Biology subjects

Rege, M.

Publications and source records attributed to Rege, M..

3 recordsLinked to original sources

bioRxiv2023

A novel method of testing the antimicrobial potentials of Exiguobacterium aurantiacum, Lysinibacillus boronitolerans and Bacillus megaterium

Microorganisms can be an effective source for antimicrobial compounds including peptides that provide an evolutionary advantage to them in specific niches. Prior studies have noted the antimicrobial properties of Exiguobacterium aurantiacum, Lysinibacillus boronitolerans and Bacillus megaterium but they used time- and resource-intensive procedures to prepare the extracts (2, 10). We wanted to explore a more cost-effective, time-effective and simpler method of testing the antimicrobial potential of bacterial extracts. Our extraction protocol is a one-step incubation of the organism in the solvent overnight, followed by a standard well diffusion based assay to test its antimicrobial effect. We tested this method with three cultures isolated from the premises of Mumbai railway stations: E. aurantiacum, L. boronitolerans and Bacillus megaterium. These extracts were tested against human pathogens Staphylococcus aureus and Enterococcus faecalis. E. aurantiacum, L. boronitolerans and B. megaterium inhibited S. aureus by 9.17 {+/-} 0.42, 9.25 {+/-} 0.48 and 10.50 {+/-} 1.5 mm, respectively, and E. faecalis by 15.79 {+/-} 2.25, 14.21 {+/-} 0.88 and 17.5 {+/-} 2.89 mm, respectively. This approach is therefore suggested to be effective for screening the antimicrobial activity of these bacteria.

microbiology↗

bioRxiv2020

SWI/SNF antagonizes SIR heterochromatin to promote transcription of genes expressed during mitotic exit in Saccharomyces cerevisiae

Heterochromatin is a repressive, specialized chromatin structure that is central to eukaryotic transcriptional regulation and genome stability. In the budding yeast, Saccharomyces cerevisiae, heterochromatin formation requires Sir2p, Sir3p, and Sir4p, and these Sir proteins create specialized chromatin structures at telomeres and silent mating type loci. Previously, we reported that the SWI/SNF chromatin remodeling enzyme can evict Sir3 from chromatin fibers in vitro, though whether this activity contributes to the role of SWI/SNF as a transcriptional activator at euchromatic loci is unknown. Here, we characterize genetic interactions between the SIR genes (SIR2, SIR3, and SIR4) and genes encoding subunits of the chromatin remodelers SWI/SNF and INO80C, as well genes encoding the histone deacetylases Hst3 and Hst4. We find that loss of SIR genes partially rescues the growth defects of swi2, ino80, and hst3/hst4 mutants during replication stress conditions. Interestingly, partial suppression of swi2, ino80, and hst3 hst4 mutant phenotypes is due to the pseudo-diploid state of sir mutants, but a significant portion is due to more direct functional interactions. Consistent with this view, transcriptional profiling of strains lacking Swi2 or Sir3 identifies a set of genes whose expression in the M/G1 phase of the cell cycle requires SWI/SNF to antagonize the repressive impact of Sir3.

genetics↗

bioRxiv2018

LADL: Light-activated dynamic looping for endogenous gene expression control

Mammalian genomes are folded into tens of thousands of long-range looping interactions1,2. The cause and effect relationship between looping and genome function is poorly understood, and the extent to which chromatin loops are dynamic on short time scales remains a fundamental unanswered question. Currently available strategies for loop engineering involve synthetic transcription factors tethered to dCas93,4 or zinc fingers5,6, which are constitutively expressed5,6 or induced on long time scales by the presence of a small molecule3. Here we report a new class of 3-D optoepigenetic tools for the directed rearrangement of 3-D chromatin looping on short time scales using blue light. We create synthetic architectural proteins by fusing the CIBN protein subunit from Arabidopsis thaliana with enzymatically dead Cas9 (dCas9). We target our light-activated dynamic looping system (LADL) to two genomic anchors with CRISPR guide RNAs and engineer their spatial co-localization via light-induced heterodimerization of the cryptochrome 2 (CRY2) protein with dCas9-CIBN. We apply LADL to redirect a stretch enhancer (SE) away from its endogenous Klf4 target gene and to the Zfp462 promoter. Looping changes occur as early as four hours after light induction. Using single molecule RNA FISH, we observe a LADL-induced increase in the total nascent Zfp462 transcripts and the number of Zfp462 alleles expressing simultaneously per cell. Moreover, LADL also increased synchronous Sox2 expression after reinforcement of a known Sox2-SE looping interaction. LADL facilitates loop synchronization across a large population of cells without exogenous chemical cofactors and can enable future efforts to engineer reversible and oscillatory looping on short time scales.

molecular biology↗