late 1990s. Beyond a new environmental niche, these emergent populations displayed increased virulence and resulted in a different pattern of clinical disease. In particular, severe pulmonary infections predominated in contrast to presentation with neurologic disease as seen previously elsewhere. We employed population-level whole-genome sequencing and analysis to explore the genetic relationships and gene content of the PNW C. gattii populations. We provide evidence that the PNW strains originated from South America and identified numerous genes potentially related to habitat adaptation, virulence expression, and clinical presentation. Characterization of these genetic features may lead to improved diagnostics and therapies for such fungal infections. The data indicate that there were multiple recent introductions of C. gattii into the PNW. Public health vigilance is warranted for emergence in regions where C. gattii is not thought to be endemic

Investigation of an outbreak of disease compatible with scurvy in a male penitentiary in the state of Ceará, Brazil, 2019-2020: a case-control study

ABSTRACT Objective: to identify the occurrence of an outbreak compatible with scurvy and exposure factors associated with typical signs/symptoms of hypovitaminosis that occurred in a male penitentiary in Ceará, Brazil between 2019-2020. Methods: this was a population-based case-control study; we used clinical records and interviews with compatible cases - based on sign/symptom onset during the study period - and with controls; we carried out multivariate analysis. Results: out of 62 cases, mean age was 40.6 years (SD = 10.8); main signs/symptoms were edema and pain in the lower limbs (100.0%), difficulty in walking (91.9%), hematoma/ecchymosis in the lower limbs (90.3%) and fever (88.7%); we identified being over 40 years old as an associated factor (aOR = 1.10; 95%CI 1.05;1.17; p-value = 0.001); and as protective factors: working (aOR = 0.11; 95%CI 0.03;0.36; p-value < 0.001) and taking part in classes (aOR = 0.21; 95%CI 0.08;0.59; p-value = 0.003) in the prison. Conclusion: we considered the penitentiary outbreak to be compatible with scurvy due to characteristic signs/symptoms, associated with the identified factors; we recommended regular provision of a diet rich in vitamin C to all male inmates and clinical follow-up of cases

Surto de varicela entre imigrantes venezuelanos alojados em abrigos e ocupações no estado de Roraima, 2019: um estudo descritivo

Objective: To describe the chickenpox outbreak among Venezuelan immigrants in shelters and occupations in the municipalities of Pacaraima and Boa Vista, Roraima, Brazil, and the control measures implemented. Methods: Descriptive case series study, that happened between november 21 and december 13, 2019, using secondary database from the investigation of the outbreak, made available by the General Coordination of the National Immunization Program. Descriptive analysis was performed, using simple and relative frequency measures, and calculating measures of central tendency and dispersion. Results: Of the 9,591 immigrants, 38 active cases and 1,500 susceptible to chickenpox were detected. Among the active cases, 23 were female and the most affected age group those under 9 years old (17 cases). Conclusion: The identification of susceptible people in the investigation led to the adoption of immunization actions that controlled the transmission, preventing serious cases, deaths, and the overload of the local health care network.Objetivo: Descrever o surto de varicela entre imigrantes venezuelanos em abrigos e ocupações nos municípios de Pacaraima e Boa Vista, Roraima, Brasil, e as medidas de controle implementadas. Métodos: Estudo descritivo de tipo ‘série de casos’, realizado entre 21 de novembro e 13 de dezembro de 2019, sobre banco de dados secundários da investigação do surto disponibilizado pela Coordenação-Geral do Programa Nacional de Imunizações. Na análise descritiva, utilizou-se medidas de frequência simples e relativa e foram calculadas medidas de tendência central e dispersão. Resultados: Dos 9.591 imigrantes, detectaram-se 38 casos ativos e 1.500 suscetíveis à varicela. Dos casos ativos, 23 eram do sexo feminino e a faixa etária mais acometida foi a de menores de 9 anos (17 casos). Conclusão: Identificou-se pessoas suscetíveis à varicela na investigação; foram adotadas ações de imunização que controlaram a transmissão, evitando casos graves, óbitos e sobrecarga da rede de assistência à saúde local

The Astropy Problem

The Astropy Project (http://astropy.org) is, in its own words, "a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages." For five years this project has been managed, written, and operated as a grassroots, self-organized, almost entirely volunteer effort while the software is used by the majority of the astronomical community. Despite this, the project has always been and remains to this day effectively unfunded. Further, contributors receive little or no formal recognition for creating and supporting what is now critical software. This paper explores the problem in detail, outlines possible solutions to correct this, and presents a few suggestions on how to address the sustainability of general purpose astronomical software

BRCA1 and BRCA2 5′ noncoding region variants identified in breast cancer patients alter promoter activity and protein binding

© 2018 The Authors. Human Mutation published by Wiley Periodicals, Inc. The widespread use of next generation sequencing for clinical testing is detecting an escalating number of variants in noncoding regions of the genome. The clinical significance of the majority of these variants is currently unknown, which presents a significant clinical challenge. We have screened over 6,000 early-onset and/or familial breast cancer (BC) cases collected by the ENIGMA consortium for sequence variants in the 5′ noncoding regions of BC susceptibility genes BRCA1 and BRCA2, and identified 141 rare variants with global minor allele frequency \u3c 0.01, 76 of which have not been reported previously. Bioinformatic analysis identified a set of 21 variants most likely to impact transcriptional regulation, and luciferase reporter assays detected altered promoter activity for four of these variants. Electrophoretic mobility shift assays demonstrated that three of these altered the binding of proteins to the respective BRCA1 or BRCA2 promoter regions, including NFYA binding to BRCA1:c.-287C\u3eT and PAX5 binding to BRCA2:c.-296C\u3eT. Clinical classification of variants affecting promoter activity, using existing prediction models, found no evidence to suggest that these variants confer a high risk of disease. Further studies are required to determine if such variation may be associated with a moderate or low risk of BC

Coorte retrospectiva de crianças e adolescentes hospitalizados por COVID-19 no Brasil do início da pandemia a 1º de agosto de 2020

Objectives: To characterize the study population, estimating the in-hospital lethality rate by state and analysing associated factors with COVID-19-related deaths. Methods: a retrospective cohort study was carried out of hospitalised children and adolescents diagnosed with COVID-19, confirmed by RT-PCR, whose outcome was death by COVID-19 or recovery, from 2020 March 1 to August 1. The data source was the Influenza Epidemiological Surveillance Information System (SIVEP-Gripe in Brazilian acronym), where patients with Severe Acute Respiratory Syndrome (SARS) are notified. Children were defined as those between the ages of 0 and 11, and adolescents those between 12 and 18. A bi and multivariate analysis were performed using Poisson Regression with robust variance, with adjusted Relative Risk as the final association measure. Results: A total of 4,930 cases were analysed; 2,553 (51.8%) were males, 2,335 (47.4%) were brown-skinned. The Federative Unit of Roraima presented the highest in-hospital case-fatality rate, with 68.8% (n=11/16). Multivariate analysis showed that belonging to the age group adolescent (RR = 1.59; 95% CI 1.12 - 2.25; p=0.009), SARS-critical patient (RR = 4.56; 95% CI 2, 77 - 7.51; p&lt;0.001) and presenting immunological disorders (RR = 2.24; 95% CI 1.58 - 3.17; p&lt;0.001) as comorbidities, were associated factors with death by COVID-19. Conclusion: it was observed that adolescents, SARS-critical patients, and presence of immunological disorders were important factors associated with death. Active surveillance and differentiated care are recommended for patients with chronic diseases and special immunological conditions.Objetivos: Caracterizar a população do estudo, estimar a taxa de letalidade intra-hospitalar por estado e analisar fatores associados aos óbitos por COVID-19. Métodos: Foi realizado estudo de coorte retrospectiva de crianças e adolescentes hospitalizados com diagnóstico de COVID-19, confirmados por RT-PCR, tendo como desfecho óbito por COVID-19 ou recuperado, entre 1º de março a 1º de agosto de 2020. A fonte de dados foi Sistema de Informação de Vigilância Epidemiológica da Gripe (SIVEP-Gripe), onde são notificados pacientes internados com Síndrome Respiratória Aguda Grave (SRAG). Considerou-se crianças aqueles com idade entre 0 e 11 anos completos e adolescentes aqueles com idade entre 12 e 18 anos completos. Realizou-se análise bi e multivariável&nbsp;por meio de Regressão de Poisson com variância robusta, sendo utilizado como medida de associação final o Risco Relativo ajustado (RRa). Resultados: Dos 4.930 casos analisados, 2.553 (51,8%) eram do sexo masculino. A raça/cor autodeclarada parda foi a mais frequente com 2.335 (47,4%). A Unidade Federativa de Roraima apresentou a maior taxa de letalidade intra-hospitalar com 68,8% (n=11/16). Análise multivariada mostrou que pertencer ao grupo etário adolescente (RR= 1,59; IC95% 1,12 – 2,25; p=0,009), ter sido classificado como SRAG-crítico (RR= 4,56; IC95% 2,77 – 7,51; p&lt;0,001) e apresentar imunopatia (RR= 2,24; IC95% 1,58 – 3,17; p&lt;0,001) como comorbidade se configuraram como fatores associados ao óbito pela COVID-19. Conclusão: Observou-se que ser adolescente, ter classificação de SRAG-crítico e imunopatia como comorbidade foram importantes fatores associados ao óbito. Recomenda-se vigilância ativa e cuidados diferenciados a portadores de doenças crónicas e condições imunológicas especiais

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts