Bryan J. Killinger's research while affiliated with Washington State University and other places

... In addition, first reports on the use of ABPP or related approaches for studying microbial communities and isolating functionally active subpopulations, with a focus on host-associated microbial communities, have been made [42][43][44]. Among these, few studies on the gut microbiome have implemented a combination of ABPP with metagenomics to facilitate the identification of enzymes related to chronic inflammation, drug toxicity, or dietary fiber metabolism in the gastrointestinal tract by employing a metaproteome database that was either constructed from publicly available genomes or self-constructed based on metagenome sequencing [45][46][47]. ABPP of environmental microbial communities, by contrast, is largely unknown and is usually achieved by profiling isolated strains of environmental microbes rather than by direct profiling of complex communities [48][49][50][51][52]. Recently, activity-based imaging of ammonia-and alkane-oxidizing bacteria in complex microbial communities with the ABP 1,7-octadiyne was reported [53]. ...

... Activity-based protein profiling (ABPP) for functional annotation of microbial communities can better address the disconnect of genomics to phenotype [10,11]. ABPP uses activity-based probes (ABPs), which are small-molecule substrates composed of a reactive warhead group that selectively and covalently binds to active enzymes, and a reporter tag attached through a linker that permits characterization through fluorescence visualization of the bound, active enzyme [12][13][14][15]. ABPs have strong specificity when attaching to enzymes performing a function of interest. ...

... However, condensing peptide measurements into a single protein report may potentially obscure biologically relevant differences between related protein isoforms (87,88). To avoid these problems with protein-based quantification, some researchers have advocated for working more directly with peptide abundances to identify significant differences between samples (89)(90)(91)(92). As peptide-centric methods have yet to be used in SCP, this review will focus on protein-level quantification. ...

... We especially highlight stable isotope probing (SIP; Bernard et al. 2007;Dumont and Murrell 2005;Pepe-Ranney et al. 2016), new ultrahigh-resolution metabolomics (Tfaily et al. 2017, activity-based protein profiling (ABPP, Killinger et al. 2019), and machine learning as new classes of technologies deserving of further development and broader consideration. Briefly, microbial applications of SIP use substrates enriched in heavy isotopes (e.g. 13 C, 18 O, 15 N) amended to microbial communities to reveal isotope-labeled biomarkers of active microbial populations (Bernard et al. 2007;Dumont and Murrell 2005;Pepe-Ranney et al. 2016). ...

... In line our data, the up-regulation of GSTP1 contributes to an increase in detoxification functions and altered apoptotic pathways of urothelial bladder cells [49]. It is interesting that exposure to potentially carcinogenic compounds such as benzo[a]pyrene and tobacco smoke induces the expression of GSTP1 to eliminate toxic substances in urothelial bladder cells [50,51]. However, GSTP1 not only has both physiologic and pathologic functions but also can be considered as a potential marker for UBC. ...

... Cobalamin and thiamine are vitamins B that are only produced by prokaryotic organisms, especially bacteria (Warren et al. 2002) Cobalamin and thiamine given by symbiotic bacteria are assumed to be able to support the growth of microalgae due to the function of these two vitamins. Cobalamin which plays an important role in protein synthesis, and thiamine which plays an important role in the formation of amino acids and carbohydrates can increase cell growth and division because cell growth is controlled by these compounds (Konopka et al. 2015;Rosnow et al. 2018). So, the presence of bacteria is assumed to be able to increase microalgae cell density and its biomass. ...

... Here, we establish photoaffinity labeling of GSTs as an easy way to detect GSTs in various tissues of model plants, crops and weeds. We took advantage of a glutathione-based photoaffinity probe that successfully labeled recombinant human GSTs and endogenous GSTs from mouse liver and lung tissues (Stoddard et al. 2017). This photoaffinity probe contains glutathione, a benzophenone photoreactive group and an alkyne minitag that can be labeled with a fluorophore of biotin via click chemistry. ...