San Mateo, CA, United States
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Udy D.B.,University of California at San Francisco | Voorhies M.,University of California at San Francisco | Chan P.P.,Maverix Biomics | Chan P.P.,University of California at Santa Cruz | And 3 more authors.
PLoS ONE | Year: 2015

The rat kangaroo (long-nosed potoroo, Potorous tridactylus) is a marsupial native to Australia. Cultured rat kangaroo kidney epithelial cells (PtK) are commonly used to study cell biological processes. These mammalian cells are large, adherent, and flat, and contain large and few chromosomes - and are thus ideal for imaging intra-cellular dynamics such as those of mitosis. Despite this, neither the rat kangaroo genome nor transcriptome have been sequenced, creating a challenge for probing the molecular basis of these cellular dynamics. Here, we present the sequencing, assembly and annotation of the draft rat kangaroo de novo transcriptome. We sequenced 679 million reads that mapped to 347,323 Trinity transcripts and 20,079 Unigenes. We present statistics emerging from transcriptome- wide analyses, and analyses suggesting that the transcriptome covers full-length sequences of most genes, many with multiple isoforms. We also validate our findings with a proof-of-concept gene knockdown experiment. We expect that this high quality transcriptome will make rat kangaroo cells a more tractable system for linking molecular-scale function and cellular-scale dynamics. Copyright: © 2015 Udy et al.


Grant
Agency: Department of Health and Human Services | Branch: National Institutes of Health | Program: STTR | Phase: Phase I | Award Amount: 149.95K | Year: 2015

DESCRIPTION provided by applicant The broad objective of this project is to develop an integrated wet lab dry lab kit for high throughput detection of RNA modifications The final product will provide all required molecular biology reagents a set of simple and robust experimental manipulations for facile analysis of modifications and researcher friendly analytic cloud based software requiring no special bioinformatics skills or computing hardware Emerging data suggests that post transcriptional modifications of many types of cellular RNA play an important and largely unexplored role in biology and in development and maintenance of the nervous system In particular a notable variety of neural diseases are due to specific defects in RNA modification including autosomal recessive intellectual disability ARID non syndromic X linked mental retardation myoclonus epilepsy ragged red fibers MERRF mitochondrial encephalopathy lactic acidosis with stroke like episodes MELAS and familial dysautonomia Initial evidence for the links between RNA modification regulation and gene expression mRNA splicing nuclear export and protein translation suggest much broader unknown effects given that modification states for most RNAs in most cell types are not well defined High throughput RNA sequencing has revolutionized the study of gene expression but it has not been widely applied to identifying most types of RNA modifications due to lack of methods for detection of modifications that are suitable for commercial use and lack of methods for complex post sequencing analytics This Phase proposal focuses on developing such methodology for three types of biologically relevant but relatively understudied RNA modifications with the following Specific Aims I Develop methods for identifying RNA sites with m A m C or andapos O methylation II Develop an analysis pipeline to identify sites with andapos O methylation m A or m C To achieve these aims a novel biochemical approach will be employed for detecting and mapping andapos O methylation leveraging a known chemical reaction coupled with ligation methods to enrich for these sites A distinct novel approach will be applied to detect m A and m C modifications by differential analysis of reverse transcription between enzymatically treated samples An integrated cloud based platform with custom analytic pipelines will be developed for processing and interpreting the RNA sequencing data to simplify complex analyses required to identify modifications with precision Together these all inclusive kits will form both pre and post sequencing means for large scale RNA modification detection with turn key ease of use PUBLIC HEALTH RELEVANCE This project will advance research on RNA modifications a key type of processing events that plays an important role in the development of the nervous system and many neurological diseases Researchers will be able to use the tools developed by this work to detect multiple types of RNA modifications in the cells of human and other model species using a high throughput robust commercial kit Broad application of this technology should significantly advance the knowledge of RNA modification and its many effects on gene regulation and human health


Grant
Agency: Department of Health and Human Services | Branch: National Institutes of Health | Program: STTR | Phase: Phase I | Award Amount: 219.66K | Year: 2016

Project Summary Antibiotic resistance has become a pressing public health concern due to the rise of pathogenic bacterial strains with mutations that reduce or eliminate the effectiveness of drugs to treat infections Beta lactamases produced by some bacteria provide resistance by degrading beta lactams one of most widely used class of antibiotics Originally restricted to penicillins mutant beta lactamases that confer resistance to antibiotics including monobactams and most cephalosporins known as extended spectrum beta lactamases or ESBLs are widespread Clinical isolates are currently characterized for ESBL resistance using inhibition zone tests against a panel of lactam antibiotics but the results produced by these tests are difficult to standardize and do not translate consistently into clinical practice In addition these tests typically produce no information about the genetic basis for the observed resistance nor the relatedness to other potentially characterized strains Here we propose the development of a sequence based analysis platform and knowledgebase for analyzing molecular signatures of extended spectrum beta lactamase resistance that can initially market to health institutions and companies monitoring the spread of EBSL resistance The platform will consist of an analysis kit that extracts positively selected variants beta lactamase sequences and other genomic information relevant to the ESBL phenotype from whole genome sequences of clinical samples A total of samples will be analyzed of which ESBL resistant samples provided by the Mercy Center at UC Merced will be newly sequenced and the rest will be obtained from a published study from the University of Washington A cloud based searchable database with interactive visualization will be served as the repository of the ESBL resistant features identified in the clinical samples By leveraging the metadata exchange standards being developed for broad sharing of human genomic data the rapidly expanding Global Alliance for Genomics and Health application program interface our work will represent the initial extension of this API for sharing microbial centric data The ultimate goal of this project is to create an accurate predictive resistance classifier using beta lactamase gene sequences and other genomic markers that are linked to known treatment outcomes and strain phenotypes We will develop this new classifier based on published methods found to be effective with HIV genotype phenotype prediction ESBL resistant features obtained from the clinical samples in this study will be used for training and testing of the classifier The powerful combination of sharable database and analytic tools in a single platform will significantly advance knowledge of antibiotic resistant bacteria facilitate epidemiological monitoring of the spread of ESBL resistance and represents a key first step to develop a diagnostic tool to counter ESBL resistance using whole genome sequences !Project Narrative Infectious diseases caused by antibiotic resistant bacteria are difficult to treat and represent a serious threat to human health world wide This project will develop a platform of pathogen search tools with simple interfaces for clinical researchers to rapidly match and analyze molecular signatures of extended spectrum beta lactamase resistance Broad application of this cloud based database and search technology should significantly advance knowledge of antibiotic resistant bacteria enable more effective targeted treatment and limit future outbreaks by establishing real time pathogen signature data sharing


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Partnerskmarkiewicz2016-01-13T17:25:35+00:00 Maverix works with several partners to provide an end-to-end solution from bio sample through discovery. Interested in partnering with Maverix? Click herefor more information ...


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mRNA-seq Expression Analysisheaththomas2016-01-13T11:39:07+00:00 RNA sequencing is a high-throughput sequencing technology that provides a genome-wide assessment of the RNA content of an organism, tissue or cell. mRNA-seq can be used to measure gene expression levels, assist in new gene and transcript discovery, and identify novel splice variants ...


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Maverix Dxkmarkiewicz2016-01-14T07:48:10+00:00 The Maverix Dx Platform leverages the best-in-class analytics of WAVES, but is designed to support clinical diagnostic applications where the sample collection and sequencing will be done in one or more geographically distributed CLIA lab environments, using Illumina, Ion Torrent and other sequencing technologies. Weve added on a front-end system and LIMS interface that is specifically designed for clinical diagnostic and testing applications, including integrating patient information and sample IDs in a secure and confidential manner ...


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Translational Research/Medicinekmarkiewicz2016-01-14T08:37:54+00:00 Utilizing NGS in developing diagnostics and treatments? Maverix solutions will help! NGS can be an excellent tool to assist in translating scientific discoveries into practical (clinical) applications, such as the creation of diagnostics or medicinal treatments. The National Institute of Environmental Health Sciences (NIEHS) has established a framework for developing translational and interdisciplinary research, helping to structure to the practice of translational research, including five categories of effort: Mechanistic Understanding (MC), Emerging Technology (ET), Phenotypic Validation (PV), Application & Intervention (AI), and Clinical Assessment (CA) ...


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Basic Researchkmarkiewicz2016-01-14T07:35:35+00:00 We share your passion for great science! At Maverix, we take great pains to ensure superb handling of big data and the efficient processing of data, and we also care deeply about the science. We realize that if youre utilizing NGS and youre on a quest for a fundamental understanding of genomics, you may be engaged in either pure basic research or use-inspired basic research, depending on whether you have considerations for the use of the technology, and we can help you to achieve your goals ...


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