Biology subjects

Patel, P. H.

Publications and source records attributed to Patel, P. H..

11 recordsLinked to original sources

bioRxiv2026

Application of the Bradley-Terry model to quantify components of sperm competition

In many species with female sperm storage, ejaculates from multiple males overlap in the female reproductive tract, making sperm competitive ability a key component of male reproductive fitness and a target of rapid evolutionary change in the underlying genes. Here, we used controlled laboratory assays of Drosophila melanogaster sperm competition, with doubly-mated females and paternity assignment of offspring, to ask whether a Bradley-Terry framework can effectively summarize and predict competitive outcomes. The Bradley-Terry model is a probabilistic approach that estimates a latent "ability" score for each contestant based on outcomes of pairwise contests, and thus is naturally suited to data from sperm competition, which are intrinsically pairwise. We selected five distinct male genotypes: four carried strongly expressed RFP or GFP markers that allowed us to distinguish their heterozygous offspring under UV illumination, and the fifth was Canton-S, a standard wild-type genotype that served as our reference. Using Canton-S females, we assayed all 20 ordered pairwise combinations of first and second male, recorded successful double matings, and quantified the offspring sired by each male. We then extended the Bradley-Terry model to estimate genotype-specific competitive success separately for first-male "defense" (fertilization success following initial mating, also called "P1") and second-male "offense" (fertilization success following a remating, also called "P2"). This framework provides a flexible and efficient way to integrate results across large arrays of pairwise mating tests and to derive predictive scores for sperm competitive performance.

evolutionary biology↗

bioRxiv2025

Recognition of pathogenic bacteria by intestinal progenitors promotes adult Drosophila midgut regeneration via PGRP-MKK3-p38 signalling.

When enteropathogenic bacteria breach the intestinal epithelium, they are recognized by epithelial and immune cells that elicit an intestinal regenerative response. However, less is known about whether and how intestinal progenitors directly detect invading pathogenic bacteria and couple this to their proliferation. Here we show that adult Drosophila midgut progenitors recognise peptidoglycan from pathogenic bacteria through the peptidoglycan recognition proteins, PGRP-LC and PGRP-LE, and translate this to ISC proliferation by stimulating MKK3-p38 signalling. Moreover, we find that PGRP-LC/LE-MKK3-p38 signalling in progenitors regulates p38 activation throughout the midgut epithelium after infection, indicating that progenitors can influence the regenerative niche in a non-cell autonomous manner. Whilst it was previously thought that ISC proliferation in both mammals and flies is driven solely by damage-induced signals after infection, our work reveals that progenitors can directly recognise pathogenic bacteria and mount a strong parallel regenerative response that spreads throughout the midgut epithelium. Increased ISC proliferation after bacterial recognition may also serve as a strategy to repopulate the epithelium with uninfected cells.

developmental biology↗

bioRxiv2025

Orthologs of an essential orphan gene vary in their capacities for function and subcellular localization in Drosophila melanogaster

Orphan genes evolve rapidly, raising questions about whether their functions remain conserved or diverge across species. To address this, we investigated goddard (gdrd), an orphan gene essential for spermatogenesis in Drosophila melanogaster. Within the Drosophila genus, Gdrd proteins retain a conserved core structure but display substantial variation in length and primary sequence. Here we perform cross-species gene-swap assays in D. melanogaster testes to examine how these lineage-specific changes affect Gdrd function. Strikingly, the highly divergent D. mojavensis ortholog fully rescues fertility in gdrd null flies, suggesting that ancestral Gdrd acted within a conserved spermatogenesis pathway. By contrast, several orthologs, including one from a more closely related species, cannot substitute for the melanogaster gene. Cytological analysis shows that all divergent Gdrd orthologs retain some ability to interact with axonemes and ring centrioles, consistent with the proteins structural conservation, but many non-complementing orthologs display weaker axonemal binding. Furthermore, all tested orthologs exhibit divergent localizations to organellar structures. Using computational analyses and molecular dynamics simulations, we identified intrinsic protein qualities that may account for several observations made in the gene swap assays. Rescuing orthologs bear motifs with shared physicochemical properties in their intrinsically disordered regions, while non-rescuing variants exhibit structural instabilities. Taken together, these findings show that while Gdrds ancestral structure and interactions are conserved, several orthologs have undergone lineage-specific evolutionary changes.

genetics↗

bioRxiv2025

Damage recognition by intestinal stem cells via Draper-Src-Shark-STAT signalling promotes adult Drosophila midgut regeneration.

Regeneration after injury is crucial for maintaining epithelial structure and function. In order to facilitate this, a regenerative niche forms upon damage that produces cues to induce stem cell proliferation to replace damaged or lost cells. Whereas much is known about this process, less is understood about how stem cells themselves sense damage, translate this into their proliferation and shape the regenerative niche. In the adult Drosophila midgut, the non-receptor tyrosine kinase Src42A is required in progenitors to promote ISC proliferation after pathogenic bacterial infection. Although STAT is necessary for Src42A-driven ISC proliferation, the mechanism by which Src42A activates STAT in progenitors remains unclear. Here we show that Draper-Src-Shark signalling acts in ISCs to recognise midgut damage and is required for full STAT activation in ISCs to promote their proliferation. Unlike its role in phagocytes, we find that the engulfment receptor Draper in ISCs does not promote the engulfment of dying midgut epithelial cells but rather is required for ISC proliferation only in the presence of apoptotic enterocytes. Moreover, we uncover that Draper-Src-Shark signalling in progenitors regulates STAT activity non-cell autonomously in the visceral muscle, indicating that progenitors can shape the regenerative niche. As both Src and Stat are activated in the mammalian intestinal epithelium after damage and tumour formation, our work likely extends to mammalian organisms and may aid in developing therapies for tissue regeneration, inflammatory diseases and cancer.

cell biology↗

bioRxiv2024

A newly evolved gene is essential for efficient sperm entry into eggs in Drosophila melanogaster

While spermatogenesis has been extensively characterized in the Drosophila melanogaster model system, very little is known about the genes required for fly sperm entry into eggs. We identified a lineage-specific gene, which we named katherine johnson (kj), that is required for efficient fertilization. Males that do not express kj produce and transfer sperm that are stored normally in females, but sperm from these males enter eggs with severely reduced efficiency. Using a tagged transgenic rescue construct, we observed that the KJ protein localizes around the edge of the nucleus at various stages of spermatogenesis but is undetectable in mature sperm. These data suggest that kj exerts an effect on sperm development, the loss of which results in reduced fertilization ability. Interestingly, KJ protein lacks detectable sequence similarity to any other known protein, suggesting that kj could be a lineage-specific orphan gene. While previous bioinformatic analyses indicated that kj was restricted to the melanogaster group of Drosophila, we identified putative orthologs with conserved synteny, male-biased expression, and predicted protein features across the genus, as well as likely instances of gene loss in some lineages. Thus, kj was likely present in the Drosophila common ancestor and subsequently evolved an essential role in fertility in D. melanogaster. Our results demonstrate a new aspect of male reproduction that has been shaped by a lineage-specific gene and provide a molecular foothold for further investigating the mechanism of sperm entry into eggs in Drosophila. Article SummaryHow fruit fly sperm enter eggs is poorly understood. Here, we identify a gene required for efficient fertilization. Sperm from males lacking this genes function cannot enter eggs. The gene appears to act during sperm production, rather than in mature sperm. Interestingly, the gene is undetectable outside of genus Drosophila, and its encoded protein shows no discernable similarity to other proteins. This study provides insights into sperm-egg interactions and illustrates how lineage-specific genes can impact important aspects of reproduction.

genetics↗

bioRxiv2024

Enhanced mucosal mitochondrial function corrects dysbiosis and OXPHOS metabolism in IBD

BackgroundMitochondrial (Mito) dysfunction in IBD reduces mucosal O2 consumption and increases O2 delivery to the microbiome. Increased enteric O2 promotes blooms of facultative anaerobes (eg. Proteobacteria) and restricts obligate anaerobes (eg. Firmicutes). Dysbiotic metabolites negatively affect host metabolism and immunity. Our novel compound (AuPhos) upregulates intestinal epithelial cell (IEC) mito function, attenuates colitis and corrects dysbiosis in humanized Il10-/- mice. We posit that AuPhos corrects IBD-associated dysbiotic metabolism. MethodsPrimary effect of AuPhos on mucosal Mito respiration and healing process was studied in ex vivo treated human colonic biopsies and piroxicam-accelerated (Px) Il10-/- mice. Secondary effect on microbiome was tested in DSS-colitis WT B6 and germ-free 129.SvEv WT or Il10-/- mice reconstituted with human IBD stool (Hu-Il10-/-). Mice were treated orally with AuPhos (10- or 25- mg/kg; q3d) or vehicle, stool samples collected for fecal lipocalin-2 (f-LCN2) assay and microbiome analyses using 16S rRNA sequencing. AuPhos effect on microbial metabolites was determined using untargeted global metabolomics. AuPhos-induced hypoxia in IECs was assessed by Hypoxyprobe-1 staining in sections from pimonidazole HCl-infused DSS-mice. Effect of AuPhos on enteric oxygenation was assessed by E. coli Nissle 1917 WT (aerobic respiration-proficient) and cytochrome oxidase (cydA) mutant (aerobic respiration-deficient). ResultsMetagenomic (16S) analysis revealed AuPhos reduced relative abundances of Proteobacteria and increased blooms of Firmicutes in uninflamed B6 WT, DSS-colitis, Hu-WT and Hu-Il10-/- mice. AuPhos also increased hypoxyprobe-1 staining in surface IECs suggesting enhanced O2 utilization. AuPhos-induced anaerobiosis was confirmed by a significant increase in cydA mutant compared to WT (O2-utlizing) E.coli. Ex vivo treatment of human biopsies with AuPhos showed significant increase in Mito mass, and complexes I and IV. Further, gene expression analysis of AuPhos-treated biopsies showed increase in stem cell markers (Lgr4, Lgr5, Lrig1), with concomitant decreases in pro-inflammatory markers (IL1{beta},MCP1, RankL). Histological investigation of AuPhos-fed Px-Il10-/- mice showed significantly decreased colitis score in AuPhos-treated Px-Il10-/- mice, with decrease in mRNA of pro-inflammatory cytokines and increase in Mito complexes (ND5, ATP6). AuPhos significantly altered microbial metabolites associated with SCFA synthesis, FAO, TCA cycle, tryptophan and polyamine biosynthesis pathways. AuPhos increased pyruvate, 4-hydroxybutyrate, 2-hydroxyglutarate and succinate, suggesting an upregulation of pyruvate and glutarate pathways of butyrate production. AuPhos reduced IBD-associated primary bile acids (BA) with concomitant increase in secondary BA (SBA). AuPhos treatment significantly decreased acylcarnitines and increased L-carnitine reflective of enhanced FAO. AuPhos increases TCA cycle intermediates and creatine, energy reservoir substrates indicating enhanced OxPHOS. Besides, AuPhos also upregulates tryptophan metabolism, decreases Kynurenine and its derivatives, and increases polyamine biosynthesis pathway (Putresceine and Spermine). ConclusionThese findings indicate that AuPhos-enhanced IEC mitochondrial function reduces enteric O2 delivery, which corrects disease-associated metabolomics by restoring short-chain fatty acids, SBA, AA and IEC energy metabolism. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/584471v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@41e437org.highwire.dtl.DTLVardef@1eddf37org.highwire.dtl.DTLVardef@1d9bff3org.highwire.dtl.DTLVardef@c925f0_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2024

Prophages block cell surface receptors to ensure survival of their viral progeny

In microbial communities, viruses compete for host cells to infect, and thus evolved diverse ways to inhibit their competitors. One mechanism is Superinfection exclusion (Sie), whereby a virus that has established an infection prevents a secondary infection. We identified a Pseudomonas prophage Sie protein that alters pilus dynamics through the pilus assembly chaperone, PilZ. This protein, known as Zip for PilZ interacting protein, does not abrogate pilus activity, but fine tunes it, providing strong phage resistance without a fitness cost. This tuning is modulated through quorum sensing, which coordinates Zip production in concert with bacterial cell density to ensure maximal protection when bacterial populations are at the highest risk of phage infection. Most notably, Zip activity prevents internalization and destruction of phage progeny. We refer to this as the "anti-Kronos effect" after the Greek god who devoured his own children and show that it is a conserved feature of diverse prophage-encoded Sie systems.

microbiology↗

bioRxiv2021

A putative de novo evolved gene required for spermatid chromatin condensation in Drosophila melanogaster

Comparative genomics has enabled the identification of genes that potentially evolved de novo from non-coding sequences. Many such genes are expressed in male reproductive tissues, but their functions remain poorly understood. To address this, we conducted a functional genetic screen of over 40 putative de novo genes with testis-enriched expression in Drosophila melanogaster and identified one gene, atlas, required for male fertility. Detailed genetic and cytological analyses showed that atlas is required for proper chromatin condensation during the final stages of spermatogenesis. Atlas protein is expressed in spermatid nuclei and facilitates the transition from histone- to protamine-based chromatin packaging. Complementary evolutionary analyses revealed the complex evolutionary history of atlas. The protein-coding portion of the gene likely arose at the base of the Drosophila genus on the X chromosome but was unlikely to be essential, as it was then lost in several independent lineages. Within the last [~]15 million years, however, the gene moved to an autosome, where it fused with a conserved non-coding RNA and evolved a non-redundant role in male fertility. Altogether, this study provides insight into the integration of novel genes into biological processes, the links between genomic innovation and functional evolution, and the genetic control of a fundamental developmental process, gametogenesis. Author SummaryGenomes are in flux, as genes are constantly added and lost throughout evolution. New genes were once thought to arise almost exclusively via the modification or duplication of existing genes. Recently, however, interest has grown in alternative modes of new gene origination, such as de novo evolution from genetic material that previously did not encode proteins. Many de novo genes are expressed in male reproductive tissues, but their significance for fertility is not well understood. We screened likely de novo genes expressed in the Drosophila testis for reproductive roles and found one gene, atlas, essential for male fertility. We leveraged genetic and cell biological experiments to investigate roles for Atlas protein in reproduction and found that it is required during sperm development for proper packaging of DNA in the sperm nucleus. Evolutionary analyses of this gene revealed a complicated history, including loss in some lineages, movement between chromosomes, and fusion with a non-protein-coding gene. Studying both the functions and evolutionary histories of new proteins illustrates how they might evolve critical roles in biological processes despite their relative novelty. Furthermore, the study of atlas identifies an essential genetic player in the fly testis, an important model system for understanding how gametes are produced.

genetics↗

bioRxiv2021

Structural and functional characterization of a putative de novo gene in Drosophila

Comparative genomic studies have repeatedly shown that new protein-coding genes can emerge de novo from non-coding DNA. Still unknown is how and when the structures of encoded de novo proteins emerge and evolve. Combining biochemical, genetic and evolutionary analyses, we elucidate the function and structure of goddard, a gene which appears to have evolved de novo at least 50 million years ago within the Drosophila genus. Previous studies found that goddard is required for male fertility. Here, we show that Goddard protein localizes to elongating sperm axonemes and that in its absence, elongated spermatids fail to undergo individualization. Combining modelling, NMR and CD data, we show that Goddard protein contains a large central -helix, but is otherwise partially disordered. We find similar results for Goddards orthologs from divergent fly species and their reconstructed ancestral sequences. Accordingly, Goddards structure appears to have been maintained with only minor changes over millions of years.

evolutionary biology↗

bioRxiv2021

OPA1 Deletion in Brown Adipose Tissue Improves Thermoregulation and Systemic Metabolism via FGF21

Adrenergic stimulation of brown adipocytes alters mitochondrial dynamics, including proteolytic processing of the mitochondrial fusion protein optic atrophy 1 (OPA1). However, direct mechanisms linking OPA1 to brown adipose tissue (BAT) physiology are incompletely understood. By deleting OPA1 selectively in BAT (OPA1 BAT KO), we demonstrate that OPA1 is required for cold-induced thermogenesis. Unexpectedly, OPA1 deficiency induced fibroblast growth factor 21 (FGF21) as a BATokine in an activating transcription factor 4 (ATF4)- dependent manner. BAT-derived FGF21 mediates an adaptive response in OPA1 BAT KO mice, by inducing browning of white adipose tissue (WAT), increasing resting metabolic rates, and improving thermoregulation. However, FGF21 does not mediate the resistance to diet-induced obesity observed in these animals. These findings reveal a requirement for OPA1 in BAT thermogenesis, and uncovers a homeostatic mechanism of BAT-mediated metabolic protection governed by an ATF4-FGF21 axis, that is activated independently of BAT thermogenic function.

physiology↗

bioRxiv2020

Vps54 regulates Drosophila neuromuscular junction development and controls postsynaptic density composition via a Rab7-dependent mechanism

Vps54 is a subunit of the Golgi-associated retrograde protein (GARP) complex, which is involved in tethering endosome-derived vesicles to the trans-Golgi network (TGN). In the wobbler mouse, a model for human motor neuron (MN) disease, reduction in the levels of Vps54 causes neurodegeneration. However, it is unclear how disruption of GARP-mediated vesicle transport leads to MN dysfunction and ultimately neurodegeneration. To better understand the role of Vps54 in MNs, we have disrupted expression of the Vps54 ortholog in Drosophila and examined the impact on the larval neuromuscular junction (NMJ). Here, we show that both null mutants and MN-specific knockdown of Vps54 leads to NMJ overgrowth. Reduction of Vps54 partially disrupts localization of the t-SNARE, Syntaxin-16, to the TGN but has no impact on endosomal pools. Presynaptic knockdown of Vps54 in MNs combined with overexpression of the small GTPases Rab5, Rab7, or Rab11 suppresses the Vps54 NMJ phenotype. Conversely, knockdown of Vps54 combined with overexpression of dominant negative Rab7 causes axonal and behavioral abnormalities including a decrease in postysynaptic Dlg and GluRIIB levels without any effect on GluRIIA. Taken together, these data suggest that Vps54 controls larval MN axon development and postsynaptic density composition by modulating Rab7-mediated endosomal trafficking.

neuroscience↗