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Full-Text Articles in Gastroenterology
Acafinder: Genome Mining For Anti-Crispr-Associated Genes, Bowen Yang, Jinfang Zheng, Yanbin Yin
Acafinder: Genome Mining For Anti-Crispr-Associated Genes, Bowen Yang, Jinfang Zheng, Yanbin Yin
Food for Health: Publications
Anti-CRISPR (Acr) proteins are encoded by (pro)viruses to inhibit their host’s CRISPR-Cas systems. Genes encoding Acr and Aca (Acr associated) proteins often colocalize to form acr-aca operons. Here, we present AcaFinder as the first Aca genome mining tool. AcaFinder can (i) predict Acas and their associated acr-aca operons using guilt-by-association (GBA); (ii) identify homologs of known Acas using an HMM (Hidden Markov model) database; (iii) take input genomes for potential prophages, CRISPR-Cas systems, and self-targeting spacers (STSs); and (iv) provide a standalone program (https://github.com/boweny920/AcaFinder) and a web server (http://aca .unl.edu/Aca). AcaFinder was applied to mining over …
The Unique Seed Protein Composition Of Quality Protein Popcorn Promotes Growth Of Beneficial Bacteria From The Human Gut Microbiome, Nate Korth, Leandra Parsons, Mallory J. Van Haute, Qinnan Yang, Preston Hurst, James C. Schnable, David R. Holding, Andrew K. Benson
The Unique Seed Protein Composition Of Quality Protein Popcorn Promotes Growth Of Beneficial Bacteria From The Human Gut Microbiome, Nate Korth, Leandra Parsons, Mallory J. Van Haute, Qinnan Yang, Preston Hurst, James C. Schnable, David R. Holding, Andrew K. Benson
Food for Health: Publications
The effects of fiber, complex carbohydrates, lipids, and small molecules from food matrices on the human gut microbiome have been increasingly studied. Much less is known about how dietary protein can influence the composition and function of the gut microbial community. Here, we used near-isogenic maize lines of conventional popcorn and quality-protein popcorn (QPP) to study the effects of the opaque-2 mutation and associated quality-protein modifiers on the human gut microbiome. Opaque-2 blocks the synthesis of major maize seed proteins (α-zeins), resulting in a compensatory synthesis of new seed proteins that are nutritionally beneficial with substantially higher levels …
The Chromosome-Level Rambutan Genome Reveals A Significant Role Of Segmental Duplication In The Expansion Of Resistance Genes, Jinfang Zheng1, Lyndel W. Meinhardt, Ricardo Goenaga, Tracie Matsumoto, Dapeng Zhang, Yanbin Yin
The Chromosome-Level Rambutan Genome Reveals A Significant Role Of Segmental Duplication In The Expansion Of Resistance Genes, Jinfang Zheng1, Lyndel W. Meinhardt, Ricardo Goenaga, Tracie Matsumoto, Dapeng Zhang, Yanbin Yin
Food for Health: Publications
Rambutan (Nephelium lappaceum var. lappaceum), a tropical fruit tree native to southeastern Asia, belongs to the family Sapindaceae. Rambutan is a popular table fruit and is also processed into preserves, juices, wines, and sorbets [1]. At present, only three Sapindaceae genomes are publicly available: Xanthoceras sorbifolium [2], Dimocarpus longan (longan) [3], and Acer yangbiense [4]. During the process of submitting this manuscript, the genome paper for the rambutan cultivar Baoyan7 became available online, but its genome sequence has not yet been released [5].