5 research outputs found
QPromoters: sequence based prediction of promoter strength in Saccharomyces cerevisiae
No full textPromoters play a key role in influencing transcriptional regulation for fine-tuning the expression of genes. Heterologous promoter engineering has been a widely used concept to control the level of transcription in all model organisms. The strength of a promoter is mainly determined by its nucleotide composition. Many promoter libraries have been curated, but few have attempted to develop theoretical methods to predict the strength of promoters from their nucleotide sequence. Such theoretical methods are not only valuable in the design of promoters with specified strength but are also meaningful in understanding the mechanistic role of promoters in transcriptional regulation. In this study, we present a theoretical model to describe the relationship between promoter strength and nucleotide sequence in Saccharomyces cerevisiae. We infer from our analysis that the −49–10 sequence with respect to the Transcription Start Site represents the minimal region that can be used to predict promoter strength. https://qpromoters.com/ and a standalone tool https://github.com/DevangLiya/QPromoters to quickly quantify the strength of Saccharomyces cerevisiae promoters
Spike selection in SARS-CoV-2 variants across different geographical regions reveals unique signature patterns and differential stability with drug interaction
No full textThe evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus since its emergence in 2019 has yielded several new viral variants with varied infectivity, disease severity, and antigenicity. Although most mutations are expected to be relatively neutral, mutations at the Spike region of the genome has shown to have a major impact on the viral transmission and infection in humans. Therefore, it is crucial to survey the structures of spike protein across the global virus population to contextualize the rate of therapeutic success against these variants. In this study, high-frequency mutational variants from different geographic regions were pooled in order to study the structural evolution of the spike protein through drug docking and MD simulations. We investigated the mutational burden in the spike sub regions and have observed that the different variants harbour unique signature patterns in the spike sub regions, with certain domains being highly prone to mutations. Further, the MD simulations and docking study revealed that different variants show differential stability when docked for the same set of drug targets. This work sheds light on the mutational burden and the stability landscape of the spike protein across the variants from different geographical regions
A Comprehensive SARS-CoV-2 Genomic Analysis Identifies Potential Targets for Drug Repurposing
No full textBackground:
The
severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which is a novel
human coronavirus strain (HCoV) initially reported in December 2019 in Wuhan
City, China causing pneumonia-like symptoms and other respiratory tract
illness. It’s higher transmission and infection rate has successfully enabled
it to have a global spread over a matter of small time. With 6,529,240 cases
and about 385,264 deaths, this pandemic has become a global concern with
certain drugs and vaccines failing at later clinical trials.
Materials
and Methods: Phylogenetic
Analysis, Haplotype Network, Analysis of conserved genes and population-level
variants, Using conserved genes as targets for drug designing, Docking studies
and Molecular Dynamics (MD) simulations to predict the stability of Drug-Ligand
Complex.
Results:
We
identified the most common haplotypes from the haplotype network and at least
seven different clusters were found signifying seven different viral lineages
across the globe. We studied the mutation frequency across the SARS-CoV-2 viral
genome. The conserved genes and population level variants were analyzed and
NSP10, Nucleoprotein, Plpro and 3CLpro which were conserved at the highest
threshold were used as drug targets for molecular dynamics simulations.
Darifenacin, Nebivolol, Bictegravir, Alvimopan and Irbesartan are among the
potential drugs which are suggested for further pre-clinical and clinical trials.
Significance:
This
particular study provides a comprehensive targeting of the conserved genes as a
novel approach for drug targeting. The conserved gene approach could also be of
a big use while designing vaccines and cure. Mutations in the viral genome make
the designing of the drugs a challenging task which has a higher risk of
failure at later clinical trials. This approach of targeting the stable genes
for drug discovery would provide a better therapeutic approach and confidence
in the successive clinical trials. We also identified the global level spread
of SARS-CoV-2 and mutation frequencies across the viral genome. Our study gives
insights of the origin and global spread of the SARS-CoV-2. The data provided
in this study can further be used by other groups to understand and combat
Covid 19.</p
Drug repurposing and sequence analysis in S-glycoprotein variants reveals critical signature patterns and destabilization of receptor-binding domain in omicron variant
No full textThe evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus since its emergence in 2019 has yielded several new viral variants with varied infectivity, disease severity, and antigenicity. Although most mutations are expected to be relatively neutral, mutations at the Spike region of the genome have shown to have a major impact on the viral transmission and infection in humans. Therefore, it is crucial to survey the structures of spike protein across the global virus population to contextualize the rate of therapeutic success against these variants. In this study, high-frequency mutational variants from different geographic regions were pooled in order to study the structural evolution of the spike protein through drug docking and MD simulations. We investigated the mutational burden in the spike subregions and have observed that the different variants harbour unique signature patterns in the spike subregions, with certain domains being highly prone to mutations. Further, the MD simulations and docking study revealed that different variants show differential stability when docked for the same set of drug targets. This work sheds light on the mutational burden and the stability landscape of the spike protein across the variants from different geographical regions. Communicated by Ramaswamy H. Sarma</p
Robust estimation of bacterial cell count from optical density
No full textOptical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data
