Biology subjects

Shah, D.

Publications and source records attributed to Shah, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Dynamic flux balance analysis of cancer metabolism using expression-based human cell line models

Aberrant metabolism that supports dysregulated growth is a key feature of cancer. Flux balance analysis, a computational approach that can predict genome-scale metabolic rates based on stoichiometry and mass conservation, has proven valuable in the prediction of pathway utilization and possible drug targets in cancer cells, but deep insight into growth dynamics under physiologically relevant conditions has been limited. To address this gap, we revisited the human metabolism model and its integration of gene-expression data, and we implemented simulations of metabolism in multiple cancer cell lines using static and dynamic flux balance analysis. Our models predict a substantial dependence of intracellular and exchange fluxes, and of the timing of resource utilization, on growth media and specific cell-line makeup. Secretions include lactate and other metabolites that could contribute to shaping the tumor microenvironment. Despite these differences in flux phenotypes, virtual genetic knockout screens predict high similarity of lethality across cell lines and media, and suggest a handful of possible cell-line specific targets. We finally demonstrate the power of dynamic simulations by setting virtual competition assays, which form the foundation for future extensions into dynamic simulations of tumor-stromal interactions in spatially-structured environment.

systems biology↗

bioRxiv2026

Urea is a dynamic and functional component of mammalian breast milk

Urea is a constituent of human milk, yet its regulation and interactions with the infant gut microbiome remain unclear. Combining three human cohorts, a controlled mouse model, and complementary microbiome analyses, we show that milk urea increases across lactation, is conserved across mammals, and is not explained by circulating urea levels or maternal diet. Instead, we identify lactation-dependent remodeling of mammary urea-metabolism and transport pathways, including dynamic AQP3 localization in secretory epithelium, indicative of regulated transfer of circulating urea into breast milk. Alongside urea, maternal milk and stool provide complementary reservoirs of urea-metabolizing bacteria that help establish the infant "ureabiome", whose urea-utilization capacity is supported by metagenomics. This maternal-infant axis is context-dependent: infant formulas provide substantially higher urea levels than human milk, while functional assays show that urea supports both commensal and opportunistic bacteria in a concentration-dependent manner. Together, these findings define a maternal nitrogen axis through which lactation can shape the assembly and function of the infant gut microbiome.

microbiology↗

bioRxiv2026

Inferring the relative contributions of evolutionary processes shaping X chromosome dynamics in the common marmoset (Callithrix jacchus) in the presence of twinning and hematopoietic chimerism

The common marmoset (Callithrix jacchus) is a biomedically important species that is characterized by two unusual biological traits -- a high frequency of twin births and hematopoietic chimerism -- that preclude the application of many commonly used population genomic approaches for quantifying evolutionary processes. In this study, we directly account for both factors in order to estimate fine-scale mutation and recombination rate maps, as well as to infer the demographic and selective processes shaping variation, on the common marmoset X chromosome. Comparing our findings to estimates recently inferred on the autosomes of this species, we find reduced rates of mutation and recombination on the X, as expected. Furthermore, population sex ratios are inferred to be nearly equal, and the appropriately rescaled autosomal population history fits the X chromosome well. Finally, we report evidence of recent selective sweeps targeting a number of X-linked genes, including several of significant biomedical relevance. Overall, these analyses provide novel insights into the evolutionary processes shaping X chromosome evolution in this biomedically-relevant primate model.

evolutionary biology↗

bioRxiv2026

TRPML1 loss drives lysosomal calcium failure and astrocyte dysfunction across Alzheimer's Disease progression

Astrocytes are among the earliest cells to exhibit dysfunction in Alzheimers disease (AD), developing profound calcium signalling deficits before amyloid plaques have formed, yet the underlying mechanisms remain unknown. Lysosomal dysfunction is a hallmark of AD, but whether it initiates this early functional impairment or arises as a consequence of established pathology remains unresolved. Here, we find that astrocytic cytosolic calcium activity is suppressed prior to amyloid plaque deposition and is accompanied by reduced lysosomal acidification in vivo. Using a lysosome-targeted calcium indicator selectively expressed in astrocytes, we directly visualise lysosomal calcium dynamics in vivo and reveal a profound early loss of lysosomal calcium release, identifying lysosomal failure as an initiating event in astrocyte dysfunction in AD. Reduced expression of the lysosomal calcium channel TRPML1 provides the mechanistic basis for this deficit. Astrocyte-specific restoration of TRPML1 expression rescues lysosomal homeostasis and cytosolic calcium signalling and prevents astrocyte reactivity and morphological hypertrophy. Strikingly, early TRPML1 restoration prevents both the initial calcium hypoactivity observed before plaque formation and the later hyperactivity that characterises post-plaque disease, demonstrating that lysosomal calcium homeostasis stabilises astrocyte function across the disease trajectory. TRPML1 restoration also reduces amyloid plaque burden, indicating that astrocytic lysosomal competence directly shapes disease pathology. These findings identify lysosomal calcium failure as an early organelle-level mechanism linking amyloid stress to astrocyte dysfunction in AD, and position TRPML1-mediated lysosomal calcium signalling as a tractable target for limiting disease progression.

neuroscience↗

bioRxiv2026

Profilin-1 Promotes Chromophobe Renal Cell Carcinoma Malignancy

Chromophobe renal cell carcinoma (ChRCC) accounts for 5% of all renal cancer cases. Despite its generally indolent behavior and low mutational burden, there is no targeted therapy for metastatic ChRCC. Profilin-1 (Pfn1), a cytoskeletal regulator of actin and tubulin dynamics, has emerged as a potential oncogenic driver in several cancers including RCC, but its role in ChRCC, remains undefined. We observed elevated Pfn1 expression in stage IV ChRCC patients, implicating Pfn1 in advanced disease progression. To investigate this, we manipulated Pfn1 expressions in two ChRCC cell lines UOK276 and RCJ41M. Pfn1 knockdown (KD) significantly reduced proliferation, invasion, and colony formation, whereas Pfn1 overexpression (OE) in UOK276 enhanced ChRCC aggressive phenotypes. Pharmacological inhibition of Pfn1 significantly suppressed proliferation and clonogenic growth in both cell lines. Additionally, Pfn1 KD increased intracellular ROS accumulation, while overexpressed reduced ROS levels, linking cytoskeletal regulation to oxidative stress control. Together, these findings position Pfn1 as a critical mediator of ChRCC progression, linking cytoskeletal remodeling to aggressive tumor behavior. This work highlights Pfn1 as a potential therapeutic target and establishes a framework for cytoskeletal-focused strategies in advanced ChRCC.

cancer biology↗

bioRxiv2026

Targeting ZC3H12C improves T cell persistence and antitumor function in adoptive T cell therapy

Adoptive T cell therapy (ACT) has achieved remarkable clinical responses in hematologic malignancies but remains limited by progressive T cell dysfunction under chronic antigen stimulation. Here, we identify ZC3H12C as a conserved feature of dysfunctional T cells and show that its disruption enhances the durability and antitumor activity of engineered T cells. By integrating single-cell chromatin accessibility and transcriptomic profiling of human tumor-infiltrating lymphocytes (TILs), we identified the ZC3H12C locus as selectively remodeled in exhausted T cells. ZC3H12C induction is largely absent across acute T cell activation contexts, indicating regulation that is specific to chronic antigen-driven dysfunction. Genetic disruption of ZC3H12C improves T cell expansion, cytotoxicity, and expression of effector molecules during repeated in vitro stimulation, translating into enhanced tumor control in vivo across both T cell receptor (TCR) and chimeric antigen receptor (CAR) T cell therapy platforms. Improved efficacy is observed in hematologic, solid, and metastatic tumor models and is accompanied by increased T cell persistence. Further, ZC3H12C is enriched in clinical pre-infusion CAR T cell products associated with non-response. Together, these findings identify ZC3H12C as a T cell dysfunction-specific target to improve ACT performance.

immunology↗

bioRxiv2026

Systematic Screening of a Glycolysis-targeting Small-molecule Library Identifies Novel Inhibitors of Fungal Morphogenesis in Candida albicans

Fungal infections are an increasing global health concern, with Candida albicans emerging as a leading cause of mucosal and life-threatening systemic infections. C. albicans relies on yeast-to-hyphae transition, to establish systemic infections in the host. Our recent work demonstrated that glycolysis is a key regulator of hyphal differentiation in C. albicans. Leveraging this knowledge, we screened a small-molecule compound library containing glycolysis inhibitors for their ability to block fungal morphogenesis and identified multiple inhibitors of glycolysis that robustly block hyphal differentiation without compromising overall growth. While early glycolysis pathway inhibitors showed moderate effects, two compounds (NPD10084 and PKM2-IN-6) targeting pyruvate kinase activity emerged as the most potent inhibitors of fungal morphogenesis, completely blocking hyphal differentiation, in multiple filamentation-inducing conditions. Comparative RNA-Seq analysis revealed that pyruvate kinase inhibition using PKM2-IN-6 resulted in the repression of multiple genes associated with fungal morphogenesis, biofilm formation, and virulence. These transcriptional changes were accompanied by a significant reduction in biofilm formation and increased sensitivity to conventional antifungal drugs, including amphotericin B and fluconazole, in the presence of PKM2-IN-6. Furthermore, administration of PKM2-IN-6 significantly improved the survival of mice in a systemic model of murine candidiasis underscoring the in vivo efficacy of this compound. Molecular docking analysis showed stable binding of both compounds to the ATP-binding pocket of pyruvate kinase, suggesting ATP-competitive inhibition as the mode of action. Collectively, our study has identified novel inhibitors of fungal morphogenesis in C. albicans that target pyruvate kinase activity to increase antifungal susceptibility and attenuate the virulence of C. albicans. ImportanceCandida albicans is a major fungal pathogen that causes fatal infections, particularly in immunocompromised individuals. The increasing prevalence of antifungal resistance and the limited availability of effective antifungal therapies underscore the need for new treatment strategies. In this study, we identify pyruvate kinase, a key glycolytic enzyme, as an important regulator of fungal morphogenesis and virulence. Pharmacological inhibition of pyruvate kinase blocked hyphal differentiation without affecting fungal growth, impaired biofilm formation, and enhanced the activity of clinically relevant antifungal drugs. Transcriptomic analysis further revealed broad repression of genes involved in filamentation, biofilm formation, cell adhesion, antifungal resistance, and virulence, providing a molecular basis for these phenotypes. Importantly, pyruvate kinase inhibition also improved host survival in a murine model of systemic candidiasis. Together, our findings identify pyruvate kinase as a promising therapeutic target and demonstrate the potential of targeting fungal metabolism to effectively combat C. albicans infections.

microbiology↗

bioRxiv2026

Chromatin remodelling enables enhancer resetting to facilitate the ERK transcriptional response

During development, cellular identity is ultimately determined by transcriptional output: lineage-specific genes must be activated, while genes associated with alternative fates must be repressed. This process depends on the activity of chromatin remodelling complexes, which regulate the accessibility of transcription factors to chromatin regulatory elements. In addition, cellular identity is shaped by exposure to intercellular signals. Understanding the mechanisms by which extracellular signals are translated into changes in the transcriptional program is essential for understanding cell fate decisions during development, as well as in disease conditions such as cancer. Here we describe a rapid and widespread enhancer resetting event in response to ERK signalling in mouse ES cells. This process occurs in two distinct phases: an immediate, genome-wide alteration in transcription factor binding dynamics at regulatory regions which is dependent on the release of paused RNA Polymerase II, followed by the re-establishment of a context appropriate, stable chromatin state. We demonstrate that the chromatin remodelling complex NuRD is required for this reestablishment phase and for the appropriate transcriptional response to ERK signalling. We propose that enhancer resetting places genomic regulatory regions in a state which is permissive to the exchange of transcription factors in order to establish a new, stable enhancer topology enabling rapid yet precise transcriptional response to extracellular signals.

molecular biology↗

bioRxiv2026

Compromised striatal structure and function in mouse models of RARB-related disorder

Dominant variants in the retinoic acid receptor beta (RARB) gene cause a complex disorder known as RARB-related disorder (RARB-RD), characterized by multiple congenital anomalies, global developmental delay, and dystonia. RARB-RD variants have been classified as either gain-of-function (GOF) or dominant-negative (DN) based on their cell-based transcriptional responses to retinoids. To investigate the mechanisms underlying this disorder, we generated mouse models carrying either the p.R387C or p.L402P RARB-RD variant, previously categorized as GOF and DN, respectively. Homozygous mice for either RARB-RD variant died perinatally with colonic aganglionosis, while heterozygous mice survived and recapitulated several features of RARB-RD. In addition to microphthalmia, both RarbR387C/+and RarbL402P/+ mice exhibited progressive coordination deficits, increased active-phase locomotor activity, and cognitive impairment in the novel object recognition test. In contrast, mice heterozygous for a null allele of Rarb (Rarb+/-) did not display these abnormalities. In the brain, Rarb is predominantly expressed in the two major populations of projection neurons of the striatum recognizable by the expression of dopamine receptors D1R/Drd1 and D2R/Drd2. Marker analysis revealed a reduction in Drd2-expressing neurons without changes in Drd1-expressing neurons in both RARB-RD models. Furthermore, RARB-RD mice showed partial resistance to the cataleptic effects of haloperidol, a D2R-specific antagonist. These behavioral, cellular, and dopaminergic deficits--though not the cognitive impairments--have previously been observed in Rarb-/- mice. To determine whether the in vitro effects of RARB-RD variants correlate with distinct transcriptional signatures in vivo, we compared the striatal transcriptome of RarbR387C/+, RarbL402P/+, Rarb-/- and Rarb+/-mice with their littermate controls. We found that the heterozygous RARB-RD variants and the homozygous null allele affected a large subset of common genes, with putative direct RARB targets predominantly downregulated. Notably, the transcriptional impact of the RARB-RD variants was more profound than that of the null allele, regardless of zygosity. Additionally, transcriptional changes in RARB-RD mice extensively overlapped with those observed in mouse models of Huntingtons disease, suggesting shared mechanisms affecting neuronal survival in the striatum. We conclude that the p.R387C and p.L402P variants similarly compromise striatal integrity and function, likely through a DN mechanism. Progressive emergence of most neurologic deficits highlights a potential therapeutic window. Our results support the development of strategies aimed at silencing RARB-RD alleles.

neuroscience↗

bioRxiv2026

Modular mRNA LNP design integrates RNA, lipid, and antigen engineering for protective vaccination

mRNA-lipid nanoparticle (LNP) vaccines are programmable, multi-component systems in which immune outcomes emerge from coupled control of nanoparticle chemistry, RNA regulatory architecture, and antigen design. Here we establish an integrated engineering framework that quantitatively maps how ionizable lipid identity, untranslated region (UTR) configuration, and 5' cap structure shape innate activation landscapes and thereby tune the magnitude, cellular distribution, and polarization of adaptive immunity. Benchmarking three ionizable lipids shows that lipid chemistry imprints distinct cytokine and chemokine milieus during dendritic cell-T cell priming that mirror downstream T cell activation phenotypes, identifying lipid structure as a determinant of pathway-selective activation; notably, our first-in-study lipid exhibits benchmark-comparable immunostimulatory profiles, supporting further translational evaluation. Using Crimean-Congo hemorrhagic fever virus (CCHFV) as a model high-consequence pathogen, we show that UTRs act as modular regulatory elements that redirect cytokine outputs, tuning effector versus proliferative programs and expanding helper polarization in an antigen-dependent manner. Cap structure functions primarily as a quantitative gain control, scaling cellular and humoral response magnitude without overriding antigen-defined polarization. Within this optimized platform, antigen architecture defines functional constraints on protection: structural modifications reshape immune hierarchies and antibody quality. Integrating these design axes yields an optimized mRNA-LNP vaccine encoding the CCHFV secreted glycoprotein complex (sGCs) that achieves 90% protection in an immunosuppressed murine lethal-challenge model with minimal clinical signs. Together, these data define generalizable design principles for rational, multi-parameter optimization of mRNA-LNP vaccines.

microbiology↗

bioRxiv2025

A Conserved Metabolic Network Regulates Titan Cell Formation in Cryptococcus neoformans

Cryptococcus neoformans is an opportunistic fungal pathogen that causes pulmonary infections and life-threatening meningoencephalitis in immunocompromised individuals. In addition to the polysaccharide capsule and melanin, titan cell formation is a key virulence trait that promotes immune evasion and disease progression. Despite the established role of titan cells in C. neoformans pathogenesis, the molecular mechanisms governing their formation remain poorly understood. Here, we demonstrate that glycolysis is critical for titan cell formation in C. neoformans. Pharmacological inhibition or genetic disruption of glycolysis significantly impaired titanization, whereas exogenous cAMP add-back restored the defect. To elucidate the underlying mechanism, we performed comparative RNA-seq analyses of wild- type, hxk2{Delta}, and hxk2{Delta} supplemented with cAMP under titan cell inducing conditions. Transcriptomic analyses revealed significant downregulation of a large subset of calcineurin- responsive genes in the hxk2{Delta} mutant, many of which were restored upon cAMP supplementation. Consistent with these findings, pharmacological inhibition of calcineurin using FK506 or cyclosporin A markedly reduced titan cell formation, establishing an essential role for calcineurin signaling in this morphological transition. Furthermore, supplementation with CaCl2 rescued the titanization defect of the hxk2{Delta} mutant, whereas chelation of extracellular calcium with EGTA significantly inhibited titanization in wild-type cells. Using the calcium-sensitive dye, we found that intracellular calcium levels were substantially reduced in the hxk2{Delta} mutant and were restored by CaCl2 or cAMP supplementation. Collectively, our findings uncover a previously unrecognized glycolysis-calcineurin regulatory axis that governs titan cell formation and establishes a direct mechanistic link between central carbon metabolism, calcium homeostasis and fungal morphogenesis. SummaryTitan cell formation is a critical virulence trait that promotes immune evasion and disease progression of Cryptococcus neoformans. However, the mechanisms governing this morphological transition remain poorly understood. Here, we demonstrate that glycolysis is essential for titan cell formation and uncover a previously unrecognized link between glycolysis, calcium homeostasis, and calcineurin signaling. Comparative transcriptomics, pharmacological perturbation, calcium rescue experiments, and intracellular calcium measurements reveal that disruption of glycolysis attenuates calcineurin signaling by reducing intracellular calcium levels, thereby impairing titanization. These findings establish a novel glycolysis-calcineurin regulatory axis controlling fungal morphogenesis in C. neoformans.

microbiology↗

bioRxiv2025

The chromatin remodeller CHD4 controls both nucleosome integrity and transcription factor binding to promote activity of active regulatory elements and to prevent activation of silent enhancers

Chromatin organisation and transcriptional regulation are tightly coordinated processes that are essential for maintaining cellular identity and function. ATP-dependent chromatin remodelling proteins play critical roles in control of genome structure and in regulating transcription across eukaryotes. Their essential nature, however, has made it difficult to define exactly how these functions are mediated. The chromatin remodeller CHD4 has been shown to be capable of sliding nucleosomes in vitro, and to regulate chromatin accessibility and gene expression in vivo. Using an inducible depletion system, here we identify a second mechanism of action for CHD4 in actively restricting the residence time of transcription factors on chromatin. Together these activities result in distinct, context-dependent outcomes: at highly accessible regulatory elements, CHD4 limits transcription factor binding to maintain regulatory function, while at low-accessibility euchromatic regions, it prevents transcription factor engagement and sustains chromatin compaction, thereby silencing cryptic enhancers. Collectively, these mechanisms enable CHD4 to reduce transcriptional noise while preserving the responsiveness of active regulatory networks.

molecular biology↗

bioRxiv2025

HP1β and densely packed chromatin form separate microdomains in mouse ES cells, which are reconfigured upon exit from naive pluripotency

Heterochromatin proteins play a key role in establishing local chromatin structure to control the transcription of target genes. Here we uncover a surprising segregation between regions of high DNA- and high heterochromatin protein 1{beta} (HP1{beta})-density in mouse ES cells. DNA-low/HP1{beta}-high foci retain freely diffusing HP1{beta}, and form via condensation through a multitude of weak interactions on top of HP1{beta} that is bound stably to chromatin. DNA-high/HP1{beta}-low foci exclude freely diffusing HP1{beta} and display reduced chromatin mobility, suggesting a higher degree of chromatin self-interaction and a more repressive environment. Finally, the two types of environments are intertwined in DNA-high/HP1{beta}-high foci, where HP1{beta} maintains heterochromatin in a more compact yet dynamic chromatin state. During the exit from naive pluripotency HP1{beta} is lost from regions of high DNA density as cells transition through the formative state, which might facilitate the reconfiguration of genome structure accompanying a change in cell state that we observed previously. Subsequently, as cells enter primed pluripotency, canonical heterochromatin is established.

molecular biology↗

bioRxiv2025

Using phylogenetic relationships to assess conservation priorities for birds in India

In the midst of the ongoing biodiversity crisis, setting conservation priorities has moved beyond the conventional approaches. The need to incorporate phylogeny-based metrics that capture evolutionary rarity with extinction risk for prioritization of global conservation efforts has been widely recognized. Such metrics are even more important in megadiverse countries of the Global South, where conservation spending is limited despite high conservation value. Here, we reassess global avian threatened evolutionary history with an updated phylogeny, using the EDGE metric. The EDGE metric or score combines evolutionary distinctiveness of a species with its extinction risk. We focus on India to identify species and regions that represent high avian EDGE scores. We find that the Bengal Florican (Houbaropsis bengalensis) had the highest median EDGE score of 18.83 MY (millions of years). To identify spatial conservation priorities, we mapped avian EDGE scores at a 10 km x 10 km scale. Northeastern India is exceptional in its richness of evolutionary unique and threatened species. We also scored IBAs and PAs, finding that IBA, as well as PA, with the maximum EDGE score, was Intaki or Ntangki National Park in Nagaland, accumulating [~]250 MY of threatened evolutionary history in India. Habitats of the top 5% of EDGE species in India are currently not adequately protected. Our study offers a preliminary basis for a quantitatively informed and phylogeny-driven conservation prioritization approach for researchers, practitioners, and policymakers to safeguard threatened evolutionary history of birds in India.

evolutionary biology↗

bioRxiv2025

Parental exposure to wet and dry conditions shapes the viability and thermotolerance of eggs in Aedes aegypti

Aedes aegypti, a primary vector of dengue, Zika, and chikungunya, displays remarkable adaptability across ecological gradients. Central to this resilience is the egg stage, which must withstand fluctuating moisture and temperature conditions. Environmental transitions, particularly changes in moisture availability, significantly influence egg hatching success in mosquitoes. This study investigates how parental exposure to variable hydration conditions shapes key reproductive traits in Ae. aegypti. Using four environmental regimes, continuous wet, continuous dry, wet-to- dry, and dry-to-wet, we assessed egg output, hatching success, thermotolerance, and egg nutrient composition across three Ae. aegypti populations. Our results show that oviposition timing and egg production are significantly affected by the hydration environment experienced by the parental generation. While the wet, dry, and dry-to-wet groups exhibited a consistent oviposition peak beginning four days post-blood feeding, the wet-to-dry group showed delayed reproductive investment, with peak egg production occurring later. Egg output was highest under continuous wet conditions and significantly reduced in the dry and wet-to-dry treatments across all populations. Interestingly, the wet-to-dry group showed significantly higher egg-thermotolerance than any other group, and this pattern was consistent across all three populations under high- temperature stress conditions (41{degrees}C and 45{degrees}C). Nutritional composition showed an increased glycogen level in eggs when parents were exposed to wet conditions before blood feeding. By integrating physiological and ecological metrics such as hatching rates and thermal stress resilience, we demonstrate how parental environments shape subsequent egg performance, highlighting adaptive responses that enable Ae. aegypti persistence under increasing climate variability.

physiology↗

bioRxiv2025

Glycolysis-dependent Sulfur Metabolism Orchestrates Morphological Plasticity and Virulence in Fungi

Fungi exhibit remarkable morphological plasticity, which allows them to undergo reversible transitions between distinct cellular states in response to changes in their environment. This phenomenon, termed fungal morphogenesis, is critical for fungi to survive and colonize diverse ecological niches and establish infections in a variety of hosts. Despite significant advancements in the field with respect to understanding the gene regulatory networks that control these transitions, the metabolic determinants of fungal morphogenesis remain poorly characterized. In this study, we uncover a previously uncharacterized, conserved dependency between central carbon metabolism and de novo biosynthesis of sulfur-containing amino acids that is critical for fungal morphogenesis, in two key fungal species. Using a multidisciplinary approach, we demonstrate that glycolytic flux is crucial to drive fungal morphogenesis in a cAMP-independent manner and perturbation of this pathway leads to a significant downregulation in the expression of genes involved in de novo biosynthesis of sulfur-containing amino acids. Remarkably, exogenous supplementation of sulfur-containing amino acids robustly rescues the morphogenesis defect induced by the perturbation of glycolysis in both Saccharomyces cerevisiae and Candida albicans, underscoring the pivotal role of de novo biosynthesis of sulfur-containing amino acid as a downstream effector of morphogenesis. Furthermore, a C. albicans mutant lacking the glycolytic enzyme, phosphofructokinase-1 (Pfk1) exhibited significantly reduced survival within murine macrophages and attenuated virulence in a murine model of systemic candidiasis. Overall, our work elucidates a previously uncharacterized coupling between glycolysis and sulfur metabolism that is critical for driving fungal morphogenesis, contributing to our understanding of this conserved phenomenon.

microbiology↗

bioRxiv2025

Interpreting patterns of X chromosomal relative to autosomal diversity in aye-ayes(Daubentonia madagascariensis)

We here present high-quality, population-level sequencing data from the X chromosome of the highly-endangered aye-aye, Daubentonia madagascariensis. Using both polymorphism- and divergence-based inference approaches, we quantify fine-scale mutation and recombination rate maps, study the demographic and selective processes additionally shaping variation on the X chromosome, and compare these estimates to those recently inferred from the autosomes in this species. Results suggest that an equal sex ratio is most consistent with observed patterns of variation, and that no sex-specific demographic patterns are needed to fit the empirical site frequency spectrum. Further, reduced rates of recombination were observed relative to the autosomes as would be expected, whereas mutation rates were inferred to be similar. Utilizing the estimated population history together with the mutation and recombination rate maps, we evaluated evidence for both recent and recurrent selective sweeps as well as balancing selection across the X chromosome, finding no significant evidence supporting the action of these episodic processes. Overall, these analyses provide new insights into the evolution of the X chromosome in this species, which represents one of the earliest splits in the primate clade.

evolutionary biology↗

bioRxiv2025

MitoEdit: a pipeline for optimizing mtDNA base editing and predicting bystander effects

Short Structured AbstractO_ST_ABSMotivationC_ST_ABSHuman mitochondrial DNA (mtDNA) mutations are causally implicated in maternally inherited mitochondrial respiratory disorders; however, the role of somatic mtDNA mutations in both late-onset chronic diseases and cancer remains less clear. Although recent advances in mtDNA base editing technology have the potential to model and characterize many of these mutations, current editing approaches are complicated by the potential for multiple unintentional edits (bystanders) that are only identifiable through empirical trial and error, thereby sacrificing valuable time and effort towards suboptimal construct development. ResultsWe developed MitoEdit, a novel tool that incorporates empirical base editor patterns to facilitate identification of optimal target windows and potential bystander edits. MitoEdit allows users to input DNA sequences in a text-based format, specifying the target base position and its desired modification. The program generates a list of candidate target windows with a predicted number of bystander edits and their functional impact, along with flanking nucleotide sequences designed to bind TALE (transcription activator-like effectors) array proteins. In silico evaluations indicate that MitoEdit can predict the majority of bystander edits, thereby reducing the number of constructs that need to be tested empirically. To the best of our knowledge, MitoEdit is the first tool to automate prediction of base edits. Availability and implementationMitoEdit is freely available at Kundu Lab GitHub (https://github.com/Kundu-Lab/mitoedit). ContactCorresponding email: Gang.Wu@stjude.org; Mondira.Kundu@stjude.org Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗