High-throughput sequencing of black pepper root transcriptome

Background: Black pepper (Piper nigrum L.) is one of the most popular spices in the world. It is used in cooking and the preservation of food and even has medicinal properties. Losses in production from disease are a major limitation in the culture of this crop. The major diseases are root rot and foot rot, which are results of root infection by Fusarium solani and Phytophtora capsici, respectively. Understanding the molecular interaction between the pathogens and the host's root region is important for obtaining resistant cultivars by biotechnological breeding. Genetic and molecular data for this species, though, are limited. In this paper, RNA-Seq technology has been employed, for the first time, to describe the root transcriptome of black pepper. Results: The root transcriptome of black pepper was sequenced by the NGS SOLiD platform and assembled using the multiple-k method. Blast2Go and orthoMCL methods were used to annotate 10338 unigenes. The 4472 predicted proteins showed about 52% homology with the Arabidopsis proteome. Two root proteomes identified 615 proteins, which seem to define the plant's root pattern. Simple-sequence repeats were identified that may be useful in studies of genetic diversity and may have applications in biotechnology and ecology. Conclusions: This dataset of 10338 unigenes is crucially important for the biotechnological breeding of black pepper and the ecogenomics of the Magnoliids, a major group of basal angiosperms.Rede Paraense de Genomica e Proteomica (Governo do Estado do Para/SEDECT/FAPESPA)Rede Paraense de Genomica e Proteomica (Governo do Estado do Para/SEDECT/FAPESPA)PROPESP/UFPAPROPESP/UFPAFADESPFADESPFINEPFINEPCoordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES)CAPES (Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior

De novo transcriptome analysis of Hevea brasiliensis tissues by RNA-seq and screening for molecular markers

Abstract\ud \ud Background\ud The rubber tree, Hevea brasiliensis, is a species native to the Brazilian Amazon region and it supplies almost all the world’s natural rubber, a strategic raw material for a variety of products. One of the major challenges for developing rubber tree plantations is adapting the plant to biotic and abiotic stress. Transcriptome analysis is one of the main approaches for identifying the complete set of active genes in a cell or tissue for a specific developmental stage or physiological condition.\ud \ud \ud Results\ud Here, we report on the sequencing, assembling, annotation and screening for molecular markers from a pool of H. brasiliensis tissues. A total of 17,166 contigs were successfully annotated. Then, 2,191 Single Nucleotide Variation (SNV) and 1.397 Simple Sequence Repeat (SSR) loci were discriminated from the sequences. From 306 putative, mainly non-synonymous SNVs located in CDS sequences, 191 were checked for their ability to characterize 23 Hevea genotypes by an allele-specific amplification technology. For 172 (90%), the nucleotide variation at the predicted genomic location was confirmed, thus validating the different steps from sequencing to the in silico detection of the SNVs.\ud \ud \ud Conclusions\ud This is the first study of the H. brasiliensis transcriptome, covering a wide range of tissues and organs, leading to the production of the first developed SNP markers. This process could be amplified to a larger set of in silico detected SNVs in expressed genes in order to increase the marker density in available and future genetic maps. The results obtained in this study will contribute to the H. brasiliensis genetic breeding program focused on improving of disease resistance and latex yield.CNPqPROSULCAPESFUNDHER

Impact of COVID-19 on cardiovascular testing in the United States versus the rest of the world

Objectives: This study sought to quantify and compare the decline in volumes of cardiovascular procedures between the United States and non-US institutions during the early phase of the coronavirus disease-2019 (COVID-19) pandemic. Background: The COVID-19 pandemic has disrupted the care of many non-COVID-19 illnesses. Reductions in diagnostic cardiovascular testing around the world have led to concerns over the implications of reduced testing for cardiovascular disease (CVD) morbidity and mortality. Methods: Data were submitted to the INCAPS-COVID (International Atomic Energy Agency Non-Invasive Cardiology Protocols Study of COVID-19), a multinational registry comprising 909 institutions in 108 countries (including 155 facilities in 40 U.S. states), assessing the impact of the COVID-19 pandemic on volumes of diagnostic cardiovascular procedures. Data were obtained for April 2020 and compared with volumes of baseline procedures from March 2019. We compared laboratory characteristics, practices, and procedure volumes between U.S. and non-U.S. facilities and between U.S. geographic regions and identified factors associated with volume reduction in the United States. Results: Reductions in the volumes of procedures in the United States were similar to those in non-U.S. facilities (68% vs. 63%, respectively; p = 0.237), although U.S. facilities reported greater reductions in invasive coronary angiography (69% vs. 53%, respectively; p < 0.001). Significantly more U.S. facilities reported increased use of telehealth and patient screening measures than non-U.S. facilities, such as temperature checks, symptom screenings, and COVID-19 testing. Reductions in volumes of procedures differed between U.S. regions, with larger declines observed in the Northeast (76%) and Midwest (74%) than in the South (62%) and West (44%). Prevalence of COVID-19, staff redeployments, outpatient centers, and urban centers were associated with greater reductions in volume in U.S. facilities in a multivariable analysis. Conclusions: We observed marked reductions in U.S. cardiovascular testing in the early phase of the pandemic and significant variability between U.S. regions. The association between reductions of volumes and COVID-19 prevalence in the United States highlighted the need for proactive efforts to maintain access to cardiovascular testing in areas most affected by outbreaks of COVID-19 infection

Risk profiles and one-year outcomes of patients with newly diagnosed atrial fibrillation in India: Insights from the GARFIELD-AF Registry.

BACKGROUND: The Global Anticoagulant Registry in the FIELD-Atrial Fibrillation (GARFIELD-AF) is an ongoing prospective noninterventional registry, which is providing important information on the baseline characteristics, treatment patterns, and 1-year outcomes in patients with newly diagnosed non-valvular atrial fibrillation (NVAF). This report describes data from Indian patients recruited in this registry. METHODS AND RESULTS: A total of 52,014 patients with newly diagnosed AF were enrolled globally; of these, 1388 patients were recruited from 26 sites within India (2012-2016). In India, the mean age was 65.8 years at diagnosis of NVAF. Hypertension was the most prevalent risk factor for AF, present in 68.5% of patients from India and in 76.3% of patients globally (P < 0.001). Diabetes and coronary artery disease (CAD) were prevalent in 36.2% and 28.1% of patients as compared with global prevalence of 22.2% and 21.6%, respectively (P < 0.001 for both). Antiplatelet therapy was the most common antithrombotic treatment in India. With increasing stroke risk, however, patients were more likely to receive oral anticoagulant therapy [mainly vitamin K antagonist (VKA)], but average international normalized ratio (INR) was lower among Indian patients [median INR value 1.6 (interquartile range {IQR}: 1.3-2.3) versus 2.3 (IQR 1.8-2.8) (P < 0.001)]. Compared with other countries, patients from India had markedly higher rates of all-cause mortality [7.68 per 100 person-years (95% confidence interval 6.32-9.35) vs 4.34 (4.16-4.53), P < 0.0001], while rates of stroke/systemic embolism and major bleeding were lower after 1 year of follow-up. CONCLUSION: Compared to previously published registries from India, the GARFIELD-AF registry describes clinical profiles and outcomes in Indian patients with AF of a different etiology. The registry data show that compared to the rest of the world, Indian AF patients are younger in age and have more diabetes and CAD. Patients with a higher stroke risk are more likely to receive anticoagulation therapy with VKA but are underdosed compared with the global average in the GARFIELD-AF. CLINICAL TRIAL REGISTRATION-URL: http://www.clinicaltrials.gov. Unique identifier: NCT01090362

Mutational screening in the LDLR gene among patients presenting familial hypercholesterolemia in the Southeast of Brazil

Zanette, Dalila Lucíola. “Documento produzido em parceria ou por autor vinculado à Fiocruz, mas não consta à informação no documento”.Submitted by Ana Maria Fiscina Sampaio ([email protected]) on 2018-03-27T12:36:58Z No. of bitstreams: 1 Molfetta GA Mutational screening in the LDLR gene....pdf: 342859 bytes, checksum: 9e8d92035643cdd905392bba319d042d (MD5)Approved for entry into archive by Ana Maria Fiscina Sampaio ([email protected]) on 2018-03-27T12:59:07Z (GMT) No. of bitstreams: 1 Molfetta GA Mutational screening in the LDLR gene....pdf: 342859 bytes, checksum: 9e8d92035643cdd905392bba319d042d (MD5)Made available in DSpace on 2018-03-27T12:59:07Z (GMT). No. of bitstreams: 1 Molfetta GA Mutational screening in the LDLR gene....pdf: 342859 bytes, checksum: 9e8d92035643cdd905392bba319d042d (MD5) Previous issue date: 2017Universidade de São Paulo. Faculdade de Medicina de Ribeirão Preto. Departamento de Genética. Ribeirão Preto, SP, Brasil / Universidade de São Paulo. Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto. Centro de Medicina Genômica. Ribeirão Preto, SP, Brasil / Universidade de São Paulo. Instituto Nacional de Ciência e Tecnologia em Células-Tronco e Terapia Celular. Fundação Hemocentro de Ribeirão Preto. Ribeirão Preto, SP, BrasilUniversidade de São Paulo. Faculdade de Medicina de Ribeirão Preto. Departamento de Genética. Ribeirão Preto, SP, Brasil / Universidade de São Paulo. Instituto Nacional de Ciência e Tecnologia em Células-Tronco e Terapia Celular. Fundação Hemocentro de Ribeirão Preto. Ribeirão Preto, SP,Universidade de São Paulo. Faculdade de Medicina de Ribeirão Preto. Departamento de Clínica Médica. Ribeirão Preto, SP, BrasilUniversidade de São Paulo. Faculdade de Medicina de Ribeirão Preto. Departamento de Genética. Ribeirão Preto, SP, Brasil / Universidade de São Paulo. Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto. Centro de Medicina Genômica. Ribeirão Preto, SP, Brasil / Universidade de São Paulo. Instituto Nacional de Ciência e Tecnologia em Células-Tronco e Terapia Celular. Fundação Hemocentro de Ribeirão Preto. Ribeirão Preto, SP, BrasilFamilial hypercholesterolemia (FH) is a dominant, autosomal disease characterized by high LDL levels in blood plasma, and is caused by a defect in the gene encoding the LDL receptor (LDLR). The clinical diagnosis is based on personal and familial history, physical examination findings, and measures of high LDL cholesterol concentrations. LDLR is a cell-surface glycoprotein that controls the level of blood plasma cholesterol and triglyceride by LDLR-mediated endocytosis. Here we sequenced the entire LDLR gene-coding region to screen for mutations in 32 patients diagnosed with FH, and we have found 20 mutations including synonymous, missense, and intronic mutations. Six of them were characterized as pathogenic mutations (D178Y, C184Y, S326C, C681X, IVS7+10G>C, and IVS11-10G>A). We have also found one intronic mutation not described so far (IVS11-63C>A). Our study corroborates the broad spectrum of mutations distributed along the entire LDLR gene, and we suggest that the genes APOB and PCSK9 should also be screened for mutations when considering the diagnosis of FH. It is already known that different types of mutations are directly associated with the phenotype heterogeneity presented by patients. Considering that Brazilian population is highly admixed, it is important to determine the geographic spectrum of LDLR mutations to provide information on the prognosis and treatment of each FH patient

Computational framework to support integration of biomolecular and clinical data within a translational approach

Background The use of the knowledge produced by sciences to promote human health is the main goal of translational medicine. To make it feasible we need computational methods to handle the large amount of information that arises from bench to bedside and to deal with its heterogeneity. A computational challenge that must be faced is to promote the integration of clinical, socio-demographic and biological data. In this effort, ontologies play an essential role as a powerful artifact for knowledge representation. Chado is a modular ontology-oriented database model that gained popularity due to its robustness and flexibility as a generic platform to store biological data; however it lacks supporting representation of clinical and socio-demographic information. Results We have implemented an extension of Chado – the Clinical Module - to allow the representation of this kind of information. Our approach consists of a framework for data integration through the use of a common reference ontology. The design of this framework has four levels: data level, to store the data; semantic level, to integrate and standardize the data by the use of ontologies; application level, to manage clinical databases, ontologies and data integration process; and web interface level, to allow interaction between the user and the system. The clinical module was built based on the Entity-Attribute-Value (EAV) model. We also proposed a methodology to migrate data from legacy clinical databases to the integrative framework. A Chado instance was initialized using a relational database management system. The Clinical Module was implemented and the framework was loaded using data from a factual clinical research database. Clinical and demographic data as well as biomaterial data were obtained from patients with tumors of head and neck. We implemented the IPTrans tool that is a complete environment for data migration, which comprises: the construction of a model to describe the legacy clinical data, based on an ontology; the Extraction, Transformation and Load (ETL) process to extract the data from the source clinical database and load it in the Clinical Module of Chado; the development of a web tool and a Bridge Layer to adapt the web tool to Chado, as well as other applications. Conclusions Open-source computational solutions currently available for translational science does not have a model to represent biomolecular information and also are not integrated with the existing bioinformatics tools. On the other hand, existing genomic data models do not represent clinical patient data. A framework was developed to support translational research by integrating biomolecular information coming from different “omics” technologies with patient’s clinical and socio-demographic data. This framework should present some features: flexibility, compression and robustness. The experiments accomplished from a use case demonstrated that the proposed system meets requirements of flexibility and robustness, leading to the desired integration. The Clinical Module can be accessed in http://dcm.ffclrp.usp.br/caib/pg=iptrans webcite

American Journal of Human Biology

Texto completo. Acesso restrito. p.551–563Estimates of African, European, and Amerindian contributions to the gene pool of 11 predominantly African-derived South American populations were obtained using five autosomal and one Y chromosome hypervariable loci, as well as mitochondrial DNA (sequences of the first hypervariable segment of the control region, plus two restriction sites and the presence or absence of the CoII/tRNALys intergenic 9-bp deletion). The three latter characteristics are reported here for the first time for 42 individuals living in three Brazilian populations. Thirty-eight sequences were identified in these persons; 17 (45%) could be classified as being of African, 4 (11%) of Amerindian, and 2 (5%) of European origin. Evidence for asymmetrical matings in relation to sex and ethnic group was obtained for nine of the 11 populations. The most consistent finding was the introduction of European genes through males, but the results differ in the several communities, indicating the importance of local factors in such interactions.Salvado

Microarray profiles of ex vivo expanded hematopoietic stem cells show induction of genes involved in noncanonical Wnt signaling

Zanette, Dalila Lucíola. “Documento produzido em parceria ou por autor vinculado à Fiocruz, mas não consta à informação no documento”.Submitted by Ana Maria Fiscina Sampaio ([email protected]) on 2018-04-13T17:59:31Z No. of bitstreams: 1 Zanette DL Microarray profiles of ex vivo expanded....pdf: 429718 bytes, checksum: 44af439761969d8585f1abad49511734 (MD5)Approved for entry into archive by Ana Maria Fiscina Sampaio ([email protected]) on 2018-04-13T18:12:41Z (GMT) No. of bitstreams: 1 Zanette DL Microarray profiles of ex vivo expanded....pdf: 429718 bytes, checksum: 44af439761969d8585f1abad49511734 (MD5)Made available in DSpace on 2018-04-13T18:12:41Z (GMT). No. of bitstreams: 1 Zanette DL Microarray profiles of ex vivo expanded....pdf: 429718 bytes, checksum: 44af439761969d8585f1abad49511734 (MD5) Previous issue date: 2013FAPESP and CNPqUniversidade de São Paulo. Faculdade de Medicina de Ribeirão Preto. Departamento de Genética. Ribeirão Preto, SP, Brasil / Centro de Terapia Celular, Centro Regional de Hemoterapia. Ribeirão Preto, SP, BrasilUniversidade de São Paulo. Faculdade de Medicina de Ribeirão Preto. Departamento de Genética. Ribeirão Preto, SP, Brasil / Centro de Terapia Celular, Centro Regional de Hemoterapia. Ribeirão Preto, SP, BrasilUniversidade de São Paulo. Faculdade de Medicina de Ribeirão Preto. Departamento de Genética. Ribeirão Preto, SP, Brasil / Centro de Terapia Celular, Centro Regional de Hemoterapia. Ribeirão Preto, SP, BrasilUniversidade de São Paulo. Faculdade de Medicina de Ribeirão Preto. Departamento de Genética. Ribeirão Preto, SP, Brasil / Centro de Terapia Celular, Centro Regional de Hemoterapia. Ribeirão Preto, SP, BrasilUniversidade de São Paulo. Faculdade de Medicina de Ribeirão Preto. Departamento de Genética. Ribeirão Preto, SP, Brasil / Centro de Terapia Celular, Centro Regional de Hemoterapia. Ribeirão Preto, SP, BrasilCentro de Terapia Celular, Centro Regional de Hemoterapia. Ribeirão Preto, SP, Brasil / Universidade de São Paulo. Faculdade de Medicina de Ribeirão Preto. Departamento de Clínica Médica Ribeirão Preto, SP, BrasilUniversidade de São Paulo. Faculdade de Medicina de Ribeirão Preto. Departamento de Genética. Ribeirão Preto, SP, Brasil / Centro de Terapia Celular, Centro Regional de Hemoterapia. Ribeirão Preto, SP, BrasilCentro de Terapia Celular, Centro Regional de Hemoterapia. Ribeirão Preto, SP, Brasil / Universidade de São Paulo. Faculdade de Medicina de Ribeirão Preto. Departamento de Clínica Médica Ribeirão Preto, SP, BrasilThe low number of hematopoietic stem cells (HSC) in umbilical cord blood (UCB) is directly related to increased risk of transplant failure. Effective ex vivo expansion of HSC has been tried for many years, with conflicting results because of the inability to reproduce in vitro HSC proliferation in the same way it occurs in vivo. We compared freshly isolated HSC with their expanded counterparts by microarray analysis and detected activation of the noncanonical Wnt (wingless-type MMTV integration site family) pathway. Study of early alterations during ex vivo UCB-HSC expansion could contribute to improvement of ex vivo expansion systems