The recent emergence of previously unknown coronavirus (SARS-CoV-2), first identified in the Chinese city of Wuhan in December 2019 has had a major public health and economic consequences. Although 61 888 confirmed cases were reported in Brazil by 28 April 2020, little is known about the SARS-CoV-2 epidemic in this country.
To better understand the recent epidemic in both populous state in southeast Brazil – Minas Gerais (MG) – we sequenced the complete 40 SARS-CoV-2 genome of MG case and reviewing epidemiological data from three Brazilian states. Both the analysis of genomic and geographical distribution of the reported cases provide evidence for multiple independent introductions MG.
epidemiological estimates of the number of reproduction (R) use different data sources and the theoretical assumptions indicate a potential ongoing transmission of the virus even though the reduction R of the first reported cases of the end of April 2020. Estimated date of SARS-CoV-2 introduction to Brazil is consistent with epidemiological data from the first case of travelers returning from Lombardy, Italy. These findings highlight the nature of the epidemic in COVID-19 MG and reinforces the need for real-time and continuously genome surveillance strategies to better understand and prepare for the deployment of emerging pathogenic virus epidemic.
Development of new approaches to regulate the expression of angiotensin-converting enzyme 2 (ACE2) and transmembrane protease serine 2 (TMPRSS2) is becoming increasingly important in the context of the ongoing 19th COVID pandemic because this enzyme plays an important role in cell infection. In this work we are looking for suspected ACE2 expression and regulatory networks TMPRSS2 mediated by various miRNA isoforms (isomiR) throughout the different human organs using the data miRNA / mRNA sequencing paired publicly available from The Cancer Genome Atlas (TCGA) project.
As a result, we identified several families miRNA targeting ACE2 and TMPRSS2 gene in several tissues. Specifically, we found that the lysine specific demethylase 5B (JARID1B), encoded by the gene KDM5B, can indirectly affect the expression of ACE2 / TMPRSS2 by repressing transcription of HSA-let-7e / HSA-miR-125A and HSA-miR-141 / HSA -mir-200 gene targeting miRNA family.
The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing
Development and validation of Houston Methodist Variant Viewer version 3: update our application for next-generation sequencing data interpretation
Objective: Informatics tools support generation sequencing workflows are essential to provide timely interpretation of somatic variants in cancer. Here, we explain the significant updates to our development laboratory and bioinformatics pipeline data management application called Houston Methodist Varian Viewer (HMVV).
Materials and methods: We collect feature requests and suggestions for improvement workflows from end users of version 1.5 HMVV 1. Over the years, we iteratively apply these features in five successive updates to HMVV version 3.
Results: We improve application performance and data throughput while reducing the chance for manual data entry errors. We enabled end-user workflows for pipeline monitoring, variants of interpretation and explanation, and integration with our laboratory information system. maintenance enhanced through improved reporting system defects, high data security, and improved code modularity and environmental systems.
PinPoint-HR System for Platform Cell Line Generation & Retargeting of AAVS1 Safe Harbor Locus (includes PIN410A-1, GE601A-1, PIN200A-1, PIN510A-1, & PIN600A-1)
PinPoint-HR System for Platform Cell Line Generation & Retargeting of AAVS1 Safe Harbor Locus (includes PIN410A-1, CAS601A-1, PIN200A-1, PIN510A-1, & PIN600A-1)
Description: Description of target: SCFR(Mast/stem cell growth factor receptor), also known as proto-oncogene c-Kit or tyrosine-protein kinase Kit or CD117, is a protein that in humans is encoded by the KIT gene. KIT was first described as the cellular homolog of the feline sarcoma viral oncogene v-kit. The KIT gene is mapped on 4q12. Kit was expressed on the surface of germ cells up to the pachytene stage. Signaling from the KIT receptor tyrosine kinase is essential for primordial germ cell growth both in vivo and in vitro. Determination of the KIT effectors acting in primordial germ cells has been hampered by the lack of effective methods to manipulate easily gene expression in these cells.;Species reactivity: Mouse;Application: ELISA;Assay info: ;Sensitivity: <10pg/ml
Description: Description of target: This gene encodes the human homolog of the proto-oncogene c-kit. C-kit was first identified as the cellular homolog of the feline sarcoma viral oncogene v-kit. This protein is a type 3 transmembrane receptor for MGF (mast cell growth factor, also known as stem cell factor). Mutations in this gene are associated with gastrointestinal stromal tumors, mast cell disease, acute myelogenous lukemia, and piebaldism. Multiple transcript variants encoding different isoforms have been found for this gene.;Species reactivity: Human;Application: ELISA;Assay info: Assay Methodology: Quantitative Sandwich ELISA;Sensitivity: 0.61 ng/mL
Description: Description of target: This gene encodes the human homolog of the proto-oncogene c-kit. C-kit was first identified as the cellular homolog of the feline sarcoma viral oncogene v-kit. This protein is a type 3 transmembrane receptor for MGF (mast cell growth factor, also known as stem cell factor). Mutations in this gene are associated with gastrointestinal stromal tumors, mast cell disease, acute myelogenous lukemia, and piebaldism. Multiple transcript variants encoding different isoforms have been found for this gene.;Species reactivity: Human;Application: ELISA;Assay info: ;Sensitivity: < 0.61ng/mL
Description: Description of target: The c-Kit proto-oncogene is the cellular homolog of the transforming gene of a feline retrovirus (v-Kit). The c-kit protein includes characteristics of a protein kinase transmembrane receptor. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.;Species reactivity: Mouse;Application: ELISA;Assay info: ;Sensitivity: < 0.063ng/mL
Discussion and conclusion: Validate any updates HMVV carried out in accordance with expert guidance. We turned the 8 × reduction in bioinformatics pipeline computing time to test our longest. Our molecular pathologists to interpret the test results of at least two days faster than was previously possible.
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