Biology subjects

Shukla, S.

Publications and source records attributed to Shukla, S..

At least 19 recordsLinked to original sources

bioRxiv2026

A CTCF-LDHB axis converts nuclear lactate availability into an H3K18 acylation switch that directs alternative splicing in hypoxic breast cancer

Lactate accumulating in hypoxic tumours lactylates histones, coupling metabolic state to chromatin. Why it differs between tumours of comparable glycolytic rate has remained unresolved. Here we show that nuclear, rather than total intracellular, lactate availability determines histone H3K18 lactylation in breast cancer, and that CCCTC-binding factor (CTCF) and lactate dehydrogenase B (LDHB) jointly set it. CTCF sustains glycolytic gene expression under hypoxia and drives LDHB in triple-negative breast cancer (TNBC), whereas a CTCF-ER complex represses LDHB in non-TNBC. LDHB consumes lactate favouring H3K18 acetylation; where LDHB is low, CTCF-dependent MCT1 delivers lactate into the nucleus and sustains lactylation. At a CTCF site downstream of TACC3 exon 3, an invariant polymerase II pause couples kinetic and adaptor control of splicing, with the mark deciding the outcome: H3K18la recruits SMARCA4 and hnRNPA1 to skip the exon, generating an isoform that drives EMT, whereas H3K18ac recruits TRIM33 and SRSF10 to include it, generating one that confers stemness. Inhibiting LDHB restores exon skipping and suppresses tumour growth in vivo. Nuclear lactate availability therefore acts as a metabolic switch that converts hypoxic stress into subtype-specific splicing decisions and identifies LDHB as a tractable target in TNBC.

cancer biology↗

bioRxiv2026

NeuroGraphBench: Interacting with Drosophila Connectomes at Scale for Exploring the Functional Logic of Neural Circuits

Drosophila connectomic datasets provide increasingly comprehensive maps of neuronal morphology and synaptic connectivity, offering an unprecedented opportunity to explore the structural organization of its neural circuits. This calls for designing automated tools to interact with connectomic datasets at scale for efficiently exploring structural features embedded in the vast amount of data. Yet the central challenge remains the understanding of the functional logic of neural circuits. In order to understand how elements of the functional logic may emerge from this structural organization, it is critical to (i) characterize the objects in the natural environment in which brain circuits operate, and (ii) formulate how brain circuits represent and process the defined objects in the natural environment. To develop and demonstrate a methodology for these requirements, we focus on the Drosophila looming-evoked escape pathway. We modeled the trajectory of looming objects that are on a collision course (direct-hits) or pass-by the fly (near-misses): their projected images on the retina can be characterized by the solid angle (angular size) and elevation. We then analyzed the pathway's morphology across the OpticLobe, Hemibrain, and FlyWire connectome datasets. By abstracting their sub-neuronal structure and retinotopic organization, we constructed an executable circuit model that maps each structural element to a processing block. We demonstrate that this model separates direct hits from near misses well before the angular size could tell them apart. To accelerate the connectomic analysis step, we developed a Python toolset with an agentic, code-free workspace interface called NeuroGraphBench (NGB). NGB provides four composable morphology-analysis primitives and an AI agent that composes them to interactively respond to natural-language queries aided by visualization on an interactive 3D canvas. Thus, NGB automates tedious and repetitive tasks to enable faster and scalable connectomic exploration, keeping human reasoning, instead of writing code, at the center of an open-ended research inquiry.

neuroscience↗

bioRxiv2026

Sanjeevani: A manually curated anti-cancerous phytochemical database integrated with downstream analysis tools.

BackgroundCancer continues to pose a massive global health burden. While plant-derived phytochemicals offer promising therapeutic leads, existing natural product databases often lack cancer specificity, dataset downloadability, and integrated screening tools. MethodsWe developed Sanjeevani, an integrative web platform cataloguing 4,823 curated anticancer phytochemicals. Using a balanced dataset of 9,646 molecules, we trained Support Vector Machine (SVM), Random Forest, and K-Nearest Neighbours classifiers using a hybrid feature representation of RDKit descriptors and 2048-bit ECFP4 fingerprints. The platform also integrates AutoDock Vina for web-based molecular docking for binding affinity, poses prediction and ADMET-AI for pharmacokinetics estimation. ResultsThe SVM model demonstrated the strongest predictive capability, achieving a top test accuracy of 0.966 and a ROC-AUC of 0.992. Benchmarking across five docking tools confirmed that AutoDock Vina successfully balanced computational automation with literature-consistent binding affinity replication. The final architecture provides rapid interactive 2D/3D visualizations integrated with downstream analysis tools. ConclusionSanjeevani provides an open-access, one-stop pipeline that bridges the gap between raw natural product data and actionable computational screening, accelerating natural product-based oncology drug discovery. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/732344v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@77183borg.highwire.dtl.DTLVardef@d7e465org.highwire.dtl.DTLVardef@1d3dfd7org.highwire.dtl.DTLVardef@10cc94d_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2026

Projections from subfornical organ to infralimbic cortex modulate carbon dioxide associated fear

Most of our mechanistic understanding of threat responding and defensive fear behaviors is based on exposure to aversive stimuli in the environment. However, unpleasant, within-the body interoceptive signals can also regulate threat and emotion although underlying cell-circuit mechanisms are not well understood. Abnormal interoceptive sensitivity is associated with fear-associated psychiatric conditions such as panic disorder and PTSD. The ventromedial infralimbic (IL) subdivision of the prefrontal cortex plays a key role in threat appraisal and fear, however, IL engagement in interoceptive threat response and contributory afferent mechanisms are not known. Here, using an interoceptive clinical panicogen, carbon dioxide (CO2) inhalation, we report IL-mediated regulation of fear in mice via afferents from the subfornical organ (SFO), a key viscero-humoral circumventricular organ lacking a traditional blood brain barrier. Chemogenetic inhibition of SFO-to-IL (but not SFO-to-BNST) projections regulated defensive behaviors during CO2 inhalation and associative contextual fear. Notably, the SFO-IL circuit also modulated delayed CO2 effects on contextual fear conditioning-extinction, but not startle, neuroendocrine response or motivated behaviors. We also established more specifically that SFO angiotensin II receptor type-1 (AT-1R)+ve neuronal afferents to the IL regulate CO2-associated fear and long-term deficits in contextual fear extinction. CO2 inhalation reduced neuronal activation within the IL and optogenetic activation of SFO neurons activated inhibitory parvalbumin (PV) (but not somatostatin (SST)) interneurons in the IL. Collectively, these data reveal that aversive interoceptive signals can be directly conveyed to the IL via the SFO, a sensory hub for systemic perturbations, to regulate spontaneous and long-term fear. Our findings provide important mechanistic insights into fear-associated disorders with abnormal interoceptive threat sensitivity such as panic disorder and PTSD.

neuroscience↗

bioRxiv2026

Dual-compartment engagement of STAR-family proteins SAM68 and QKI by LINC00941 sustains oncogenic fitness in RAS-driven lung cancer

Long non-coding RNAs (lncRNAs) are increasingly recognised as effectors of oncogenic signalling, yet the transcriptional programmes through which driver mutations regulate lncRNA expression remain poorly defined. Here we identify LINC00941 as a direct transcriptional target of FOSL1, an AP-1 transcription factor downstream of the KRAS-MAPK pathway, establishing the first FOSL1-regulated lncRNA in lung adenocarcinoma (LUAD). LINC00941 is significantly upregulated in LUAD across multiple independent cohorts, and its depletion via siRNAs, shRNAs, and antisense oligonucleotides (ASOs) induces proliferative arrest and stress-induced premature senescence, accompanied by transcriptomic suppression of cell cycle and DNA damage response (DDR) genes. Mechanistically, LINC00941 operates through a dual-compartment mechanism engaging two STAR-family RNA-binding proteins in distinct subcellular contexts. In the nucleus, LINC00941 binds SAM68 through its 700-1300 nucleotide region and shields it from proteasomemediated degradation, thereby sustaining SAM68-dependent PARP1 activation and DDR competency; RNF123 is identified as a candidate E3 ligase mediating SAM68 turnover in the absence of LINC00941. In the cytoplasm, LINC00941 sequesters QKI, preventing its nuclear translocation; LINC00941 depletion releases QKI to the nucleus, driving alternative splicing dysregulation including validated NUMB exon 12 exclusion, and QKI co-depletion rescues the anti-proliferative phenotype both in vitro and in xenograft models. Multi-cohort survival analysis across three independent LUAD datasets (n=649) identifies LINC00941 as an independent prognostic factor for poor overall survival. Gymnotic ASO-mediated targeting of LINC00941 significantly suppresses xenograft tumour growth without systemic toxicity, providing preclinical proof-of-concept for therapeutic tractability. Together, these findings establish LINC00941 as a compartment-specific oncogenic scaffold within the KRAS-FOSL1 transcriptional axis and a tractable therapeutic target in LUAD.

cancer biology↗

bioRxiv2026

Tie2 signaling in the tumor microenvironment orchestrates breast cancer cell dissemination through TMEM doorways

During breast cancer metastasis, tumor cells migrate toward intratumoral blood vessels and intravasate through stable structures known as TMEM (Tumor Microenvironment of Metastasis) doorways. TMEM doorways, composed of a Mena-expressing tumor cell, a Tie2hi/VEGFhi macrophage, and an endothelial cell, are clinically validated prognostic markers of distant metastasis in breast cancer and represent the exclusive sites of tumor cell intravasation. We previously demonstrated that Tie2 signaling is essential for TMEM doorway function and tumor cell intravasation. In this study, we investigated how Tie2 signaling promotes tumor cell intravasation and metastasis. Because all three TMEM doorway-associated cell types can express Tie2, we sought to determine which of these cells contribute to the Tie2 signaling-dependent vascular opening at TMEM doorways and tumor cell dissemination. We found that endothelial cells associated with TMEM doorways secrete Ang2, which stimulates VEGF-A expression in Tie2hi macrophages. Elevated VEGF-A levels at TMEM doorways increase vascular permeability, facilitating tumor cell entry into the bloodstream. Using tissue staining and line-scan analysis of Tie2 and lineage markers in human and mouse breast cancer models, we observed Tie2 expression in macrophages, tumor cells, and endothelial cells. To assess functional contributions, we selectively disrupted Tie2 in macrophages, endothelial cells, and cancer cells using CRISPR-Cas9 and RNAi approaches and tested in which of these cell-knockouts of Tie2 expression affected transendothelial migration in vitro. Macrophage-specific Tie2 deletion had the greatest impact on tumor cell intravasation. To confirm this finding in vivo, we generated a mouse model with inducible, macrophage-specific Tie2 knockout. Acute, targeted loss of Tie2 specifically in macrophages significantly reduced TMEM doorway associated vascular opening and tumor cell intravasation. Together, these findings establish macrophage Tie2 signaling as a critical driver of TMEM doorway-mediated vascular permeability and metastatic dissemination in breast cancer.

cancer biology↗

bioRxiv2026

Enforced ZFP281 expression delays breast cancer initiation and can provide lifelong protection against breast cancer metastasis

Breast cancer metastatic reactivation and its links to mammary development are largely unknown. Here, using conditional knockout and overexpression in normal and HER2+ mammary glands, we show that the dormancy regulator ZFP281 promotes branching and dissemination while suppressing growth, and its overexpression can even override HER2-driven cancer initiation. Notably, while ZFP281 does not limit HER2-driven early dissemination, it constrains DCC plasticity, confining cells to a dormant mesenchymal/hybrid-like state and effectively suppressing metastasis throughout the mouse lifespan. ZFP281 is induced by estrogen, progesterone, and glucocorticoid signaling, and RNA sequencing of early lesions revealed that it regulates glutathione metabolism and ferroptosis, potentially supporting fitness during dormancy, while repressing angiogenesis, Th17-like inflammation, innate immune genes, and pro-inflammatory programs that might otherwise trigger awakening. Integrating these findings with human data, we show that DCIS and IBC (invasive breast cancer) lesions that later relapse are selectively enriched for ZFP281-regulated M-like and dormancy signatures and, after pregnancy, depleted for a ZFP281-induced stress-autophagy module, indicating that erosion or imbalance of these programs marks lesions that seed DCCs with higher reactivation potential. We propose that ZFP281 acts as a hormone-regulated dormancy gatekeeper that uncouples dissemination from growth, enforcing a metabolically fit, angiogenesis-low, immune-evasive dormant state in breast DCCs, thereby shaping the timing of metastatic relapse and potentially exploitable for durable prevention of metastasis. STATEMENT OF SIGNIFICANCEZFP281, a hormone-regulated dormancy gatekeeper, uncouples dissemination from growth and constrains DCCs into long-term arrest, defining human gene signatures that distinguish dormancy-prone from awakening-prone lesions and predict breast cancer relapse dynamics.

cancer biology↗

bioRxiv2026

Analysis of the heterogenous structural states of the hexameric ATPase PilU of the Type IV pili from Vibrio cholerae

Type IV pili (T4P) mediate surface motility, host interactions, and DNA uptake through cycles of extension and retraction. While the primary retraction ATPase PilT has been extensively characterized, its homolog PilU remains less well understood despite being demonstrated as a PilT-dependent retraction ATPase. Here, we determined six PilU structures by cryo-electron microscopy and X-ray crystallography. The structures reveal a homohexameric assembly stabilized by interactions between the C-terminal catalytic domain of one subunit and the N-terminal PAS-like domain of a neighboring subunit. PilU adopts multiple conformational states, exhibiting digerent combinations of open and closed interfaces even in the absence of nucleotide. Comparison with PilT highlights structural features that likely underlie PilUs weak ATPase activity and its dependence on PilT for function. Together, these findings provide a structural framework for understanding PilUs role within the T4P retraction machinery.

molecular biology↗

bioRxiv2026

Root-Suppressed Phenotype of Tomato Rs Mutant is Seemingly Related to Expression of Root-Meristem-Specific Sulfotransferases

Root development and growth are governed by a complex interplay between a plants genetic makeup and its ambient environment. In this study, we characterised a radiation-induced root-suppressed (Rs) mutant mapped on chromosome 4 of tomato. Rs seedlings had a dwarf stature, and mature plants exhibited abnormalities in their leaves, flowers, and fruits. The partial rescue of seedling root elongation by H2S donors or L-cysteine hinted that its root defect is linked to disrupted sulfur metabolism. The metabolite profiling of organs revealed altered homeostasis, analogous to that of plants subjected to sulfur starvation. Whole-genome sequencing revealed that the Rs genome was replete with genetic lesions; therefore, the pleiotropic morphological abnormalities likely emanate from mutations in other genes, including those related to sulfur. Among S-related genes, two sulfotransferase genes (Solyc04g028380 and Solyc04g028390) localised on chromosome 4 showed mutations in their promoters. The expression of both sulfotransferases is confined to the root meristem, suggesting a causal connection with the suppression of root growth. These sulfotransferases belonged to a distinct subset exclusively expressed in the root meristem and were distinct from the tyrosine sulfotransferase involved in the sulfation of root growth factors. Our study suggests that a sulfur-related module, other than tyrosine sulfotransferase, may regulate root development.

plant biology↗

bioRxiv2025

An Autophagy-Inducing Compound Reduces Tau Pathology, Microglia Reactivity, and Rescues Working Memory in 3xTg AD Mice

BackgroundRecent advancements in Alzheimers disease (AD) therapeutics have validated the use of amyloid beta (A{beta})-clearing antibodies, which reduce A{beta} pathology but leave other disease hallmarks largely unaddressed. Since AD involves multiple pathological processes, additional strategies are needed to target complementary mechanisms. One such target is autophagy, a lysosomal mediated degradation pathway essential for cellular homeostasis that removes toxic protein aggregates and damaged organelles. This process is implicated in AD, as impaired lysosomal function promotes A{beta} and tau accumulation. Our laboratory recently identified a novel natural mitophagy-inducing compound (MIC) that may serve as a therapeutic intervention for AD. MethodsWe evaluated the effects of MIC in aged 3xTgAD mice, a transgenic model displaying both A{beta} and tau pathology. Mice received either standard diet or diet containing MIC beginning at age 4 months until 20 months on alternating weeks. Age-matched non-transgenic (NonTg) controls were included under standard and MIC-supplemented diets to assess compound effects during normal aging. Neuropathological changes were assessed using immunohistochemistry (IHC) for A{beta}, phosphorylated tau (pTau), and microglial reactivity. Cognitive performance was evaluated using the Morris Water Maze (MWM) to assess spatial learning and memory and the Y-maze to measure working memory. ResultsAt 20 months of age, our neuropathological assessment showed that 3xTgAD mice fed an MIC-supplemented diet had a significant reduction in pTau accumulation and microglial reactivity, although A{beta} burden remained unchanged. At 15 months, MIC diet also improved spatial learning and memory in aged NonTg controls but not in 3xTgAD mice. However, in younger 8-month-old 3xTgAD mice, MIC restored working memory performance to NonTg levels, indicating an age-dependent therapeutic response. ConclusionMIC emerges as a potential modulator of tau pathology and neuroinflammation. As a naturally derived compound, MIC offers potential for combination therapy with FDA-approved A{beta}-clearing antibodies, enabling a multimodal approach to AD treatment that addresses amyloid, tau, and microglia-related pathology.

neuroscience↗

bioRxiv2025

Synaptic high-frequency jumping synchronises vision to high-speed behaviour

During high-speed behaviour, animals must synchronise perception and action despite rapid environmental and self-generated motion. How neural systems achieve such precision remains unclear. Here we show how the housefly (Musca domestica) maintains visual accuracy during fast motion. Using intracellular and photomechanical recordings during saccade-like stimulation, we traced information flow from photoreceptors to large monopolar cells (LMCs). Visual neurons achieved record-high information sampling ([~]2,500 bits{middle dot}s-1) and synaptic transmission ([~]4,100 bits{middle dot}s-1), far exceeding previous estimates. We identify a previously unknown mechanism - synaptic high-frequency jumping - in which photoreceptor-LMC synapses dynamically shift transmission toward higher frequencies during saccades, extending visual bandwidth to [~]1,000 Hz, effectively eliminating synaptic delays, and quadrupling classical flicker-fusion limits ([~]230 Hz). Behavioural experiments show flies respond synchronously within [~]13-20 ms, even before photoreceptor responses peak. A biophysically realistic model reveals how photomechanical-stochastic-refractory quantal sampling co-adapts with saccadic behaviour: through self-motion, flies efficiently translate image motion into temporally-precise, predictive high-speed vision.

neuroscience↗

bioRxiv2025

Oxidative Stress, Hypoxia and Cellular Metabolism: Unraveling the Effects of Fentanyl on Lung Cancer Cells

Fentanyl, a widely used opioid analgesic for cancer pain management, is effective but requires cautious administration due to its potential for respiratory depression. Beyond its analgesic properties, fentanyls broader impact on cancer biology and biochemical alterations in lung carcinoma cells remains underexplored. This study investigates fentanyls influence on oxidative stress, mitochondrial function, hypoxia-inducing factors, apoptosis, and cytokine production in A549 lung cancer cells. Our findings reveal that fentanyl increases reactive oxygen species (ROS) generation, disrupts cellular homeostasis, induces DNA damage, and alters key signaling pathways, potentially affecting tumor metabolism and progression. Our "Ramanomics" data further highlight fentanyl-driven changes in key ions (inorganic phosphate, calcium) and biomolecules (glycogen, phospholipids, proteins, nucleic acids, and enzymes) at subcellular mitochondrial levels. These insights contribute to understanding fentanyls mechanistic impact on lung cancer progression and may inform optimized therapeutic strategies. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/665412v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@1fb7aaaorg.highwire.dtl.DTLVardef@13255deorg.highwire.dtl.DTLVardef@1a398cdorg.highwire.dtl.DTLVardef@184d63e_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

TGFb Regulated Small GTPase RHOV interact with PEAK1 and drive MYC Expression to Promote Cellular Proliferation, Migration and Etoposide resistance

1.Non-small cell lung cancer (NSCLC) remains a leading cause of cancer-related mortality, driven by tumor heterogeneity, metastasis, and therapeutic resistance. While Rho GTPases are well-established regulators of oncogenic processes, the role of the atypical GTPases in NSCLC remains unexplored. Here, we identified RHOV as one of the commonly upregulated Rho GTPases in NSCLC. Analysis of four independent patient cohorts revealed that elevated RHOV expression serves as a robust and independent prognosticator of NSCLC patients specifically early-stage disease. Functionally, RHOV knockdown significantly inhibited cell proliferation, whereas its overexpression enhanced proliferation. Similarly, RHOV depletion suppressed cell migration by disrupting cytoskeletal dynamics, while its overexpression promoted migratory capacity. Mechanistically, we demonstrated that RHOV is a direct transcriptional target of the TGF{beta}-SMAD3 signaling pathway. RNA-seq analysis identified MYC as a critical downstream mediator of RHOV; RHOV knockdown reduced MYC expression, impairing mitochondrial oxidative phosphorylation and inducing ROS-mediated DNA damage--a phenotype rescued by MYC overexpression. Furthermore, RHOV inhibition sensitized NSCLC cells to etoposide but not doxorubicin. immunoprecipitation coupled with LC-MS revealed PEAK1 as a key interactor of RHOV. The RHOV-PEAK1 complex proved essential for NSCLC proliferation, as PEAK1 silencing abolished RHOV- driven MYC upregulation and tumor growth. This axis sustains MYC levels and activates PI3K/MAPK signaling. Intriguingly, PEAK1 depletion elevated TGF-{beta} levels, which suppressed RHOV expression, establishing a negative feedback loop wherein PEAK1 maintains RHOV by inhibiting TGF-{beta} signaling. Collectively, our findings establish RHOV as a prognostic biomarker and a driver of NSCLC progression via the RHOV-PEAK1-MYC axis, highlighting its potential as a therapeutic target. HighlightsO_LIRHOV upregulation predicts poor NSCLC survival, particularly in early-stage disease. C_LIO_LIThe RHOV-PEAK1 interaction is crucial for NSCLC growth and cell migration. C_LIO_LIRHOV inhibition sensitizes NSCLC cells to Etoposide treatment. C_LIO_LIRHOV expression is sustained via a PEAK1-TGF{beta} negative feedback loop. C_LI

cancer biology↗

bioRxiv2025

Molecular mechanism for cargo-mediated initiation of kinesin-1 activation

Kinesin-1 is a dynamic heterotetrameric assembly of two heavy and two light chains (KHC and KLC) that mediates microtubule-based intracellular transport of many different cargoes. The complex adopts a compact, autoinhibited state that is activated by cargo-adaptor proteins containing specific short linear peptide motifs (SLiMs). These motifs interact with the tetratricopeptide repeat (TPR) domains of the KLCs. The mechanism coupling SLiM recognition to activation-associated conformational changes in the complex is unknown. Here we combine protein design, computational modelling, biophysical analysis, and electron microscopy to examine the structural and mechanistic consequences of SLiM binding to the KLC-TPR domain within the complete heterotetrameric holoenzyme. We show that coiled coil 1 (CC1) of the KHC docks KLC TPR domains in the autoinhibited complex, forming the shoulder feature observed in electron microscopy. Disrupting this interaction or binding an activating SLiM dislocates the TPR shoulder, freeing the motor domains and promoting transition between its closed, inactive, and open states. Opening the kinesin-1 complex facilitates binding to the microtubule-associated kinesin-1 cofactor, MAP7. Therefore, cargo-mediated dislocation of the TPR shoulder serves as a key initial step in kinesin-1 activation, allosterically linking cargo binding to motor dynamics.

biochemistry↗

bioRxiv2025

Effect of perchlorate on biocementation capable bacteria and Martian bricks

With the recent discovery of perchlorate (0.5-1%) in Martian regolith, more experiments related to the impact of perchlorate on microbial life are crucial to understanding the possibility of earth life forms that could sustain on the Martian terrain. While we are familiar with the idea of bioconsolidated Martian bricks made via Microbially Induced Calcite Precipitation (MICP), studies on the effect of perchlorate on Martian bricks & biocementation capable microbes have been obscure. In this work, we investigated the effect of perchlorate (MgClO4- salt) on a lab-isolated biocementation capable bacteria & Martian bricks bioconsolidated by the same, with 1% perchlorate in Mars Global Simulant-1 (MGS-1). The screening of biocementation-capable bacteria involved phenol red assay for urease activity followed by Scanning Electron Microscopy (SEM) and X-ray diffraction (XRD) study of the precipitate formed through MICP via ureolytic pathway. The biocementation capable bacterium SI_IISc_isolate was found phylogenetically closest to Sporosarcina pasteurii strain S2135, its draft genome being approximately 3.69 Mb. To understand the effect of perchlorate on SI_IISc_isolate, we majorly relied on Gram-staining & SEM. The negative effect of perchlorate stress on the isolate was evident by its decreased growth in the presence of varying concentrations of perchlorate through plate assays, growth curve studies in broth & live-dead staining. Gram-staining study and SEM both revealed that perchlorate induces the release of extracellular matrix (ECM) and promotes clustering of cells by the bacteria, which we termed as multicellularity-like behavior. Further, we constructed Martian bricks with Martian Global Simulant (MGS-1) along with 1% perchlorate, utilizing the microbially induced calcite precipitation ability of the Sporosarcina sp. strain SI_IISc_isolate via ureolysis, following an established protocol at our lab. The bioconsolidation experiments showed that in the presence of a natural adhesive - guar gum, perchlorate tends to significantly improve the compressive strength of Martian bricks. However, the end result eventually relies on the overall effect of various additives in the regolith.

bioengineering↗

bioRxiv2025

MRPL47 Deficiency Drives Mitochondrial Dysfunction via ROS/p38-MAPK/CDKN1A Signaling in Non-Small Cell Lung Cancer

Mitoribosomes play a pivotal role in cellular energy metabolism by synthesizing proteins involved in oxidative phosphorylation (OXPHOS) system. Dysregulation of mitoribosomes has been linked to Cancer, yet there have been no studies demonstrating the genetics and epigenetic landscape of mitoribosomal proteins (MRPs). In this study, we conducted a comprehensive analysis of expression, copy number variations, mutations, data from TCGA NSCLC patients to elucidate the genetic mechanism regulating MRPs in NSCLC. Consequently, we identified MRPL47, a significantly amplified and overexpressed mitoribosomal gene. We also found significant correlation of MRPL47 expression and copy number with patients survival. Functionally, we showed that inhibition of MRPL47 was associated with reduced cell proliferation and migration. Furthermore, silencing MRPL47 impaired the enzymatic activity of electron chain complex I & III leading to a defective OXPHOS system and elevated mitochondrial ROS level. Further, we showed ROS-mediated increase in CDKN1A through the p38 MAPK pathway. The increased CDKN1A level induced G1 cell cycle arrest by inhibiting E2F activity. RNA sequencing analysis further confirmed that MRPL47 hinders cell growth by inhibiting E2F pathway. Additionally, we found that MRPL47 selectively regulates mitochondrial translation of specific OXPHOS proteins rather than influencing all mitochondrial proteins. Altogether, these findings suggest that MARPL47, is amplified and overexpressed in NSCLC and plays a critical role in tumor progression by regulating ROS signaling pathways.

cancer biology↗

bioRxiv2025

Multimodal Neuroimaging Reveals Distinct Characteristics of Levodopa-Induced Dyskinesias in de novo Parkinsons Disease Patients

Levodopa-induced dyskinesia (LID) is a significant treatment complication that affects a substantial proportion of Parkinsons disease (PD) patients. Our understanding of the neural basis of LID remains limited, partly due to the small sample sizes in existing neuroimaging studies. In this study, we utilized structural MRI data from the Parkinsons Progression Markers Initiative (PPMI) database, including de novo PD patients (104 non-dyskinetic for a least 3 years after diagnosis and 120 who developed dyskinesia) and 100 age- and sex-matched healthy controls. Additionally, we analyzed resting-state functional MRI data from a subset of these participants to investigate connectivity differences among the groups. Our analysis revealed no significant baseline volumetric differences between dyskinetic and non-dyskinetic PD patients. However, the thickness of frontal and sensorimotor cortices were significantly greater in dyskinetic patients. In the subcortical regions, vertex-based shape analysis identified localized surface growth in the left caudate and left pallidum, as well as surface morphology changes in the bilateral pallidum in dyskinetics. Resting-state functional connectivity analysis revealed stronger connectivity between the putamen, inferior frontal gyrus, and sensory cortex in dyskinetic PD patients compared to non-dyskinetics. These findings suggest that specific morphological and functional changes in the motor cortical-basal ganglia circuitry of de novo PD patients may predispose them to LID over time. Additionally, the altered functional connectivity patterns reinstate the role of the inferior frontal gyrus in the pathophysiology of dyskinesia and suggest that it might be a suitable target for neuromodulatory interventions, consistent with previous reports.

neuroscience↗

bioRxiv2025

Paclitaxel causes de novo induction of invasive breast cancer cells by repolarizing tumor-associated macrophages

Metastasis is the leading cause of breast cancer death, and tumor cells must migrate and invade to metastasize. Breast cancer cells that express the pro-metastatic actin regulatory protein MenaINV have an enhanced ability to migrate and intravasate within the primary tumor and extravasate at secondary sites. Though chemotherapy improves patient survival, treatment with paclitaxel leads to upregulation of MenaINV and an increase in metastasis in mice. MenaINV expression can be induced in breast cancer cells through cooperative NF-{kappa}B/ Notch1 signaling with macrophages, which are often increased in tumors in response to chemotherapy. MenaINV-expressing cells are also resistant to paclitaxel, raising the question of whether paclitaxel increases MenaINV by de novo induction or by selectively killing non-MenaINV-expressing cells. We hypothesized that paclitaxel causes de novo MenaINV induction by increasing macrophage-tumor cell NF-{kappa}B/ Notch1 signaling. Understanding this pro-metastatic effect of chemotherapy is crucial to refining treatment strategies. In this study, we demonstrate that paclitaxel increases MenaINV expression by de novo induction. Mechanistically, paclitaxel induces MenaINV by repolarizing tumor-associated macrophages towards a pro-inflammatory phenotype. These pro-inflammatory macrophages then participate in enhanced NF-{kappa}B/ Notch1 signaling with tumor cells, which leads to MenaINV induction in the tumor cells. These results lay the groundwork for novel microenvironment-based therapies to alleviate the pro-metastatic effects of chemotherapy in breast cancer.

cancer biology↗