An Atlas of the Speed of Copy Number Changes in Animal Gene Families and Its Implications

The notion that gene duplications generating new genes and functions is commonly accepted in evolutionary biology. However, this assumption is more speculative from theory rather than well proven in genome-wide studies. Here, we generated an atlas of the rate of copy number changes (CNCs) in all the gene families of ten animal genomes. We grouped the gene families with similar CNC dynamics into rate pattern groups (RPGs) and annotated their function using a novel bottom-up approach. By comparing CNC rate patterns, we showed that most of the species-specific CNC rates groups are formed by gene duplication rather than gene loss, and most of the changes in rates of CNCs may be the result of adaptive evolution. We also found that the functions of many RPGs match their biological significance well. Our work confirmed the role of gene duplication in generating novel phenotypes, and the results can serve as a guide for researchers to connect the phenotypic features to certain gene duplications

Spartan Daily, March 25, 1960

Volume 47, Issue 100https://scholarworks.sjsu.edu/spartandaily/4016/thumbnail.jp

DNA repair in bacteroides fragilis

Includes abstract.Includes bibliographical leaves (leaves 89-101).Bacteroides fragilis is a gut commensal in both humans and animals where it benefits the host through metabolizing indigestible compounds, stimulating the immune system and protecting against pathogen colonization. However, it is also an opportunistic pathogen, responsible for approximately half of anaerobic bacteraemias. Metronidazole is used to treat anaerobic infections. It diffuses into the celI as an inactive prodrug where it is reduced to form nitro anion and nitroso and hydroxylamine radicals. These chemically reactive compounds interact with DNA causing strand breaks and base mutations; the damage accumulates and leads to cell death. Mechanisms of metronidazole resistance in B. fragilis include decreased activity of oxidation/reduction enzymes, over-expression of multidrug efflux pumps and the conversion of metronidazole to non-toxic derivatives by nitroimidazole nitroreductases (encoded by nim genes). However, metronidazole resistance could also potentialIy be mediated by the over-expression or enhanced activity of DNA repair proteins. Thus, DNA repair in B. fragilis should be thoroughly investigated

Spartan Daily, October 19, 1951

Volume 40, Issue 18https://scholarworks.sjsu.edu/spartandaily/11605/thumbnail.jp

The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control.

The stable fly, Stomoxys calcitrans, is a major blood-feeding pest of livestock that has near worldwide distribution, causing an annual cost of over $2 billion for control and product loss in the USA alone. Control of these flies has been limited to increased sanitary management practices and insecticide application for suppressing larval stages. Few genetic and molecular resources are available to help in developing novel methods for controlling stable flies. This study examines stable fly biology by utilizing a combination of high-quality genome sequencing and RNA-Seq analyses targeting multiple developmental stages and tissues. In conjunction, 1600 genes were manually curated to characterize genetic features related to stable fly reproduction, vector host interactions, host-microbe dynamics, and putative targets for control. Most notable was characterization of genes associated with reproduction and identification of expanded gene families with functional associations to vision, chemosensation, immunity, and metabolic detoxification pathways. The combined sequencing, assembly, and curation of the male stable fly genome followed by RNA-Seq and downstream analyses provide insights necessary to understand the biology of this important pest. These resources and new data will provide the groundwork for expanding the tools available to control stable fly infestations. The close relationship of Stomoxys to other blood-feeding (horn flies and Glossina) and non-blood-feeding flies (house flies, medflies, Drosophila) will facilitate understanding of the evolutionary processes associated with development of blood feeding among the Cyclorrhapha

The BG News October 28, 1976

The BGSU campus student newspaper October 28, 1976. Volume 61 - Issue 23https://scholarworks.bgsu.edu/bg-news/4290/thumbnail.jp