Biology subjects

Narayan, M.

Publications and source records attributed to Narayan, M..

8 recordsLinked to original sources

bioRxiv2026

Interdependent mode of RNA recognition by the interacting KH-domain proteins KhpA and KhpB

RNA-binding proteins (RBPs) are central regulators of gene expression. In bacteria, two KH domain-containing proteins, KhpA and KhpB, are increasingly recognized as globally-acting RBPs, including in pathogens that lack well-studied RBPs, such as Hfq and ProQ. While KhpA and KhpB interact with various RNAs in diverse bacteria, their crosstalk and molecular basis of RNA recognition remain poorly understood. Here, we explored the mutual dependence between KhpA and KhpB in the food-borne pathogen Campylobacter jejuni. We demonstrate KhpA and KhpB interact in vivo, and their individual global RNA recognition is largely dependent on the presence of the partner protein. Using RNA co-immunoprecipitation, we reveal that KhpA requires a conserved KH domain motif for RNA binding, whereas KhpB relies on an atypical R3H domain. Moreover, mutating the RNA-binding domain of one protein compromises the RNA interactome of the other. Overall, we demonstrate an interdependent RNA-binding mode of KhpA and KhpB and anticipate that such KH-proteins have co-evolved to elicit joint RNA regulation in bacteria.

microbiology↗

bioRxiv2026

Molecular genetic characterization of bacterial KH-domain proteins

Post-transcriptional gene regulation is a key mechanism for bacterial stress responses and virulence, and RNA-mediated regulation frequently relies on global RNA-binding proteins (RBPs). A pair of interacting KH-domain proteins (KhpA and KhpB) have recently been identified as global RBPs in several bacterial species. To better understand their molecular functions, we employed bacterial two- and three-hybrid (B2H/B3H) assays in an E. coli reporter system to analyze protein-protein and protein-RNA interactions of KhpA/B orthologs from three human pathogens: Campylobacter jejuni, Helicobacter pylori, and Clostridioides difficile. Protein-protein interactions were conserved across all species, with KhpA-KhpB heterodimers forming more robustly than either homodimer and KhpA homodimerizing more readily than KhpB. On the other hand, protein-RNA interactions were more varied across species: C. jejuni and C. difficile KhpA bound both species-specific and non-specific RNAs, but H. pylori KhpA--and KhpB orthologs from all species--showed no RNA interaction in B3H assays. Site-directed mutagenesis experiments demonstrated that residues in the GXXG motif of KhpA are critical for RNA interaction and differences in these residues account for the distinct RNA-binding behaviors of KhpA orthologs. Collectively, these findings provide a cross-species, molecular view of how KhpA and KhpB recognize one another and RNA ligands to regulate gene expression.

molecular biology↗

bioRxiv2026

Yin Yang Interactomes Drive the Metabolic Dysfunction-Associated Liver Disease Continuum to Hepatocellular Carcinoma

The risk for hepatocellular carcinoma (HCC) arising from metabolic dysfunction- associated steatotic liver disease (MASLD)-related cirrhosis exceeds the risk for cancer developing in the kidney, heart, or lung as a consequence of end-stage disease in those organs. Both experimental and clinical studies support the existence of circulating biomarkers whose elevated expression is associated with, and supports the diagnosis of, HCC. We posit the existence of oncogenic HCC biomarkers under regulation by tumor-suppressive microRNAs (miRs), and that reduced tumor-suppressive miR expression leads to increased oncogenic biomarker expression. By interrogating the MASLD-HCC miR interactome and miRs known to regulate HCC biomarkers, we identified hsa-miR-577, hsa-miR-9500, hsa-miR-101-3p, miR-206, hsa- miR-219a-1-3p, and hsa-miR-613 as tumor-suppressive miRs whose expression is reduced across multiple cancers. Their target genes, osteopontin, Golgi protein-73, and Dickkopf-related protein 1, exhibit increased expression in HCC and display oncogenic activity. Collectively, dysregulated expression of these miRs and their downstream gene products may contribute to progression along the MASLD continuum toward HCC. HighlightsWe identified tumor suppressive miRs, hsa-miR-577, hsa-miR-9500, hsa-miR-101-3p, miR-206, hsa-miR-219a-1-3p, and hsa-miR-613 with potentially reduced expression levels in HCC. Their gene products, osteopontin, Golgi protein-73, and Dickkopf-related protein 1, exhibit oncogenic properties and increased expression levels in HCC. These miR-gene product interactions may drive the MASLD continuum to HCC. Mechanistic insights should illuminate therapies. Identification of therapeutics that interrupt these interactions may represent a therapeutic pillar for patients with MASLD. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/698028v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@1892140org.highwire.dtl.DTLVardef@1e61677org.highwire.dtl.DTLVardef@cd0488org.highwire.dtl.DTLVardef@1e48d8a_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigureC_FLOATNO MASLD-related HCC. The intersection set between the MASLD-HCC miR interactome and the set of miRs regulating biomarkers diagnostic for HCC was interrogated and tumor suppressive miRs regulating HCC biomarkers with oncogenic activity were identified. Increased risk for HCC in patients with MASLD and MASLD-cirrhosis may arise from interactions between these dysregulated miRs and their downstream gene products. C_FIG PrologueMetabolic Dysfunction-Associated Liver Disease (MASLD), the leading cause of hepatocellular carcinoma (HCC) in Sweden, is now taking epidemic proportions in South Asia. In India, there is a relatively high prevalence of pre-diabetes, diabetes and insulin resistance; body mass indices > 35 are being observed. Each of these and/or their combinations represent risk factors for MASLD. Nevertheless, both patients and providers are largely oblivious to this disease, both from a lack of general awareness and the asymptomatic nature of MASLD, at least early within its continuum. Diagnosis is often made late, and by exclusion, when presentation may include fatigue, drowsiness, mild encephalopathy (MASLD-pituitary feedback loop), prominent hepatomegaly and asciites, and with liver-specific test demonstrating stiffness, scarring and even HCC. Societal awareness and effective management of this disease are urgent needs. A strategy akin to the 4 pillars for treatment of type 2 diabetes and chronic kidney disease (CKD) needs to be implemented for treatment of patients with MASLD. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=30 SRC="FIGDIR/small/698028v1_ufig2.gif" ALT="Figure 2"> View larger version (11K): org.highwire.dtl.DTLVardef@89a77org.highwire.dtl.DTLVardef@d50c15org.highwire.dtl.DTLVardef@10c6964org.highwire.dtl.DTLVardef@1db2cfa_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigureC_FLOATNO Four-pillar Strategy for MASLD. A strategy akin to the one in place for treatment of type 2 diabetes and CKD needs to be implemented for treatment of patients with MASLD. Aspects of this strategy, viz. SGLT2i and GLP-1{+/-}GIP agonists, are already approved in MASLD. C_FIG

bioinformatics↗

bioRxiv2025

Boolean Logic Coupled with Overrepresentation Analysis Reveals Activation of the Platelet-derived Growth Factor Receptor Beta Pathway in a Model of Oliguric Acute Kidney Injury; Implications for Transition to Chronic Kidney Disease

Acute Kidney Injury (AKI) can occur secondary to insults including sepsis, ischemia and contrast dye administration. A time-sensitive increase in serum creatinine (SCr) or reduction in urine output (UO) has been used to define AKI and stage its severity. Oliguria or significantly reduced UO in AKI or oliguric AKI can have a major impact on outcomes including a transition to chronic kidney disease (CKD). We used Boolean logic coupled with overrepresentation analysis to identify the pathway activation signature associated with oliguric AKI in a published study of rat kidney-ischemia reperfusion. In the reperfused kidney, bulk transcriptomic analysis revealed 1068 differentially expressed genes (DEGs). Those DEGs that correlated with UO and SCr were submitted to gene ontology biological process overexpression analysis. The pathway activation signature associated with oliguric AKI included positive regulation of profibrotic platelet-derived growth factor receptor beta signaling (fold-enrichment >44) driven by src, hip1 and hip1r. Together these findings not only suggest that oliguric AKI may be associated with activation of a pathway leading to fibrosis and CKD but also informs an array of targets to potentially mitigate transition to CKD. HighlightsMechanistic insights should illuminate therapies. A model of rat kidney-ischemia reperfusion injury was queried by correlating kidney transcriptomics with kidney function to identify the pathway activation signature of oliguric AKI. The most striking feature associated with oliguric AKI was positive regulation of platelet-derived growth factor receptor {beta} driven by src, hip1, and hip1r. The pathway activation signature in oliguric AKI informs not only the sequel to injury but also an array of targets to mitigate the potential transition to kidney fibrosis and CKD. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=47 SRC="FIGDIR/small/680804v1_ufig1.gif" ALT="Figure 1"> View larger version (14K): org.highwire.dtl.DTLVardef@121edc1org.highwire.dtl.DTLVardef@80383borg.highwire.dtl.DTLVardef@1ebc25dorg.highwire.dtl.DTLVardef@1258145_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Unveiling the structural insights of PFAS-β-lactoglobulin binding mechanism mediating neuronal toxicity in neonates.

The strong, polar-covalent nature of C-F bonds contributes to the forever nature of per- and polyfluoroalkyl (PFAS) substances. PFAS are toxic to humans. Here, we have examined the ability of the small, globular, milk protein {beta}-lactoglobulin to bind PFAS. The protein transports hydrophobic and amphiphilic compounds, including retinol and fatty acids, for vision and brain development; therefore, underscoring its interactions with PFAS is significant. The crystal structures of {beta}-lactoglobulin complexed with PFOA (Perfluorooctanoic acid) at 2.0 ([A]), PFOS (Perfluorooctanesulfonic acid) at 2.5 ([A]), and PFDA (Perfluorodecanoic acid) at 2.0 ([A]) reveal high affinity of the compounds for the central calyx of {beta}-lactoglobulin, which is the canonical retinol and fatty acid binding site. Analyses of the data indicate significant hydrophobic interactions stabilizing the binding of the PFAS hydrophobic "tails" within the calyx and interactions between Lys60 and Lys69 and PFAS polar head groups. Comparative structural analysis revealed the presence of an open conformation of the EF loop containing the Glu89 latch residue in the complexed structures vis-a-vis the apo-form. Molecular dynamics (MD) simulations revealed high stability of the PFAS binding and attainment of energy minima in all complexes. The average binding energy of PFDA in {beta}-lactoglobulin calyx was -25 kcal/mol, which was higher than PFOS (-21 kcal/mol) and PFOA (-23 kcal/mol) due to increased van der Waals interactions of the longer hydrophobic chain of PFDA with {beta}-lactoglobulin. This work advances a mechanism by which {beta}-lactoglobulin can recruit PFAS and act as a transporter for the "forever" chemical, potentially mediating its neurotoxicity.

biophysics↗

bioRxiv2024

Densely sampled stimulus-response map of human cortex with single pulse TMS-EEG and its relation to whole brain neuroimaging measures

Large-scale networks underpin brain functions. How such networks respond to focal stimulation can help decipher complex brain processes and optimize brain stimulation treatments. To map such stimulation-response patterns across the brain non-invasively, we recorded concurrent EEG responses from single-pulse transcranial magnetic stimulation (i.e., TMS-EEG) from over 100 cortical regions with two orthogonal coil orientations from one densely-sampled individual. We also acquired Human Connectome Project (HCP)-styled diffusion imaging scans (six), resting-state functional Magnetic Resonance Imaging (fMRI) scans (120 mins), resting-state EEG scans (108 mins), and structural MR scans (T1- and T2-weighted). Using the TMS-EEG data, we applied network science-based community detection to reveal insights about the brains causal-functional organization from both a stimulation and recording perspective. We also computed structural and functional maps and the electric field of each TMS stimulation condition. Altogether, we hope the release of this densely sampled (n=1) dataset will be a uniquely valuable resource for both basic and clinical neuroscience research.

neuroscience↗

bioRxiv2022

White matter and literacy: a dynamic system in flux

Cross-sectional studies have linked differences in white matter tissue properties to reading skills. However, past studies have reported a range of, sometimes conflicting, results. Some studies suggest that white matter properties act as individual-level traits predictive of reading skill, whereas others suggest that reading skill and white matter develop as a function of an individuals educational experience. In the present study, we tested two hypotheses: a) that diffusion properties of the white matter reflect stable brain characteristics that relate to reading skills over development or b) that white matter is a dynamic system, linked with learning over time. To answer these questions, we examined the relationship between white matter and reading in a five-year longitudinal dataset and a series of large-scale, single-observation, cross-sectional datasets (N=14,249 total participants). We find that gains in reading skill correspond to longitudinal changes in the white matter. However, in the single-observation datasets, we find no evidence for the hypothesis that individual differences in white matter predict reading skill. These findings highlight the link between dynamic processes in the white matter and learning.

neuroscience↗

bioRxiv2018

Nanopore sequencing enables high-resolution analysis of resistance determinants and mobile elements in the human gut microbiome

The analysis of information rich whole-metagenome datasets acquired from complex microbial communities is often restricted by the fragmented nature of assembly from short-read sequencing. The availability of long-reads from third-generation sequencing technologies (e.g. PacBio or Oxford Nanopore) can help improve assembly quality in principle, but high error rates and low throughput have limited their application in metagenomics. In this work, we describe the first hybrid metagenomic assembler which combines the advantages of short and long-read technologies, providing an order of magnitude improvement in contiguity compared to short read assemblies, and high base-pair level accuracy. The proposed approach (OPERA-MS) integrates a novel assembly-based metagenome clustering technique with an exact scaffolding algorithm that can efficiently assemble repeat rich sequences. Based on evaluations with defined in vitro communities and virtual gut microbiomes, we show that it is possible to assemble near complete genomes from metagenomes with as little as 9x long read coverage, thus enabling high quality assembly of lowly abundant species (<1%). Furthermore, OPERA-MSs fine-grained clustering is able to deconvolute and assemble multiple genomes of the same species in a single sample, allowing us to study the complex dynamics of the human microbiome at the sub-species level. Applying nanopore sequencing to gut metagenomes of patients undergoing antibiotic treatment, we show that long reads can be obtained from stool samples in clinical studies to produce more meaningful metagenomic assemblies (up to 200x improvement over short-read assemblies), including the closed assembly of >80 putative plasmid/phage sequences and a 263kbp jumbo phage. Our results highlight that high-quality hybrid assemblies provide an unprecedented view of the gut resistome in these patients, including strain dynamics and identification of novel plasmid sequences.

bioinformatics↗