Biology subjects

Rana, B.

Publications and source records attributed to Rana, B..

4 recordsLinked to original sources

bioRxiv2025

Cryo-EM reveals a new allosteric binding site at the M5 mAChR

The M5 muscarinic acetylcholine receptor (M5 mAChR) represents a promising therapeutic target for neurological disorders. However, the high conservation of its orthosteric binding site has posed significant challenges for drug development. While selective positive allosteric modulators (PAMs) offer a potential solution, a structural understanding of the M5 mAChR and its allosteric binding sites has remained limited. Here, we present a 2.8 [A] cryo-electron microscopy structure of the M5 mAChR complexed with heterotrimeric Gq protein and the agonist iperoxo, completing the active-state structural characterization of the mAChR family. To identify the binding site of M5-selective PAMs, we implemented an integrated approach combining mutagenesis, pharmacological assays, structural biology, and molecular dynamics simulations. Our mutagenesis studies revealed that selective M5 PAMs bind outside previously characterized M5 mAChR allosteric sites. Subsequently, we obtained a 2.1 [A] structure of M5 mAChR co-bound with acetylcholine and the selective PAM VU6007678, revealing a novel allosteric pocket at the extrahelical interface between transmembrane domains 3 and 4 that was confirmed through mutagenesis and simulations. These findings demonstrate the diverse mechanisms of allosteric regulation in mAChRs and highlight the value of integrating pharmacological and structural approaches to identify novel allosteric binding sites.

pharmacology and toxicology↗

bioRxiv2024

Ecological factors that drive microbial communities in culturally diverse fermented foods

Fermented foods are increasingly recognized for their health benefits. Historically, cultures worldwide have relied on fermentation to preserve foods and enhance their digestibility, flavor, aromas, and taste. Despite the abundance of global diversity of fermented foods, the microbial communities in traditionally fermented non-European foods remain largely understudied. Here, we characterized the bacterial and fungal communities in 90 plant and animal based fermented foods from Nepal, South Korea, Ethiopia, and Kazakhstan, all traditionally prepared for household consumption. Our results reveal that these foods host diverse and intricately interconnected ecosystems of bacteria and fungi. Beyond the well-known fermenters such as lactic acid bacteria (LABs), Bacillales, and yeasts (Saccharomycetales), these foods contain additional microbes whose roles in fermentation are not well understood. While the microbial compositions of fermented foods vary by geography and preparation methods, the type of food substrate has the most significant effect on differentiating bacterial communities. Vegetable-based ferments harbor bacterial communities consisting primarily of LABs and potential pathways associated with carbohydrates degradation. Contrastingly, legumes and animal-based fermented foods are enriched with Bacillales and protein and lipid degradation pathways. Moreover, the microbial interactions, characterized via bacteria- bacteria and bacteria-fungi co-occurrence networks, differ significantly across traditionally fermented plants, legumes, and dairy products, indicating that microbial ecosystems vary between traditional fermented foods derived from different substrates. Our findings highlight the underexplored diversity of microbial communities in traditional fermented foods and underscore the need to understand the entire microbial communities present in these foods and their functions when evaluating their effect on nutrition and health.

microbiology↗

bioRxiv2024

Pharmacogenomics Guided Spaceflight: the intersection between space-flown drugs and space genes

Ten years ago, it was predicted that the multi-omics revolution would also revolutionize space pharmacogenomics. Current barriers related to the findable, accessible, interoperable, and reproducible use of space-flown pharmaceutical data have contributed to a lack of progress beyond application of earth-based principles. To directly tackle these challenges, we have produced a novel database of all the drugs flown into space, compiled from publicly available ontological and spaceflight-related datasets, to exemplify analyses for describing significant spaceflight-related targets. By focusing on mechanisms perturbed by spaceflight, we have provided a novel avenue for identifying the most relevant changes within the drug absorption, distribution, metabolism, and excretion pathways. We suggest a set of space genes, by necessity limited to available tissue types, that can be expanded and modified based on future tissue-specific and mechanistic-specific high-throughput assays. In sum, we provide the justification and a definitive starting point for pharmacogenomics guided spaceflight as a foundation of precision medicine, which will enable long-term human habitation of the Moon, Mars, and beyond. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=147 SRC="FIGDIR/small/575951v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@48f739org.highwire.dtl.DTLVardef@5ecdb0org.highwire.dtl.DTLVardef@121c93org.highwire.dtl.DTLVardef@1122b3f_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2020

Reading frame restoration at the EYS locus, and allele-specific chromosome removal after Cas9 cleavage in human embryos

The correction of disease-causing mutations in human embryos could reduce the burden of inherited genetic disorders in the fetus and newborn, and improve the efficiency of fertility treatments for couples with disease-causing mutations in lieu of embryo selection. Here we evaluate the repair outcomes of a Cas9-induced double-strand break (DSB) introduced on the paternal chromosome at the EYS locus, which carries a frame-shift mutation causing blindness. We show that the most common repair outcome is microhomology-mediated end joining, which occurs during the first cell cycle in the zygote, leading to embryos with non-mosaic restoration of the reading frame. However, about half of the breaks remain unrepaired, resulting in an undetectable paternal allele and, upon entry into mitosis, loss of one or both chromosomal arms. Thus, Cas9 allows for the modification of chromosomal content in human embryos in a targeted manner, which may be useful for the prevention of trisomies. HighlightsO_LICas9-mediated DSB induction and repair by end joining occurs within hours C_LIO_LIEnd joining provides an efficient way to restore reading frames without mosaicism C_LIO_LIUnrepaired DSBs persist through mitosis and result in frequent chromosome loss C_LI

genetics↗