Biology subjects

Dubey, D.

Publications and source records attributed to Dubey, D..

6 recordsLinked to original sources

bioRxiv2026

ScreenDMT reveals metabolites replicably associated with sleep disorders across three human cohorts

The robust replication of scientific findings across independent studies is essential, yet it remains challenging in high-dimensional biological datasets. A critical aspect of true replication requires detecting not only the repeated presence but also the consistent direction of an effect. Traditional methods for evaluating replication often ignore effect directionality or lack adequate statistical power when adjusting for multiple comparisons. To address this, we extend the directional MaxP test (DMT) and our screening-integrated procedure, ScreenDMT, to evaluate directional replication across an arbitrary number of independent studies. We mathematically prove ScreenDMT's validity for an arbitrary number of studies when the studies' sample sizes grow unbounded. Through extensive simulation studies, we demonstrate that ScreenDMT effectively controls error rates, such as the false discovery rate (FDR), in finite sample sizes and yields higher statistical power than competing methods especially for three studies. We applied the extended ScreenDMT to untargeted blood metabolomics profiles across three diverse human cohorts - ARIC (N=1,337), MESA (N=1,874), and HCHS/SOL (N=6,180) - to discover replicable biomarkers for dichotomous insomnia, long sleep, short sleep, and excessive daytime sleepiness (EDS). We found low levels of cortisol to be replicably associated with EDS, and high levels of n-formylmethionine to be associated with long sleep. Furthermore, directional pathway analysis revealed that low levels of xanthine metabolites are replicably associated with insomnia. These convergent findings validate ScreenDMT as a powerful methodology for simultaneous multi-cohort replication and offer robust insights into the metabolic signatures underlying sleep disorders across diverse populations.

bioinformatics↗

bioRxiv2025

NRF2 inhibition of alveolar macrophage MHC II expression during Mycobacterium tuberculosis infection

During Mycobacterium tuberculosis (Mtb) infection, infected alveolar macrophages (AMs) initially up-regulate a NRF2 regulated cell-protective program, which is detrimental to host control and impedes AM activation, including MHC II expression. MHC II is critical for CD4+ T cell activation and host immunity during Mtb infection. We hypothesized that NRF2 regulates the MHC II pathway and AM antigen presentation to T cells. We found that NRF2 inhibits MHC II, but not MHC I, specifically in AMs, following Mtb infection in vitro and in vivo. NRF2 dampens Ciita and H2-Ab1 gene expression in uninfected AMs, and MHC II inhibition by NRF2 is retained following innate stimuli and IFN{gamma} exposure. NRF2 expression in Mtb-infected AMs impedes their ability to activate ESAT6-specific CD4+ T cells. Thus, although NRF2 expression enhances cell-protective functions, it has the unexpected consequence of limiting innate-adaptive crosstalk, which can impair CD4+ T cell activation and host immunity during Mtb infection. HIGHLIGHTSO_LINRF2 inhibits MHC II on AMs, but not DCs, MDMs, or PMNs, during Mtb infection C_LIO_LINRF2 inhibits Ciita and H2-Ab1 and total MHC II protein in AMs, but not in BMDMs C_LIO_LINRF2 blockade of AM MHC II is retained following PAMP and IFN{gamma} stimulation C_LIO_LINRF2 impedes the activation of antigen-specific CD4+ T cells by Ams C_LI

immunology↗

bioRxiv2024

Absence of c-Maf and IL-10 enables Type I IFN enhancement of innate responses to low-dose LPS in alveolar macrophages

Alveolar macrophages (AMs) are lower-airway resident myeloid cells and are among the first to respond to inhaled pathogens. Here, we interrogate AM innate sensing to Pathogen Associated Molecular Patterns (PAMPs) and determine AMs have decreased responses to low- dose LPS compared to other macrophages, as measured by TNF, IL-6, Ifnb, and Ifit3. We find the reduced response to low-dose LPS correlates with minimal TLR4 and CD14 surface expression, despite sufficient internal expression of TLR4. Additionally, we find that AMs do not produce IL-10 in response to a variety of PAMPs due to low expression of transcription factor c- Maf and that lack of IL-10 production contributes to an enhancement of pro-inflammatory responses by Type I IFN. Our findings demonstrate that AMs have cell-intrinsic dampened responses to LPS, which is enhanced by type I IFN exposure. These data implicate conditions where AMs may have reduced or enhanced sentinel responses to bacterial infections. HIGHLIGHTSO_LIAlveolar macrophages (AMs) do not produce TNF or IL-6 in response to low-dose LPS due to minimal surface expression of TLR4 and CD14 C_LIO_LILack of AM IL-10 production is dependent on low c-Maf expression C_LIO_LIExogenous c-Maf expression increases AM IL-10 production C_LIO_LIIFN{beta} enhances AM TNF and IL-6 responses to low-dose LPS and this is dependent on a lack of IL-10 C_LI

immunology↗

bioRxiv2021

Rapid multilocus adaptation of clonal cabbage leaf curl virus populations to Arabidopsis thaliana

Cabbage leaf curl virus (CabLCV) has a bipartite single-stranded DNA genome and infects the model plant Arabidopsis thaliana. CabLCV serves as a model for the genus Begomovirus, members of which cause tremendous crop losses worldwide. We have used CabLCV as a model for within-plant virus evolution by inoculating individual plants with infectious clones of either a wild-type or mutagenized version of the CabLCV genome. Consistent with previous reports, detrimental substitutions in the Replication-associated gene (Rep) were readily compensated for by direct reversion and/or alternative mutations. A surprising number of common mutations were detected elsewhere in both viral segments (DNA-A and DNA-B) indicating convergent evolution and suggesting that CabLCV may not be as well adapted to A. thaliana as commonly presumed. Consistent with this idea, a spontaneous coat protein variant consistently rose to high allele frequency in susceptible accession Col-0, at a higher rate than in hypersusceptible accession Sei-0. Numerous high-frequency mutations were also detected in a candidate Rep binding site in DNA-B. Our results reinforce the fact that spontaneous mutation of this type of virus occurs rapidly and can change the majority consensus sequence of a within-plant virus population in weeks.

evolutionary biology↗

bioRxiv2021

Interspecies recombination has driven the macroevolution of cassava mosaic begomoviruses

Begomoviruses (family Geminiviridae, genus Begomovirus) significantly hamper crop production and threaten food security around the world. The frequent emergence of new begomovirus genotypes is facilitated by high mutation frequencies and the propensity to recombine and reassort. Homologous recombination has been especially implicated in the emergence of novel cassava mosaic begomovirus (CMB) genotypes, which cause cassava mosaic disease (CMD). Cassava (Manihot esculenta) is a staple food crop throughout Africa, and an important industrial crop in Asia, two continents where production is severely constrained by CMD. The CMD species complex is comprised of 11 bipartite begomovirus species with ample distribution throughout Africa and the Indian subcontinent. While recombination is regarded as a frequent occurrence for CMBs, a revised, systematic assessment of recombination and its impact on CMB phylogeny is currently lacking. We assembled datasets of all publicly available, full-length DNA-A (n=880) and DNA-B (n=369) nucleotide sequences from the 11 recognized CMB species. Phylogenetic networks and complementary recombination detection methods revealed extensive recombination among the CMB sequences. Six out of the eleven species have descended from unique interspecies recombination events. Estimates of recombination and mutation rates revealed that all species experience mutation more frequently than recombination, but measures of population divergence indicate that recombination is largely responsible for the genetic differences between species. Our results support that recombination has significantly impacted the CMB phylogeny and is driving speciation in the CMD species complex. IMPORTANCECassava mosaic disease (CMD) is a significant threat to cassava production throughout Africa and Asia. CMD is caused by a complex comprised of 11 recognized virus species exhibiting accelerated rates of evolution, driven by high frequencies of mutation and genetic exchange. Here, we present a systematic analysis of the contribution of genetic exchange to cassava mosaic virus diversity. Most of these species emerged as a result of genetic exchange. This is the first study to report the significant impact of genetic exchange on speciation in a group of viruses.

evolutionary biology↗

bioRxiv2018

Identification and in silico analysis of the origin recognition complex in the human fungal pathogen Candida albicans

DNA replication in eukaryotes is initiated by the orchestrated assembly and association of initiator proteins (heterohexameric Origin Recognition Complex, ORC) on the replication origins. These functionally conserved proteins play significant roles in diverse cellular processes besides their central role in ignition of DNA replication at origins. While Candida albicans, a major human fungal pathogen, is an ascomycetous, asexual, diploid budding yeast but it is significantly diverged from a much better studied model organism Saccharomyces cerevisiae. The components of the DNA replication machinery in C. albicans remain largely uncharacterized. Identification of factors required for DNA replication is essential for understanding the evolution of the DNA replication machinery. We identified the putative ORC homologs in C. albicans and determined their relatedness with those of other eukaryotes including several yeast species. Our extensive in silico studies demonstrate that the domain architecture of CaORC proteins share similarities with the ORC proteins of S. cerevisiae. We dissect the domain organization of ORC (trans-acting factors) proteins that seem to associate with DNA replication origins in C. albicans. We present a model of the 3D structure of CaORC4 to gain further insights of this proteins function.

bioinformatics↗