Biology subjects

Pal, A.

Publications and source records attributed to Pal, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Chemogenetic excitation and play promote functional recovery in juvenile spinal cord injury

Functional recovery after spinal cord injury depends on whether reorganizing descending circuits form adaptive, task-specific relays rather than maladaptive ones. The corticospinal tract undergoes competitive, activity-dependent refinement during a defined juvenile window, so the timing and polarity of cortical activity may dictate whether injured circuits rewire usefully. Whether biasing cortical activity during this window can steer reorganization toward recovery, and whether naturalistic rehabilitation supplies the activity such steering requires, remain unknown. In juvenile rats we delivered excitatory or inhibitory chemogenetic receptors, or a control vector, to the forelimb motor cortex at postnatal day 5, induced a right cervical hemisection at postnatal day 14, and gave oral clozapine-N-oxide during nightly rough-and-tumble play from postnatal day 20 to 50. Play, the rehabilitation common to all groups, did not differ between them, isolating cortical-activity polarity as the manipulated variable. Outcomes spanned forelimb dexterity, reaching kinematics, cortical output by intracortical microstimulation, descending architecture by intersectional viral tracing, and frequency-dependent depression of the Hoffmann reflex. In untreated injured animals, cortical output re-lateralized maladaptively toward the intact forelimb, driving the ipsilateral (intact) limb in 11 of 15 evoked responses and 3 of 5 animals. Excitation preserved selective drive to the impaired forelimb (38 of 39 responses; concordant-site proportion Kruskal-Wallis H = 9.08, exact P = 0.0031), and pure ipsilateral re-lateralization was absent from all nine treated animals (3 of 5 control versus 0 of 9 treated; Fisher's exact P = 0.027). Across behavioural, kinematic, and anatomical measures a consistent excitatory > control > inhibitory gradient emerged. Excitation enhanced wrist elevation and forward extension during reaching, restored frequency-dependent depression of the Hoffmann reflex, and selectively recruited three parallel lesion-bypassing relays: interhemispheric cortico-cortical-spinal, cortico-reticulo-spinal, and cortico-propriospinal (ipsilesional cortical relay neurons F(2,14) = 56.96, P < 0.0001). Inhibition yielded the weakest behavioural recovery and least relay recruitment, and did not restore contralesional cortical drive. Cortical-activity polarity during a juvenile window thus acts as a developmental switch governing whether descending reorganization is adaptive or maladaptive. Guided excitation, paired with behaviourally meaningful activity, reshapes diffuse sprouting into structured, lesion-bypassing relays and corrects the spontaneous re-lateralization that otherwise misdirects recovery. These findings provide a translational rationale for activity-paired neuromodulation in paediatric spinal cord injury.

neuroscience↗

bioRxiv2026

Coarse composition suffices: tabular in-context learning for multi-activity antimicrobial peptide profiling

Antimicrobial peptides (AMPs) often act against multiple pathogen classes, making multi-label activity prediction a more realistic screening target than binary antimicrobial classification. The ESCAPE benchmark formalizes this setting, but leading approaches typically rely on multimodal, structure-conditioned deep models that are costly to train and tune. We show that a simple, sequence-only pipeline can match and surpass these methods by combining 330 interpretable sequence descriptors with TabPFN, a tabular foundation model that performs in-context prediction in a single forward pass without gradient-based training or hyperparameter search. On ESCAPE (82,359 peptides; five labels), a label-powerset TabPFN model achieves mAP-5=77.8%, improving on the previously best reported 72.1%. A probabilistic classifier chain is the first method to match or exceed the best published average precision on each of the five labels simultaneously. The gains persist under the prior state-of-the-art single-fold training protocol, indicating they are not a training-set-size artefact, and are largest for remote homologues (+11.2 points below 30% sequence identity). Ablations further show that predicted structure is unnecessary at inference and that performance is not driven by any single descriptor family: ten global physicochemical scalars recover 91% of full-feature performance. Finally, explicitly modelling label dependence yields targeted benefits for scarce activities and supports ranking which activity to assay next from partial positive evidence.

bioinformatics↗

bioRxiv2026

A Mammalian High-Throughput Screen for AI-Designed Peptide-Guided Protein Degraders

Targeted protein degradation (TPD) offers a route to eliminate disease-driving proteins that remain inaccessible to conventional inhibitors. However, degrader discovery remains low-throughput, labor-intensive, and dependent on randomized libraries or non-human display systems, limiting functional selection in mammalian cells. Here, we present a high-throughput, human cell-based platform for screening peptide-guided ubiquibodies (uAbs). These genetically encodable, doxycycline-inducible degraders fuse peptide guides generated by protein language models to the CHIP{Delta}TPR E3 ligase domain, creating a modular, CRISPR-like system for programmable TPD. For each target, we introduce a pooled uAb library into the corresponding fluorescent reporter cell line, isolate cells with reduced target abundance by FACS, and recover enriched peptide guides by sequencing. For {beta}-catenin, enriched uAbs reduced endogenous {beta}-catenin abundance and Wnt signaling in DLD1 cells. GFAP-directed uAbs reduced endogenous GFAP abundance and cell viability in U251 glioblastoma cells, while EWS::FLI1-directed uAbs reduced fusion oncoprotein abundance, suppressed EWSAT1 expression, and increased apoptosis in Ewing sarcoma models. Finally, a screen using endogenously tagged GATA2 further identified uAbs that reduced GATA2 under native genomic regulation. Overall, our platform connects generative peptide design to functional mammalian selection and establishes a scalable strategy for CRISPR-like proteome perturbation.

synthetic biology↗

bioRxiv2026

Functional characterization of a cytosolic malic enzyme crucial for pyridine nucleotide homeostasis, redox balance, and virulence in Leishmania major

Malic enzymes (MEs) occupy a central node in metabolism, by catalyzing the reversible oxidative decarboxylation of malate to pyruvate, thereby contributing to maintenance of NADPH homeostasis. Leishmania spp. are known to encode two ME isoforms, however only one from Leishmania major has been functionally characterised till date to be a mitochondrial enzyme, playing critical role in gluconeogenesis. Here, we cloned and functionally characterized the second isoform, LmME2. Colocalization and subcellular fractionation analysis established that LmME2 localizes to the cytosol. Kinetic analyses of purified LmME2 revealed comparable rates of malate decarboxylation and pyruvate carboxylation, however, pyruvate carboxylation predominated in parasite cell lysates, indicating that the directionality of the reaction is metabolically regulated in cellular environment. Consistent with this, we identified oxaloacetate, ATP and fumarate as allosteric modulators of LmME2 activity. To dissect its physiological role, we generated CRISPR-Cas9-mediated LmME2 knockout parasites (LmME2-/-). Interestingly, LmME2 deletion did not alter NADPH levels but depleted both NADP+ and NAD+ pools, with reduction in NAD+ being more pronounced. This disruption of pyridine nucleotide homeostasis resulted in elevated intracellular ROS levels. Furthermore, inhibition of the pentose phosphate pathway, the alternative cytosolic source of NADPH, severely impaired the growth of LmME2-/- strain, highlighting the role of LmME2 in maintaining parasite fitness. These metabolic defects translated into markedly diminished intracellular survival of LmME2-/- parasites and its attenuated virulence in mice. Collectively, our findings identify LmME2 as the first functionally characterized cytosolic malic enzyme in Leishmania and establish it as a redox-associated virulence factor. These results further highlight LmME2 as a promising antileishmanial drug target.

cell biology↗

bioRxiv2026

Cell-sized droplet interfaces reorganize protein secondary structures through confinement-enhanced membrane interactions

Cell membranes can regulate protein organization, yet it remains unclear whether membrane-associated structural alterations primarily reflect membrane-induced destabilization or the reorganization of proteins that are already destabilized. How such membrane effects are amplified under cellular-scale confinement also remains poorly understood. Here, we investigate these questions using cell-sized lipid-coated droplets, where the high surface-area-to-volume ratio enhances the contribution of membrane interfaces. Native serum albumin and lysozyme showed little structural reorganization, whereas their thermally denatured forms exhibited pronounced $\beta$-sheet formation within small droplets when membrane interactions were attractive. For denatured albumin, $\beta$-sheet-rich organization increased progressively with protein--membrane attraction, while denatured lysozyme selectively formed a localized $\beta$-sheet-rich shell at a complementary anionic membrane. Circular dichroism spectroscopy independently supported the confinement-enhanced increase in $\beta$-sheet content of denatured albumin. Fluorescence recovery measurements further revealed strong interfacial arrest in both systems. Together, these results show that membrane interactions can promote structural reorganization of already destabilized proteins through electrostatic recruitment, while cell-sized confinement strongly amplifies the resulting membrane-dependent structural response. Our findings establish cell-sized droplet interfaces as a materials platform for spatially controlling protein structural organization through the interplay of interfacial chemistry and confinement.

biophysics↗

bioRxiv2026

A mitochondrial-immune axis drives the transcriptomic transition from brain aging to Alzheimer's disease

Aging is the primary risk factor for Alzheimers disease (AD), yet the molecular transitions linking normal brain aging to neurodegeneration remain poorly defined. Here, we performed integrative bulk transcriptomic analyses across a multi-region mouse aging atlas, a human aging-to-AD cohort, and an independent human AD validation dataset. Aging is associated with a progressive, region-specific increase in transcriptional perturbation, with the entorhinal cortex and choroid plexus showing the most pronounced age-associated remodeling. Females develop more extensive late-stage remodeling than males, characterized by stronger immune activation and greater suppression of mitochondrial metabolic pathways. Across cohorts, aging drives a coordinated shift toward immune activation and suppression of oxidative phosphorylation and respiratory-chain programs that is amplified in AD. Aged brains occupy an intermediate molecular state between young and AD conditions, supporting a continuum model. Together, our findings define a sex-modulated mitochondrial-immune axis linking normal aging to AD and highlight early immune-metabolic changes as potential intervention targets.

bioinformatics↗

bioRxiv2026

PFAS triggers a SpoT-associated metabolic switch that promotes persister-like phenotype in Salmonella Typhi

Per- and polyfluoroalkyl substances (PFAS) are new pollutants in the environment whose effects on bacterias physiology is not well understood. In this study, we show that exposure to PFAS causes membrane depolarization in Salmonella enterica serovar Typhi. This works as a metabolic uncoupler that breaks down proton motive force without immediately killing the cells. This disturbance results in a significant elevation of intracellular NADH and NAD levels while preserving redox equilibrium, signifying an augmented metabolic flux. At the same time, we see that {beta}-oxidation pathways are turned on, which suggests that the cells are shifting toward breaking down fats to make up for the lack of energy. Even though there are more reducing equivalents, ATP levels go down, which is what happens when respiration is uncoupled. This puts the cells in a state of "pseudo-starvation." This metabolic stress triggers the SpoT-dependent stringent response, leading to the accumulation of (p)ppGpp. Genetic analysis employing {Delta}relA and {Delta}relA{Delta}spoT mutants confirm that SpoT is necessary for this adaptive response. Functionally, PFAS-treated populations show an enhanced proportion of persister-like cells, which connects exposure to environmental pollutant in the environment to antibiotic tolerance. Our findings reveal a previously unidentified mechanism by which PFAS alters bacterial metabolism and stress responses, facilitating persistence through membrane depolarization, metabolic reconfiguration, and stringent response activation. This study underscores the potential influence of environmental pollutants on bacterial survival mechanisms and antibiotic resistance.

microbiology↗

bioRxiv2026

Development of gemcitabine-modified miR-15a as a novel, multimodal treatment strategy to overcome 5-FU and oxaliplatin resistance in colorectal cancer

BackgroundResistance to 5-fluorouracil (5-FU)-based chemotherapy is a major clinical obstacle in colorectal cancer (CRC), highlighting the urgent need to overcome established resistance mechanisms. MicroRNA-based therapeutics have emerged as compelling candidates in this context, given their inherently pleiotropic mode of action; however, their clinical translation remains hindered by poor stability and suboptimal delivery. MethodsTo address these limitations, Gem-miR-15a, a unique gemcitabine-modified tumor-suppressor microRNA-15a was designed to synergistically integrate the tumor-suppressive activity of miR-15a with the chemotherapeutic potency of gemcitabine into a single molecular entity. Therapeutic efficacy of Gem-miR-15a was evaluated across a spectrum of preclinical models, including parental and drug-resistant CRC cell lines, 3D tumor spheroids, patient-derived organoids and in vivo metastatic models. Cell viability, apoptosis and cell cycle analyses were performed, along with RNA sequencing and protein validation. Statistical analyses were conducted using Students t-test or two-way ANOVA with mixed effects, and data were presented as mean {+/-} SD. ResultsGem-miR-15a exhibited potent anti-proliferative activity with IC50 values in the low nanomolar range, achieving [~]100-5000-fold greater potency relative to 5-FU and oxaliplatin. Importantly, it retained efficacy in both 5-FU- and oxaliplatin-resistant CRC models, effectively overcoming acquired chemoresistance. Mechanistically, Gem-miR-15a induced S-phase cell cycle arrest, eliminated the G2-phase cell population, and triggered apoptosis, accompanied by suppression of key oncogenic targets including WEE1, CHK1, YAP1 and BMI1. RNA-seq analysis further demonstrated modulation of pathways such as p53 signaling and reversal of resistance-associated gene expression, that were corroborated at the protein level. In vivo, Gem-miR-15a significantly reduced tumor growth at a dose [~]12-fold lower than gemcitabine, with no observable toxicity. ConclusionGem-miR-15a represents a potent, multi-targeted therapeutic strategy capable of overcoming chemoresistance in CRC. Its enhanced stability, effective delivery and robust efficacy across resistant models and a favorable safety profile highlight its strong potential for clinical translation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC="FIGDIR/small/720825v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@c20034org.highwire.dtl.DTLVardef@9b8478org.highwire.dtl.DTLVardef@161f1dorg.highwire.dtl.DTLVardef@54d826_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2026

Developing a Multimodal miR-15a Mimic to Overcome PARP Inhibitor Resistance in Epithelial Ovarian Cancer

Epithelial ovarian cancer (EOC) is characterized by high relapse rates and the development of drug resistance, driven by adaptive DNA repair and survival pathways. Here, we develop a multimodal, chemically engineered miRNA therapeutic, MTX-5-FU-Gem-miR-15a, that integrates tumor-suppressive miR-15a activity with chemotherapeutic modifications and tumor-targeting capability. This modified miRNA exhibits potent nanomolar activity across diverse EOC models, including PARP inhibitor-resistant cells, without requiring delivery vehicles. Mechanistically, MTX-5-FU-Gem-miR-15a induces replication stress while suppressing G2/M checkpoint regulators (WEE1 and CHK1), resulting in genomic instability and apoptotic cell death. Transcriptomic and protein-level analyses revealed coordinated suppression of resistance-associated and oncogenic signaling pathways, alongside activation of DNA damage coupled with checkpoint abrogation and potential innate immune response. MTX-5-FU-Gem-miR-15a also demonstrates strong synergy with olaparib and robust antitumor efficacy in vivo. These findings establish a multimodal miRNA-based therapeutic strategy that targets replication stress and checkpoint dependency to overcome PARPi resistance in ovarian cancer.

cancer biology↗

bioRxiv2026

Broad distributions of sliding times are fingerprints of efficient target search on DNA

We investigate the target search process by proteins locating specific target sites along DNA - a phenomenon fundamental to biological functions such as gene regulation, transcription, replication, recombination, and gene-editing technologies. This process proceeds through a repetitive sequence of stochastic motions: consisting of one-dimensional (1D) sliding along the DNA contour interspersed with detachment and three-dimensional (3D) excursions in the bulk, and then reattachment to a random location on DNA. Recognizing this sequence of random events as analogous to the resetting processes widely studied in statistical physics, we employ a first-passage-renewal framework and derive general expressions for both the mean and fluctuations of the total search time. Our results are completely generic and do not depend on the detailed microscopic dynamics of either the 1D or 3D phases. Quite interestingly, we find that intermittent detachment can not only accelerate the mean search but can also regulate fluctuations around it. Our analysis reveals a universal fluctuation inequality that links the variability and mean of the sliding time to the mean excursion time, thereby identifying the fundamental conditions under which target search process becomes efficient. Notably, we find that broad distributions of sliding times emerge as a universal characteristic for optimal search efficiency--a feature emanating from the slow dynamics along the DNA. Using the facilitated diffusion mechanism as a representative example, we validate the generality of our results. These findings provide a unified theoretical framework connecting stochastic search, resetting dynamics, and biological efficiency, while also highlighting the crucial role of DNA structure such as its contour length in modulating search performance.

biophysics↗

bioRxiv2025

Vitamin D differentially modulates effector and regulatory T-cell migration across the blood-brain barrier

Multiple sclerosis (MS) is an inflammatory disease of the CNS influenced by a combination of genetic predisposition and environmental factors. Vitamin D (VitD) deficiency is considered a major risk factor for MS. While VitD is associated with immunomodulatory roles, the exact mechanisms by which VitD protects from disease are still largely unknown. CD4 T cells play a key role in MS pathogenesis with autoimmune effector T cells (Teff) infiltrating the CNS across the blood-brain barrier (BBB) and regulatory T cells (Treg) displaying impaired functions. Here we show that treatment of human CD4 T cells with the active form of VitD (1,25-Dihydroxyvitamin D3; 1,25(OH)2D3) decreased cell-surface expression of 4{beta}1- and L{beta}2-integrins on Teff but not Treg and reduced Teff adhesion to their endothelial ligands VCAM-1 and ICAM-1. By employing live cell imaging, we observed that VitD treatment reduced arrest of Teff but not Treg to the BBB as well as ICAM-1 and VCAM-1 under physiological flow in vitro and differentially affected post-arrest behaviour of Teff versus Treg on the BBB under physiological flow. Furthermore, VitD treatment favoured the migration of Treg over Teff across the BBB under static and flow conditions in vitro. In vivo live cell imaging showed that VitD reduced T cell arrest on the inflamed BBB during autoimmune neuroinflammation. Finally, VitD also reduced expression of integrins mediating CNS homing on pathogenic CD4 T cells isolated from the CSF of persons with MS (PwMS). As VitD treatment did not alter barrier properties or adhesion molecule profile of our BBB model we propose a beneficial effect of VitD supplementation in PwMS by reducing CNS trafficking of pro-inflammatory T cells while leaving CNS entry of Treg unaffected.

immunology↗

bioRxiv2025

Metagenomic Profiling of Bacterial (16S) and Fungal (ITS) Communities on D'Anjou Pears during Long-Term Controlled Atmosphere Storage

DAnjou pears are routinely stored for up to nine months under controlled atmosphere (CA) conditions to meet market demands. While this practice maintains fruit quality, limited information exists on pears natural microbiota throughout storage. The objective of this study was to describe fungal and bacterial composition on marketable and unmarketable conventional, whole, intact pears under two storage practices (bulk vs wrapped) at 3, 6, and 9 months in long-term CA cold storage. Storage practices had a significant effect on the composition and succession of both fungal and bacterial communities. Overall, fungal communities exhibited lower estimated Chao1 alpha diversity (mean 18.3) compared to bacterial communities (mean 166.4). No significant differences in Chao1 index were found between the bacterial and fungal communities on marketable or unmarketable pears. Trends in Chao1 indices of fungal and bacterial communities peaked at mid-storage and declined by 9 months, with wrapped pears showing parallel trends and bulk pears exhibiting a sharper late-stage reduction. No distinct clusters could be found for 3- and 6-month fungal communities, irrespective of marketability or being bulk or wrapped. The principal coordinate analysis of the bacterial communities showed tight clustering by time point for the individually wrapped pears, irrespective of their marketability. Bacterial communities included genera common in food-processing and plant environments, such as Pseudomonas and Acinetobacter. Fungal communities shifted over time, with spoilage-associated genera like Aureobasidium, Penicillium, Botrytis, and Mucor present at different storage stages. SignificanceThis study highlights the influence of storage duration and packaging on microbial succession, establishing initial benchmarks of pear surface microbiomes. The observed lack of significant differences in microbial diversity between marketable and unmarketable pears suggests that these baseline community profiles can serve as critical reference points for identifying other influential factors. Variables such as handling practices may exert a more direct effect on microbial dynamics and, consequently, product quality. Establishing these baselines is essential because they provide a foundation for detecting deviations linked to spoilage or safety risks. Moreover, understanding these patterns can guide the development of targeted microbial control strategies in postharvest systems, enabling interventions that maintain fruit quality, reduce losses, and improve food safety throughout the supply chain.

microbiology↗

bioRxiv2025

Cisplatin and Copper Induce Distinct Endocytic Pathways of Copper Transporter-1 and Elicits Unique Response on Copper Homeostasis Proteins

Cisplatin (CDDP), a widely used chemotherapy drug is imported in mammalian cells by copper transporter CTR1. We observed that CDDP cytotoxicity is significantly reduced in CTR1 deficient yeast and in copper loaded mammalian cells indicating its shared uptake pathway with copper. CTR1 resides on the plasma membrane undergoes endocytosis during CDDP import as in copper, involving its amino-terminal His-Met-motifs and the conserved 150MXXM154 pore motif. Unlike Copper, CDDP directs endocytosed CTR1 toward lysosomes rather than being sorted through VPS35-positive endosome. CDDP enhances lysosomal acidity and cathepsin activity. Furthermore, CDDP selectively downregulate cuproproteins, CCS and SOD1, disrupting copper homeostasis. This study highlights the unique aspects of copper versus CDDP uptake by CTR1 and its differential downstream ramification on lysosomes and cuproproteins.

cell biology↗

bioRxiv2025

Association of miR-181a-5p with Lantana camara leaf extract-mediated inhibition of proliferation, survival, and migration in luminal A-type MCF-7 cells and triple-negative type MDA-MB-231 cells

Ethnopharmacological relevanceBreast cancer has a high mortality with increasing chemoresistance and recurrence. Lantana camara has diverse medicinal properties, including anti-cancer potential; however, its role in breast cancer is not well-explored. Aim of the studyThe study aims to elucidate the role of Lantana camara leaf extract in miR-181a-5p-mediated control of proliferation, survival, and migration of breast cancer cells. Material and methodsReal-time PCR was employed for RNA expression studies. Bioinformatic tools were used for identifying miR-181a-5p target mRNAs and seed regions in the 3 prime untranslated region of target mRNAs. miR-181a-5p was overexpressed in cells using transfection method. Flow cytometry was employed for cell cycle and apoptosis assays. Scratch assay was performed to study cell migration. The 3 prime untranslated region of CDKN3 was cloned, and site-directed mutagenesis was employed to mutate miR-181a-5p seed region. Western blot analysis was employed for a reporter assay. ResultsL. camara leaf extract upregulated the expression of miR-181a-5p with concomitant decrease in mRNAs of BCL-2, MCL-1, and CDKN3 in breast cancer cells. Overexpression of miR-181a-5p induced cell death in MCF-7 and MDA-MB-231 cells, and cell death increased in the presence of leaf extract. miR-181a impeded migration in both cell lines in the presence of the extract. Reporter assay confirmed the interaction of miR-181a-5p with 3 prime untranslated region of the CDKN3 mRNA. ConclusionOur study suggests that the extract may play an important role in regulating miR-181a-5p in MCF-7 and MDA-MB-231 cells, and may have important therapeutic potential for breast cancer therapy.

cancer biology↗

bioRxiv2025

Mutations in antimicrobial peptides differently affect sleep and plasticity

Molecules implicated in host defense can, independent of their roles as immune mediators, regulate sleep. In mammals, cytokines such as Tumor Necrosis Factor (TNF ) and Interleukin 1{beta} (IL1{beta}) promote sleep. In Drosophila, infection stimulates the systemic release of a battery of anti-microbial peptides (AMPs). These fly immune effectors have been understudied as sleep modulators. We obtained mutants in different AMPs and characterized their functions in sleep and sleep dependent outputs. AMP mutants sleep less with a longer sleep latency, and lowered arousal thresholds. Group C mutant flies, doubly mutant for the anti-fungal peptides Metchinikowin (Mtk) and Drosomycin (Drs), showed the greatest impairments. These Group C mutants also showed an exaggerated sleep rebound. Sleep rebound was unaltered in other mutants. Different sets of AMP mutants exhibited specific disruptions in socialization and rocking induced sleep. These data are a detailed characterization of sleep regulation in AMP mutants. We also evaluated sleep functions. Group C mutants uniquely exhibited normal learning and memory, and lower synapse abundance, despite sleeping the least. Group C mutants are thus able to carry out some sleep functions without sleeping very much. Glial knockdown of Metchnikowin and Drosomycin mimicked the sleep phenotypes of the null mutants, these genes thus act from glia. Sleep and memory defects in AMP mutants was reversible - enhancing sleep of Bomanin mutants pharmacologically or behaviorally improved learning and memory. Together, these data suggest that AMPs are potent sleep modulators and that different classes of AMPs differently affect sleep and sleep dependent outcomes.

neuroscience↗

bioRxiv2025

Lantana camara leaf extract-mediated suppression of DNA methyltransferase 1 promotes G0/G1 cell cycle arrest and apoptosis, and impedes migration in MDA-MB-231 triple-negative breast cancer cells

BackgroundTriple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with limited therapeutic options and poor prognosis. DNA methyltransferase 1 (DNMT1) maintains aberrant silencing of tumor suppressor genes, contributing to cancer progression. Our previous work demonstrated that Lantana camara leaf extract induces G0/G1 arrest and apoptosis, while inhibiting migration in MDA-MB-231 TNBC cells (Pal et al., 2024). PurposeThis study investigated the role of DNMT1 in mediating the anticancer effects of Lantana camara extract. Study DesignAn in vitro experimental study was performed using MDA-MB-231 TNBC cells. MethodsCells were treated with the extract, and the expression of DNMT1 was analyzed at the mRNA and protein levels. Expression of tumor suppressor genes was assessed at mRNA level. Functional assays were conducted following DNMT1 overexpression to examine its impact on extract-induced effects. Expression of methyl-CpG binding domain protein 2 (MBD2), histone deacetylase 1 (HDAC1), and histone deacetylase 2 (HDAC2) was evaluated at the mRNA level. ResultsThe extract significantly downregulated DNMT1, resulting in the reactivation of multiple tumor suppressor genes. Overexpression of DNMT1 counteracted the extract-induced reduction in cell viability, reduced G0/G1 arrest, attenuated apoptosis, and enhanced migratory capacity, while suppressing the mRNA expression of tumor suppressor genes. Additionally, the extract downregulated the mRNA expression of MBD2, HDAC1, and HDAC2, suggesting broader modulation of epigenetic regulators. ConclusionSuppression of DNMT1 is a central mechanism underlying the anticancer activity of Lantana camara extract. These findings highlight its potential as a natural epigenetic modulator and a promising therapeutic candidate for TNBC.

cancer biology↗

bioRxiv2025

TIP60, a key lysine acetyltransferase, acts as a wound-induced factor essential for efficient wound response in planaria

Chromatin modifiers are essential regulators of gene expression, DNA repair, replication, and cell division. Among them, histone acetyltransferases (HATs) such as TIP60 play a central role in modulating chromatin dynamics through acetylation of histone and non-histone proteins. TIP60, a member of the MYST family of HATs, is known to regulate key cellular processes, including transcriptional activation, DNA damage response, and cell cycle progression. Although TIP60s role in stem cell maintenance and differentiation is well established, its function in stem cell-driven regeneration has remained unexplored. In this study, we characterize the role of the TIP60 homolog, SMED-TIP60, in the planarian Schmidtea mediterranea, a model organism renowned for its regenerative capacity. Biochemical assays confirmed SMED-TIP60s acetyltransferase and auto-acetylation activity. RNAi-mediated knockdown of Smed-tip60 resulted in severe defects in tissue homeostasis, survival, and regeneration, including impaired blastema formation and failure to regenerate tissues. In situ hybridization and immunofluorescence analyses revealed a marked reduction in stem cell populations and mitotic activity. Western blotting showed a peak in SMED-TIP60 expression at 5 days post-amputation, suggesting a role during regeneration. RNA-seq analysis revealed widespread dysregulation of gene expression at both anterior and posterior wounds, correlating with increased TIP60 expression post-injury. Notably, wound-response gene expression was aberrant in Smed-tip60 RNAi animals, indicating TIP60s essential role in initiating wound responses and resetting positional cues. Together, these findings establish TIP60 as a critical regulator of stem cell-mediated regeneration and wound healing in planarians.

cell biology↗

bioRxiv2025

Copy number variations in mitochondrial DNA has a potent role in parasitic immunity against Haemonchus contortus-A novel report

Mitochondria is a cellular organelle responsible for a variety of function, apart from energy production through oxidative phosphorylation, TCA cycle, apoptosis, plays a major role in iron and calcium metabolism and immune functions against pathogens (bacterial, viral or parasitic). Unlike nucleus, mitochondria exist in multiple copies, with many copies of mitochondrial DNA. A metabolically active cell possess about 103 and 104 copies of the mitochondrial genome. Lowered mtDNA copy number leads to disorders or disease, in a similar way as mutation in mtDNA causes a wide range of disease or disorders. In this current article, we estimated mtDNA copy number through QPCR analysis of cytochrome B gene and revealed that healthy individuals have better mtDNA copy number compared to that of the infected ones under natural challenge in sheep model against the parasite Haemonchus contortus infection. We diagnosed the infected animals for H. contortus primarily with symptoms, followed by Faecal egg count and final confirmation through molecular diagnosis. We had characterized the cytochrome B gene from abomasum(stomach) of sheep, which is the site of predilection of this parasite. In our lab, earlier we have documented certain immune response nuclear genes to have antiparasitic role. We had reported the mutations in cytochrome B leading to debility and disease in sheep. Quantitative expression profile for cytochrome B is an indication of the copy number of mitochondrial genes and we observed significantly better expression profile of cytochrome B in healthy sheep in comparison to infected one. Thus, mitochondrial copy number is directly associated with antiparasitic immunity, first time reported.

genomics↗