Research grade marijuana supplied by the National Institute on Drug Abuse is genetically divergent from commercially available Cannabis, bioRxiv, 2019-03-29
AbstractPublic comfort with Cannabis (marijuana and hemp) has recently increased, resulting in previously strict Cannabis regulations now allowing hemp cultivation, medical use, and in some states, recreational consumption. There is a growing interest in the potential medical benefits of the various chemical constituents produced by the Cannabis plant. Currently, the University of Mississippi, funded through the National Institutes of HealthNational Institute on Drug Abuse (NIHNIDA), is the sole Drug Enforcement Agency (DEA) licensed facility to cultivate Cannabis for research purposes. Hence, most federally funded research where participants consume Cannabis for medicinal purposes relies on NIDA-supplied product. Previous research found that cannabinoid levels in research grade marijuana supplied by NIDA did not align with commercially available Cannabis from Colorado, Washington and California. Given NIDA chemotypes were misaligned with commercial Cannabis, we sought to investigate where NIDA’s research grade marijuana falls on the genetic spectrum of Cannabis groups. NIDA research grade marijuana was found to genetically group with Hemp samples along with a small subset of commercial drug-type Cannabis. A majority of commercially available drug-type Cannabis was genetically very distinct from NIDA samples. These results suggest that subjects consuming NIDA research grade marijuana may experience different effects than average consumers.
biorxiv genetics 100-200-users 2019Research grade marijuana supplied by the National Institute on Drug Abuse is genetically divergent from commercially availableCannabis, bioRxiv, 2019-03-29
AbstractPublic comfort withCannabis(marijuana and hemp) has recently increased, resulting in previously strictCannabisregulations now allowing hemp cultivation, medical use, and in some states, recreational consumption. There is a growing interest in the potential medical benefits of the various chemical constituents produced by theCannabisplant. Currently, the University of Mississippi, funded through the National Institutes of HealthNational Institute on Drug Abuse (NIHNIDA), is the sole Drug Enforcement Agency (DEA) licensed facility to cultivateCannabisfor research purposes. Hence, most federally funded research where participants consumeCannabisfor medicinal purposes relies on NIDA-supplied product. Previous research found that cannabinoid levels in research grade marijuana supplied by NIDA did not align with commercially availableCannabisfrom Colorado, Washington and California. Given NIDA chemotypes were misaligned with commercialCannabis, we sought to investigate where NIDA’s research grade marijuana falls on the genetic spectrum ofCannabisgroups. NIDA research grade marijuana was found to genetically group with Hemp samples along with a small subset of commercial drug-typeCannabis. A majority of commercially available drug-typeCannabiswas genetically very distinct from NIDA samples. These results suggest that subjects consuming NIDA research grade marijuana may experience different effects than average consumers.
biorxiv genetics 100-200-users 2019Inhibition of mTORC1 signaling in aged rats counteracts the decline in muscle mass and reverses multiple parameters of muscle signaling associated with sarcopenia, bioRxiv, 2019-03-28
AbstractThere is a lack of pharmacological interventions available for sarcopenia, a progressive age-associated loss of muscle mass, leading to a decline in mobility and quality of life. We found mTORC1 (mammalian target of rapamycin complex 1), a well-established critical positive modulator of mass, to be hyperactivated in sarcopenic muscle. Furthermore, inhibition of the mTORC1 pathway counteracted sarcopenia as determined by observing an increase in muscle mass and fiber type cross sectional area, surprising because mTORC1 signaling has been shown to be required for muscle mass gains in some settings. Additionally, several genes related to senescence were downregulated, while gene expression indicators of neuromuscular junction denervation were diminished using a low dose of a rapalog. Therefore mTORC1 inhibition may delay the progression of sarcopenia by directly and indirectly modulating multiple age-associated pathways, implicating mTORC1 as a therapeutic target to treat sarcopenia.
biorxiv physiology 100-200-users 2019MASST A Web-based Basic Mass Spectrometry Search Tool for Molecules to Search Public Data, bioRxiv, 2019-03-28
CorrespondenceWe introduce a web-enabled small-molecule mass spectrometry (MS) search engine. To date, no tool can query all the public small-molecule tandem MS data in metabolomics repositories, greatly limiting the utility of these resources in clinical, environmental and natural product applications. Therefore, we introduce aMassSpectrometrySearchTool (MASST) (<jatsext-link xmlnsxlink=httpwww.w3.org1999xlink ext-link-type=uri xlinkhref=httpsproteosafe-extensions.ucsd.edumasst>httpsproteosafe-extensions.ucsd.edumasst<jatsext-link>), that enables the discovery of molecular relationships among accessible public metabolomics and natural product tandem mass spectrometry data (MSMS).
biorxiv bioinformatics 100-200-users 2019NanoDJ A Dockerized Jupyter Notebook for Interactive Oxford Nanopore MinION Sequence Manipulation and Genome Assembly, bioRxiv, 2019-03-28
AbstractBackgroundThe Oxford Nanopore Technologies (ONT) MinION portable sequencer makes it possible to use cutting-edge genomic technologies in the field and the academic classroom.ResultsWe present NanoDJ, a Jupyter notebook integration of tools for simplified manipulation and assembly of DNA sequences produced by ONT devices. It integrates basecalling, read trimming and quality control, simulation and plotting routines with a variety of widely used aligners and assemblers, including procedures for hybrid assembly.ConclusionsWith the use of Jupyter-facilitated access to self-explanatory contents of applications and the interactive visualization of results, as well as by its distribution into a Docker software container, NanoDJ is aimed to simplify and make more reproducible ONT DNA sequence analysis. The NanoDJ package code, documentation and installation instructions are freely available at <jatsext-link xmlnsxlink=httpwww.w3.org1999xlink ext-link-type=uri xlinkhref=httpsgithub.comgenomicsITERNanoDJ>httpsgithub.comgenomicsITERNanoDJ<jatsext-link>.
biorxiv bioinformatics 0-100-users 2019Orchestrating Single-Cell Analysis with Bioconductor, bioRxiv, 2019-03-28
AbstractRecent developments in experimental technologies such as single-cell RNA sequencing have enabled the profiling a high-dimensional number of genome-wide features in individual cells, inspiring the formation of large-scale data generation projects quantifying unprecedented levels of biological variation at the single-cell level. The data generated in such projects exhibits unique characteristics, including increased sparsity and scale, in terms of both the number of features and the number of samples. Due to these unique characteristics, specialized statistical methods are required along with fast and efficient software implementations in order to successfully derive biological insights. Bioconductor - an open-source, open-development software project based on the R programming language - has pioneered the analysis of such high-throughput, high-dimensional biological data, leveraging a rich history of software and methods development that has spanned the era of sequencing. Featuring state-of-the-art computational methods, standardized data infrastructure, and interactive data visualization tools that are all easily accessible as software packages, Bioconductor has made it possible for a diverse audience to analyze data derived from cutting-edge single-cell assays. Here, we present an overview of single-cell RNA sequencing analysis for prospective users and contributors, highlighting the contributions towards this effort made by Bioconductor.
biorxiv genomics 100-200-users 2019