Genome-Wide Screening Approaches for Biochemical Reactions Independent of Cell Growth.

Genome-wide screening is a potent approach for comprehensively understanding the molecular mechanisms of biological phenomena. However, despite its widespread use in the past decades across various biological targets, its application to biochemical reactions with temporal and reversible biological outputs remains a formidable challenge. To uncover the molecular machinery underlying various biochemical reactions, we have recently developed the revival screening method, which combines flow cytometry-based cell sorting with library reconstruction from collected cells. Our refinements to the traditional genome-wide screening technique have proven successful in revealing the molecular machinery of biochemical reactions of interest. In this article, we elucidate the technical basis of revival screening, focusing on its application to CRISPR-Cas9 single guide RNA (sgRNA) library and complementary DNA (cDNA) library screening. Finally, we also discuss the future of genome-wide screening while describing recent achievements from in vitro and in vivo screening.

Effect of Intake of Bifidobacteria and Dietary Fiber on Resting Energy Expenditure: A Randomized, Placebo-Controlled, Double-Blind, Parallel-Group Comparison Study.

Bifidobacterium animalis subsp. lactis GCL2505 in combination with inulin has been shown to have several health benefits, including an improvement in the intestinal microbiota and a reduction in human visceral fat. Previous studies have suggested that the visceral fat reduction of GCL2505 and inulin may be achieved by improving daily energy expenditure. This parallel, placebo-controlled, randomized, double-blind study was conducted to evaluate the effects of GCL2505 and inulin on resting energy expenditure (REE) in overweight or mildly obese Japanese adults (n = 44). Participants ingested 1 × 1010 colony forming units of GCL2505 and 5.0 g of inulin daily for 4 weeks. REE score at week 4 was set as the primary endpoint. At week 4, the REE score of the GCL2505 and inulin group was significantly higher than that of the placebo group, with a difference of 84.4 kcal/day. In addition, fecal bifidobacteria counts were significantly increased in the GCL2505 and inulin group. Our results indicated that the intake of GCL2505 and inulin improves energy balance, which is known to be a major factor of obesity, by modulating the microbiota in the gut. This is the first report to demonstrate the effects of probiotics and dietary fiber on REE in humans.

Dasatinib suppresses particulate-induced pyroptosis and acute lung inflammation.

Background: Humans are constantly exposed to various industrial, environmental, and endogenous particulates that result in inflammatory diseases. After being engulfed by immune cells, viz. Macrophages, such particulates lead to phagolysosomal dysfunction, eventually inducing pyroptosis, a form of cell death accompanied by the release of inflammatory mediators, including members of the interleukin (IL)-1 family. Phagolysosomal dysfunction results in the activation of the nod-like receptor family pyrin domain containing 3 (NLRP3) inflammasome, an immune complex that induces pyroptosis upon exposure to various external stimuli. However, several particulates induce pyroptosis even if the NLRP3 inflammasome is inhibited; this indicates that such inhibition is not always effective in treating diseases induced by particulates. Therefore, discovery of drugs suppressing particulate-induced NLRP3-independent pyroptosis is warranted. Methods: We screened compounds that inhibit silica particle (SP)-induced cell death and release of IL-1α using RAW264.7 cells, which are incapable of NLRP3 inflammasome formation. The candidates were tested for their ability to suppress particulate-induced pyroptosis and phagolysosomal dysfunction using mouse primary macrophages and alleviate SP-induced NLRP3-independent lung inflammation. Results: Several Src family kinase inhibitors, including dasatinib, effectively suppressed SP-induced cell death and IL-1α release. Furthermore, dasatinib suppressed pyroptosis induced by other particulates but did not suppress that induced by non-particulates, such as adenosine triphosphate. Dasatinib reduced SP-induced phagolysosomal dysfunction without affecting phagocytosis of SPs. Moreover, dasatinib treatment strongly suppressed the increase in IL-1α levels and neutrophil counts in the lungs after intratracheal SP administration. Conclusion: Dasatinib suppresses particulate-induced pyroptosis and can be used to treat relevant inflammatory diseases.

Theoretical insights into the DNA repair function of Arabidopsis thaliana cryptochrome-DASH.

Following the discovery of cryptochrome-DASH (CRYD) as a new type of blue-light receptor cryptochrome, theoretical and experimental findings on CRYD have been reported. Early studies identified CRYD as highly homologous to the DNA repair enzyme photolyases (PLs), suggesting the involvement of CRYD in DNA repair. However, an experimental study reported that CRYD does not exhibit DNA repair activity in vivo. Successful PL-mediated DNA repair requires: (i) the recognition of UV-induced DNA lesions and (ii) an electron transfer reaction. If either of them is inefficient, the DNA repair activity will be low. To elucidate the functional differences between CRYD and PL, we theoretically investigated the electron transfer reactivity and DNA binding affinity of CRYD and also performed supplementary experiments. The average electronic coupling matrix elements value for Arabidopsis thaliana CRYD (AtCRYD) was estimated to be 5.3 meV, comparable to that of Anacystis nidulans cyclobutane pyrimidine dimer PLs (AnPL) at 4.5 meV, indicating similar electron transfer reactivities. We also confirmed the DNA repair activity of AtCRYD for UV-damaged single-stranded DNA by the experimental analysis. In addition, we investigated the dynamic behavior of AtCRYD and AnPL in complex with double-stranded DNA using molecular dynamics simulations and observed the formation of a transient salt bridge between protein and DNA in AtCRYD, in contrast to AnPL in which it was formed stably. We suggested that the instability of the salt bridge between protein and DNA will lead to reduced DNA binding affinity for AtCRYD.