GenSeed-HMM: A tool for progressive assembly using profile HMMs as seeds and its application in Alpavirinae viral discovery from metagenomic data

This work reports the development of GenSeed-HMM, a program that implements seed-driven progressive assembly, an approach to reconstruct specific sequences from unassembled data, starting from short nucleotide or protein seed sequences or profile Hidden Markov Models (HMM). The program can use any one of a number of sequence assemblers. Assembly is performed in multiple steps and relatively few reads are used in each cycle, consequently the program demands low computational resources. As a proof-of-concept and to demonstrate the power of HMM-driven progressive assemblies, GenSeed-HMM was applied to metagenomic datasets in the search for diverse ssDNA bacteriophages from the recently described Alpavirinae subfamily. Profile HMMs were built using Alpavirinae-specific regions from multiple sequence alignments using either the viral protein 1 (VP1) (major capsid protein) or VP4 (genome replication initiation protein). These profile HMMs were used by GenSeed-HMM (running Newbler assembler) as seeds to reconstruct viral genomes from sequencing datasets of human fecal samples. All contigs obtained were annotated and taxonomically classified using similarity searches and phylogenetic analyses. The most specific profile HMM seed enabled the reconstruction of 45 partial or complete Alpavirinae genomic sequences. A comparison with conventional (global) assembly of the same original dataset, using Newbler in a standalone execution, revealed that GenSeed-HMM outperformed global genomic assembly in several metrics employed. This approach is capable of detecting organisms that have not been used in the construction of the profile HMM, which opens up the possibility of diagnosing novel viruses, without previous specific information, constituting a de novo diagnosis. Additional applications include, but are not limited to, the specific assembly of extrachromosomal elements such as plastid and mitochondrial genomes from metagenomic data. Profile HMM seeds can also be used to reconstruct specific protein coding genes for gene diversity studies, and to determine all possible gene variants present in a metagenomic sample. Such surveys could be useful to detect the emergence of drug-resistance variants in sensitive environments such as hospitals and animal production facilities, where antibiotics are regularly used. Finally, GenSeed-HMM can be used as an adjunct for gap closure on assembly finishing projects, by using multiple contig ends as anchored seeds

Implications of dealing with airborne substances and reactive oxygen species: what mammalian lungs, animals and plants have to say?

A gas-exchange structure interacts with the environment and is constantly challenged by contaminants that may elicit defense responses, thus compromising its primary function. It is also exposed to high concentrations of O2 that can generate reactive oxygen species (ROS). Revisiting the lung of mammals, an integrative picture emerges, indicating that this bronchi-alveolar structure deals with inflammation in a special way, which minimizes compromising the gas-exchange role. Depending on the challenge, pro-inflammatory or antiinflammatory responses are elicited by conserved molecules, such as surfactant proteins A and D. An even broader picture points to the participation of airway sensors, responsive to inflammatory mediators, in a loop linking the immunological and nervous systems and expanding the role played by respiratory organs in functions other than gas-exchange. A byproduct of exposure to high concentration of O2 is the formation of superoxide (), hydrogen peroxide (H2O2), hydroxyl radical (HO•), and other ROS, which are known to be toxic to different types of cells, including the lung epithelium. A balance between antioxidants and oxidants exists; in pulmonary epithelial cells high intracellular and extracellular levels of antioxidants are found. Antioxidant adaptations related to plant and animal life-styles involve a broad range of overlapping strategies based on well-conserved molecules. Glutathione (GSH) is an abundant and ubiquitous thiol-tripeptide antioxidant, also present in lungs, whose role in providing information on the intracellular redox state of animals and plants is well established. In these organisms, GSH influences gene expression associated with stress, maximizing defense responses. Several enzymatic antioxidants, such as glutathione peroxidase (GPx), glutathione reductase, glutathione S-transferase, and glucose 6-phosphate dehydrogenase participate in the redox system; in animals that are stress-tolerant GPx is a key element against oxidative assaults. Most importantly, alternative roles of ROS as signaling molecules have been found in all plants and animals. For example, alveolar macrophages produce that act as second messengers, in addition to having a bactericidal role. The nonradical ROS H2O2 signals inflammation in mammalian lungs, apoptosis in different animal tissues, and is also involved in stomatal closure, root development, gene expression, and defense responses of plants. Antioxidant adaptations in some water-breathing animals involve the excretion of H2O2 by diffusion through gas-exchange structures. The fine balance among a multitude of factors and cells makes the difference between damage and protection in animals and plants. Knowledge about the mechanisms and consequences of these molecular interactions is now starting to be integrated

Desenvolvimento sustentável no Brasil/ Sustainable development in Brazil

O presente trabalho corresponde a uma pesquisa de caráter descritivo-exploratório, voltado para o desenvolvimento sustentável em seus aspectos conceituais e históricos.O principal objetivo foi refletir sobre o desenvolvimento sustentável por meio da revisão literária de caráter e método de abordagem qualitativo. Assim tendo em vista que ultimamente, as questões relativas ao meio ambiente vêm se fixando no âmbito dos grandes temas contemporâneos, a principal justificativa para sua realização foi contribuir para a construção de materiais teóricos e práticos sobre o tema. Por meio da pesquisa foi possível concluir que é nítida a preocupação e difusão do desenvolvimento sustentável para a perpetuação das espécies. É preciso que a sociedade trabalhe a sustentabilidade de maneira prática e objetiva

High mobility group box 1 levels in large vessel vasculitis are not associated with disease activity but are influenced by age and statins

Introduction: Takayasu arteritis (TA) and giant cell arteritis (GCA) are large vessel vasculitides (LVV) that usually present as granulomatous inflammation in arterial walls. High mobility group box 1 (HMGB1) is a nuclear protein that acts as an alarmin when released by dying or activated cells. This study aims to evaluate whether serum HMGB1 can be used as a biomarker in LVV. Methods: Twenty-nine consecutive TA patients with 29 healthy controls (HC) were evaluated in a cross-sectional study. Eighteen consecutive GCA patients with 16 HC were evaluated at the onset of disease and some of them during follow-up. Serum HMGB1 levels were measured by enzyme-linked immunosorbent assay. Results: In GCA patients at disease onset mean serum HMGB1 levels did not differ from HC (5.74 +/- 4.19 ng/ml vs. 4.17 +/- 3.14 ng/ml; p = 0.230). No differences in HMGB1 levels were found between GCA patients with and without polymyalgia rheumatica (p = 0.167), ischemic manifestations (p = 0.873), systemic manifestations (p = 0.474) or relapsing disease (p = 0.608). During follow-up, no significant fluctuations on serum HMGB1 levels were observed from baseline to 3 months (n = 13) (p = 0.075), 12 months (n = 6) (p = 0.093) and at the first relapse (n = 4) (p = 0.202). Serum HMGB1 levels did not differ between TA patients and HC [1.19 (0.45-2.10) ng/ml vs. 1.46 (0.89-3.34) ng/ml; p = 0.181] and no difference was found between TA patients with active disease and in remission [1.31 (0.63-2.16) ng/ml vs. 0.75 (0.39-2.05) ng/ml; p = 0.281]. HMGB1 levels were significantly lower in 16 TA patients on statins compared with 13 patients without statins [0.59 (0.29-1.46) ng/ml vs. 1.93 (0.88-3.34) ng/ml; p = 0.019]. Age was independently associated with higher HMGB1 levels regardless of LVV or control status. Conclusions: Patients with TA and GCA present similar serum HMGB1 levels compared with HC. Serum HMGB1 is not useful to discriminate between active disease and remission. In TA, use of statins was associated with lower HMGB1 levels. HMGB1 is not a biomarker for LVV

Variations and particularities in cardiovascular disease mortality in Brazil and Brazilian states in 1990 and 2015 : estimates from the Global Burden of Disease

Objetivo: Analisar as variações e os diferenciais da mortalidade por doenças cardiovasculares (DCV) no Brasil e em seus estados, em 1990 e 2015. Métodos: Foram utilizados os dados de mortalidade compilados pelo Global Burden of Disease (GBD) 2015, obtidos da base de dados do Sistema de Informação sobre Mortalidade do Ministério da Saúde. Foram realizadas a correção do sub-registro de óbitos e a reclassificação dos códigos garbage por meio de algoritmos específicos. As causas cardiovasculares foram subdivididas em 10 causas específicas. As taxas de mortalidade — dos anos 1990 e 2015 — foram padronizadas pela idade, de acordo com o sexo e o estado brasileiro. Resultados: A taxa de mortalidade por DCV padronizada por idade caiu de 429,5 (1990) para 256,0 (2015) a cada 100 mil habitantes (40,4%). A redução proporcional foi semelhante em ambos os sexos, mas as taxas em homens são substancialmente mais altas do que nas mulheres. A redução da taxa padronizada por idade foi mais acentuada para a doença cardíaca reumática (44,5%), cardiopatia isquêmica (43,9%) e doença cerebrovascular (46,0%). A queda na mortalidade diferiu marcadamente entre os estados, sendo mais acentuada nos estados das regiões Sudeste e Sul do país e no Distrito Federal, e atenuada nos estados do Norte e Nordeste. Conclusão: A mortalidade por DCV padronizada por idade reduziu no Brasil nas últimas décadas, porém de forma heterogênea entre os estados e para diferentes causas específicas. Considerando a magnitude da carga de doença e o envelhecimento da população brasileira, as políticas de enfrentamento das DCV devem ser priorizadas.Objective: To analyze variations and particularities in mortality due to cardiovascular disease (CVD) in Brazil and in Brazilian states, in 1990 and 2015. Methods: We used data compiled from the Global Burden of Disease (GBD) 2015, obtained from the database of the Mortality Information System (SIM) of the Brazilian Ministry of Health. Correction of the sub-registry of deaths and reclassification of the garbage codes were performed using specific algorithms. The cardiovascular causes were subdivided into 10 specific causes. Age-standardized CVD mortality rates — in 1990 and 2015 — were analyzed according to sex and Brazilian state. Results: Age-standardized CVD mortality rate decreased from 429.5 (1990) to 256.0 (2015) per 100,000 inhabitants (40.4%). The proportional decrease was similar in both sexes, but death rates in males were substantially higher. The reduction of age-standardized mortality rate was more significant for rheumatic heart disease (44.5%), ischemic cardiopathy (43.9%), and cerebrovascular disease (46.0%). The decline in mortality was markedly different across states, being more pronounced in those of the southeastern and southern regions and the Federal District, and more modest in most states in the north and northeast regions. Conclusion: Agestandardized CVD mortality has declined in Brazil in recent decades, but in a heterogeneous way across states and for different specific causes. Considering the burden magnitude and the Brazilian population aging, policies to prevent and manage CVD should continue to be prioritized

DWORF Extends Life Span in a PLN-R14del Cardiomyopathy Mouse Model by Reducing Abnormal Sarcoplasmic Reticulum Clusters

BACKGROUND: The p.Arg14del variant of the PLN (phospholamban) gene causes cardiomyopathy, leading to severe heart failure. Calcium handling defects and perinuclear PLN aggregation have both been suggested as pathological drivers of this disease. Dwarf open reading frame (DWORF) has been shown to counteract PLN regulatory calcium handling function in the sarco/endoplasmic reticulum (S/ER). Here, we investigated the potential disease-modulating action of DWORF in this cardiomyopathy and its effects on calcium handling and PLN aggregation. METHODS: We studied a PLN-R14del mouse model, which develops cardiomyopathy with similar characteristics as human patients, and explored whether cardiac DWORF overexpression could delay cardiac deterioration. To this end, R14Δ/Δ (homozygous PLN-R14del) mice carrying the DWORF transgene (R14Δ/ΔDWORFTg [R14Δ/Δ mice carrying the DWORF transgene]) were used. RESULTS: DWORF expression was suppressed in hearts of R14Δ/Δ mice with severe heart failure. Restoration of DWORF expression in R14Δ/Δ mice delayed cardiac fibrosis and heart failure and increased life span &gt;2-fold (from 8 to 18 weeks). DWORF accelerated sarcoplasmic reticulum calcium reuptake and relaxation in isolated cardiomyocytes with wild-type PLN, but in R14Δ/Δ cardiomyocytes, sarcoplasmic reticulum calcium reuptake and relaxation were already enhanced, and no differences were detected between R14Δ/Δ and R14Δ/ΔDWORFTg. Rather, DWORF overexpression delayed the appearance and formation of large pathogenic perinuclear PLN clusters. Careful examination revealed colocalization of sarcoplasmic reticulum markers with these PLN clusters in both R14Δ/Δ mice and human p.Arg14del PLN heart tissue, and hence these previously termed aggregates are comprised of abnormal organized S/ER. This abnormal S/ER organization in PLN-R14del cardiomyopathy contributes to cardiomyocyte cell loss and replacement fibrosis, consequently resulting in cardiac dysfunction. CONCLUSIONS: Disorganized S/ER is a major characteristic of PLN-R14del cardiomyopathy in humans and mice and results in cardiomyocyte death. DWORF overexpression delayed PLN-R14del cardiomyopathy progression and extended life span in R14Δ/Δ mice, by reducing abnormal S/ER clusters.</p

Potential red-flag identification of colorectal adenomas with wide-field fluorescence molecular endoscopy

Adenoma miss rates in colonoscopy are unacceptably high, especially for sessile serrated adenomas / polyps (SSA/Ps) and in high-risk populations, such as patients with Lynch syndrome. Detection rates may be improved by fluorescence molecular endoscopy (FME), which allows morphological visualization of lesions with high-definition white-light imaging as well as fluorescence-guided identification of lesions with a specific molecular marker. In a clinical proof-of-principal study, we investigated FME for colorectal adenoma detection, using a fluorescently labelled antibody (bevacizumab-800CW) against vascular endothelial growth factor A (VEGFA), which is highly upregulated in colorectal adenomas. Methods: Patients with familial adenomatous polyposis (n = 17), received an intravenous injection with 4.5, 10 or 25 mg of bevacizumab-800CW. Three days later, they received NIR-FME. Results: VEGFA-targeted NIR-FME detected colorectal adenomas at all doses. Best results were achieved in the highest (25 mg) cohort, which even detected small adenomas ( < 3 mm). Spectroscopy analyses of freshly excised specimen demonstrated the highest adenoma-to-normal ratio of 1.84 for the 25 mg cohort, with a calculated median tracer concentration in adenomas of 6.43 nmol/mL. Ex vivo signal analyses demonstrated NIR fluorescence within the dysplastic areas of the adenomas. Conclusion: These results suggest that NIR-FME is clinically feasible as a real-time, red-flag technique for detection of colorectal adenomas

Antisense Therapy Attenuates Phospholamban p.(Arg14del) Cardiomyopathy in Mice and Reverses Protein Aggregation

Inherited cardiomyopathy caused by the p.(Arg14del) pathogenic variant of the phospholamban (PLN) gene is characterized by intracardiomyocyte PLN aggregation and can lead to severe dilated cardiomyopathy. We recently reported that pre-emptive depletion of PLN attenuated heart failure (HF) in several cardiomyopathy models. Here, we investigated if administration of a Pln-targeting antisense oligonucleotide (ASO) could halt or reverse disease progression in mice with advanced PLN-R14del cardiomyopathy. To this aim, homozygous PLN-R14del (PLN-R14 (Δ/Δ)) mice received PLN-ASO injections starting at 5 or 6 weeks of age, in the presence of moderate or severe HF, respectively. Mice were monitored for another 4 months with echocardiographic analyses at several timepoints, after which cardiac tissues were examined for pathological remodeling. We found that vehicle-treated PLN-R14 (Δ/Δ) mice continued to develop severe HF, and reached a humane endpoint at 8.1 ± 0.5 weeks of age. Both early and late PLN-ASO administration halted further cardiac remodeling and dysfunction shortly after treatment start, resulting in a life span extension to at least 22 weeks of age. Earlier treatment initiation halted disease development sooner, resulting in better heart function and less remodeling at the study endpoint. PLN-ASO treatment almost completely eliminated PLN aggregates, and normalized levels of autophagic proteins. In conclusion, these findings indicate that PLN-ASO therapy may have beneficial outcomes in PLN-R14del cardiomyopathy when administered after disease onset. Although existing tissue damage was not reversed, further cardiomyopathy progression was stopped, and PLN aggregates were resolved

Antibody dynamics and spontaneous viral clearance in patients with acute hepatitis C infection in Rio de Janeiro, Brazil

Submitted by Sandra Infurna ([email protected]) on 2017-01-18T10:31:05Z No. of bitstreams: 1 clara_yoshida_etal_IOC_2011.pdf: 146042 bytes, checksum: 8ec889224534b76d755828a99d0660c2 (MD5)Approved for entry into archive by Sandra Infurna ([email protected]) on 2017-01-18T10:59:52Z (GMT) No. of bitstreams: 1 clara_yoshida_etal_IOC_2011.pdf: 146042 bytes, checksum: 8ec889224534b76d755828a99d0660c2 (MD5)Made available in DSpace on 2017-01-18T10:59:52Z (GMT). No. of bitstreams: 1 clara_yoshida_etal_IOC_2011.pdf: 146042 bytes, checksum: 8ec889224534b76d755828a99d0660c2 (MD5) Previous issue date: 2011Innsbruck Medical University. Department of Medical Statistics, Informatics and Health Economics. Innsbruck, Austria.Harvard Medical School. Boston, MA, USA / Massachussets General Hospital. Division of Infectious Diseases. Boston, MA, USA.Harvard Medical School. Boston, MA, USA / Massachussets General Hospital. Gastrointestinal Unit. Boston, MA, USA.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Hepatites Virais. Rio de Janeiro, RJ. Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Hepatites Virais. Rio de Janeiro, RJ. Brasil.Laboratório Central de Saúde Pública Noel Nutels. Divisão de Hepatites. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Hepatites Virais. Rio de Janeiro, RJ. Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Hepatites Virais. Rio de Janeiro, RJ. Brasil / Universidade Federal do Estado do Rio de Janeiro. Hospital Universitário Gaffrée Guinle. Unidade de Hepatologia. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Desenvolvimento Tecnológico em Virologia. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Hepatites Virais. Rio de Janeiro, RJ. Brasil.Universitätsklinikum Eppendorf. Medizinische Klinik I. Hamburg, Germany.Fondation Merieux. Emerging Pathogens Laboratory. Lyon, France.University of Innsbruck. Institute of Statistics. Innsbruck, Austria.National Institute on Aging. Gerontology Research Center. Baltimore, USA.Innsbruck Medical University. Department of Medical Statistics, Informatics and Health Economics. Innsbruck, Austria.Innsbruck Medical University. Department of Medical Statistics, Informatics and Health Economics. Innsbruck, Austria.Innsbruck Medical University. Department of Medical Statistics, Informatics and Health Economics. Innsbruck, Austria.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Hepatites Virais. Rio de Janeiro, RJ. Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Hepatites Virais. Rio de Janeiro, RJ. Brasil.Background: The anti-HCV antibody response has not been well characterized during the early phase of HCV infection and little is known about its relationship to the clinical course during this period. Methods: We analyzed serial anti-HCV antibodies longitudinally obtained from a prospective cohort of 65 patients with acute HCV infection by using a microparticle enzyme immunoassay AxSYM HCV 3.0 (Abbott Diagnostics) during the first 12 months from HCV acquisition in Rio de Janeiro, Brazil. Spontaneous viral clearance (SVC) was defined as undetectable HCV RNA in serum, in the absence of treatment, for three consecutive HCV PCR tests within 12-months of follow-up. Results: Baseline antibody values were similar among patient groups with self-limiting HCV evolution (n = 34) and persistent viremia (n = 31) [median (interquartile range) signal/cut-off ratio (s/co) 78.7 (60.7-93.8) vs. 93.9 (67.8- 111.9), p = 0.26]. During 12-months follow-up, patients with acute spontaneous resolving HCV infection showed significantly lower serial antibody response in comparison to individuals progressing to chronic infection [median (interquartile range) s/co 62.7 (35.2-85.0) vs. 98.4 (70.4-127.4), p < 0.0001]. In addition, patients with self-limiting HCV evolution exhibited an expeditious, sharp decline of serial antibody values after SVC in comparison to those measured before SVC [median (interquartile range) s/co 56.0 (25.4-79.3) vs. 79.4 (66.3-103.0), p < 0.0001]. Conclusion: Our findings indicate a rapid short-term decline of antibody values in patients with acute spontaneous resolving HCV infection