We have developed VitisCyc, a grapevine-specific metabolic pathway database that allows researchers to (i) search and browse the database for its various components such as metabolic pathways, reactions, compounds, genes and proteins, (ii) compare grapevine metabolic networks with other publicly available plant metabolic networks, and (iii) upload, visualize and analyze high-throughput data such as transcriptomes, proteomes, metabolomes etc. using OMICs-Viewer tool. VitisCyc is based on the genome sequence of the nearly homozygous genotype PN40024 of Vitis vinifera “Pinot Noir” cultivar with 12X v1 annotations and was built on BioCyc platform using Pathway Tools software and MetaCyc reference database. Furthermore, VitisCyc was enriched for plant-specific pathways and grape-specific metabolites, reactions and pathways. Currently VitisCyc harbors 68 super pathways, 362 biosynthesis pathways, 118 catabolic pathways, 5 detoxification pathways, 36 energy related pathways and 6 transport pathways, 10,908 enzymes, 2912 enzymatic reactions, 31 transport reactions and 2024 compounds. VitisCyc, as a community resource, can aid in the discovery of candidate genes and pathways that are regulated during plant growth and development, and in response to biotic and abiotic stress signals generated from a plant's immediate environment. VitisCyc version 3.18 is available online at http://pathways.cgrb.oregonstate.edu.
Microplastic pollution has been observed in marine environments around the world and has the potential to negatively impact marine organisms if ingested. Blue crabs (Callinectes sapidus) are susceptible to this pollution because they feed in sediment where dense plastics accumulate. Microplastic ingestion by blue crabs was assessed in Corpus Christi Bay, TX. Crab stomachs were extracted and digested using a hydrogen‐peroxide based tissue destruction method followed by material confirmation using microattenuated total reflectance Fourier transform infrared spectroscopy (μ‐FTIR). From the 39 blue crabs sampled, 28 fully synthetic fragments and fibers and 24 semisynthetic fibers were found within their stomachs. After correcting for possible contamination, 36% of collected blue crabs contained fully synthetic fragments and fibers and semisynthetic fibers with an estimate of 0.87 items per crab. This study demonstrates the need for further studies that assess the impacts of plastic ingestion on blue crabs.
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