Search bioRxiv⌕ Search

Biology subjects

Khan, M. H.

Publications and source records attributed to Khan, M. H..

12 recordsLinked to original sources

Genetic Disruption at the CIP2A Locus Modulates T Cell Responses and Attenuates Experimental Autoimmune Encephalomyelitis

Multiple sclerosis (MS) is a chronic autoimmune disease of the central nervous system (CNS) driven by pathogenic T cell-mediated inflammation. Fingolimod (FTY720), an approved therapy for MS, is an established activator of protein phosphatase 2A (PP2A). However the contribution of PP2A in autoimmune neuroinflammation remains incompletely understood. Here, we addressed this question using experimental autoimmune encephalomyelitis (EAE), a murine model of MS, in mice carrying a genetic disruption of the locus encoding cancerous inhibitor of protein phosphatase 2A (CIP2A), an endogenous inhibitor of PP2A. Mice with disruption of the CIP2A locus, the knock out (KO) mice, exhibited attenuated EAE severity compared with wild-type (WT) controls. Histological and flow-cytometric analyses revealed markedly reduced infiltration of mononuclear cells, including CD4 and CD4CXCR6 encephalitogenic T cells, in the CNS of diseased KO mice. Reduced numbers of these T cell populations were also observed in peripheral lymphoid organs of the Cip2a-deficient mice during EAE, while T cell abundance was comparable under steady-state conditions, suggesting impaired activation-induced expansion rather than altered homeostasis or migration. Single-cell RNA sequencing of CNS and lymph node immune cells revealed changes in cell-type abundance and gene expression. Notably, Il17a expression was reduced in CNS CD8+ T cells and showed a similar trend in {gamma}{delta} T cells. Together, our findings reveal that genetic disruption at the CIP2A locus attenuates EAE, possibly by limiting the expansion and accumulation of encephalitogenic T cell populations in CNS. These results identify the CIP2A locus as a previously unrecognized regulator of T cell-driven autoimmune neuroinflammation and provide new insights into mechanisms that restrain pathogenic T cell responses during EAE.

immunology↗

CALM-VLM: CALIBRATION AND SELECTIVE PREDICTION IN VISION-LANGUAGE MODELS FOR RELIABLE BRAIN MRI CLASSIFICATION

AO_SCPLOWBSTRACTC_SCPLOWRecent advances in vision-language models (VLMs) have demonstrated strong multimodal capabilities for medical image analysis. However, their confidence in diagnostic predictions is often unclear, limiting adoption in clinical settings. We introduce CALM-VLM (CALibration Mechanism for Vision-Language Models), which integrates confidence calibration and selective prediction into a generative 3D VLM. To create CALM-VLM, we fine-tuned the Med3DVLM architecture for Alzheimers disease (AD) and stroke classification as initial test cases. To improve reliability, we incorporated temperature scaling on the VLMs generative outputs. The calibrated model then selectively abstained from predictions when uncertain; this also improved its diagnostic accuracy. Experiments across multi-site MRI datasets, from 10 countries worldwide, show that CALM-VLM improved confidence relative to uncalibrated VLMs. Coverage-adjusted test receiver-operator characteristic curve-area under the curve (ROC-AUC) increased by 5% to 13% for both diagnostic tasks across independent test sets. Our calibrated VLM achieved a test ROC-AUC of 0.951 for AD classification and 0.905 for stroke classification. These findings highlight the importance of calibrated, uncertainty-aware VLMs for trustworthy neuroimaging AI.

neuroscience↗

Assessing the impact of gamma irradiation on key biological traits of peach fruit fly, Bactrocera zonata (Diptera: Tephritidae) under laboratory conditions

Bactrocera zonata (Saunders) (Diptera: Tephritidae) poses a significant threat to global fruit production due to its high reproductive capacity and broad host range. This study aimed to evaluate the effects of gamma irradiation on key biological parameters of B. zonata. Six-day-old pupae were exposed to irradiation doses of 0, 30, 40, 50, 60, and 70 Gy, and subsequent developmental and reproductive traits were assessed to determine the impact of irradiation. Post-irradiation results revealed a dose-dependent trend. Higher doses ([≥]50 Gy) significantly reduced adult emergence, increased the incidence of partially emerged or deformed adults, and shortened adult longevity. Reproductive potential was significantly impaired in males irradiated at 60 and 70 Gy when mated with un-irradiated females, resulting in a marked decline in both fecundity and egg hatchability. Females irradiated at doses [≥]50 Gy failed to produce eggs when paired with either irradiated or non-irradiated males, indicating a high level of radio-sensitivity in female flies. Additionally, several traits in the F1 generation such as pupal recovery, pupal size, and adult development exhibited significant abnormalities and suggesting that the effects of irradiation may be transmitted to the next generation. Sterility was highest in males irradiated at 60 and 70 Gy, while females exhibited complete sterility at doses exceeding 40 Gy. The findings indicate that a dose of 70 Gy may be optimal for effective sterility induction in B. zonata. However, further detailed studies are required to standardize this dose, incorporating rigorous quality control measures to optimize its application in sterile insect technique (SIT) programs.

zoology↗

SimUrine: A Novel, Fully Defined Artificial Urinary Media for Enhanced Microbiological Research of Urinary Bacteria

Urinary tract infections represent one of the most prevalent bacterial diseases, yet current diagnostic and research methodologies are hampered by inadequate culture media that fail to replicate the bladder biochemical environment. Conventional artificial urine formulations contain undefined components, lack essential nutrients, or inadequately support urinary microbiome (urobiome) growth. To address these limitations, we developed SimUrine, a fully defined synthetic urine medium that aims to replicate human bladder chemistry while supporting diverse microbial growth requirements. SimUrine was systematically developed through iterative optimization of multi-purpose artificial urine, incorporating defined concentrations of carbon sources, vitamins, trace elements, and amino acids within physiologically relevant ranges. The modular design enables component substitution without complete reformulation, facilitating customization for culturomics, antimicrobial susceptibility testing, and microbial ecology studies, while reducing batch-to-batch variability associated with authentic urine. Performance evaluation demonstrated SimUrines capability to support growth of fastidious urobiome members, including Lactobacillus species, Aerococcus urinae, and Corynebacterium riegelii, which fail to proliferate in conventional minimal media. Physicochemical characterization confirmed that SimUrine formulation exhibits properties within normal human urine ranges for density, conductivity, osmolarity, and viscosity, ensuring physiological relevance. Clinical applications revealed reduced antibiotic susceptibility compared to standard media, suggesting more accurate representation of in vivo conditions. Co-culture experiments using Escherichia coli and Enterococcus faecalis demonstrated previously unobserved microbial interactions, highlighting SimUrines utility for investigating urobiome dynamics. SimUrine represents a significant advancement in urobiome research methodology, providing a standardized, reproducible platform for investigating urobiome under physiologically relevant conditions, potentially improving fundamental understanding and clinical diagnostic approaches. IMPORTANCEUrinary tract infections affect millions globally, yet current research and diagnostic methods rely on inadequate culture media that fail to replicate the bladders unique biochemical environment. This fundamental limitation has hindered accurate UTI research and potentially compromised clinical treatment decisions. SimUrine addresses this critical gap as the first fully defined synthetic urine medium that mimics human bladder chemistry while supporting growth of diverse urinary microbes. The breakthrough enables cultivation of urobiome organisms in a minimal medium that resembles natural conditions, revealing novel microbial interactions that influence urinary health. Crucially, SimUrine demonstrates different antimicrobial susceptibility patterns compared to standard clinical media, suggesting current testing protocols may inaccurately predict treatment outcomes. This standardized, reproducible platform eliminates the variability of authentic urine samples while maintaining physiological relevance, potentially transforming urobiome research methodology and improving clinical diagnostic accuracy for urinary tract infections worldwide.

microbiology↗

The neural mechanisms supporting the rise and fall of maternal aggression

To protect the helpless young, lactating females dramatically increase aggression towards intruders, known as maternal aggression. However, attack is costly and risky. When pups no longer exist, maternal aggression rapidly declines. Our study reveals the critical role of the pathway from posterior amygdala cells expressing estrogen receptor alpha (PAEsr1) to the ventrolateral part of ventromedial hypothalamus cells expressing neuropeptide Y receptor Y2 (VMHvlNpy2r) in the rise and fall of maternal aggression. Functional manipulations and recordings demonstrate that VMHvl-projecting PAEsr1 (PAEsr1[->]VMHvl) cells are naturally active and required for maternal aggression. During lactation, PA-VMHvlNpy2r connection strengthens, and VMHvlNpy2r excitability increases to facilitate attack. Furthermore, PAEsr1 expresses abundant oxytocin receptors, enabling oxytocin to boost PAEsr1 cell output. After pup separation, the oxytocin level drops, causing decreased maternal aggression, which can be restored by optogenetically increasing the oxytocin level. Thus, diverse forms of plasticity occur at the PAEsr1-VMHvlNpy2r circuit to support need-based maternal aggression.

neuroscience↗

HIC1 interacts with FOXP3 multi-protein complex: a novel mechanism to regulate human regulatory T cell differentiation and function

Transcriptional repressor, hypermethylated in cancer 1 (HIC1) participates in a range of important biological processes, such as tumor repression, immune suppression, embryonic development and epigenetic gene regulation. Further to these, we previously demonstrated that HIC1 provides a significant contribution to the function and development of regulatory T (Treg) cells. However, the mechanism by which it regulates these processes was not apparent. To address this question, we used affinity-purification mass spectrometry to characterize the HIC1 Interactome in human Treg cells. Altogether 61 high-confidence interactors were identified, including IKZF3, which is a key transcription factor in the development of Treg cells. The biological processes associated with these interacting proteins include protein transport, mRNA processing, non-coding (ncRNA) transcription and RNA metabolism. The results revealed that HIC1 is part of a FOXP3-RUNX1-CBFB protein complex that regulates Treg signature genes thus improving our understanding of HIC1 function during early Treg cell differentiation. HighlightsO_LISystematic characterization of HIC1 interactome in regulatory T cells by Affinity Purification-Mass Spectrometry C_LIO_LIHIC1 binds to the RUNX1 promoter and regulates its expression C_LIO_LIHIC1-a part of FOXP3-RUNX1-CBFB transcriptional complex C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=37 SRC="FIGDIR/small/540505v1_ufig1.gif" ALT="Figure 1"> View larger version (14K): org.highwire.dtl.DTLVardef@1fcb119org.highwire.dtl.DTLVardef@cf1397org.highwire.dtl.DTLVardef@10f512forg.highwire.dtl.DTLVardef@9ae94e_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

SHARPIN serine 146 phosphorylation mediates ARP2/3 interaction, cancer cell invasion, and metastasis

The adaptor protein SHARPIN is involved in a number of cellular processes and promotes cancer progression and metastasis. However, how the choice between different functions of SHARPIN is post-translationally regulated is unclear. Here we have characterized SHARPIN phosphorylation by mass spectrometry and in vitro kinase assay. Focusing on two uncharacterized phosphorylation sites, serine 131 and 146, in the unstructured linker region of SHARPIN, we demonstrate their role in SHARPIN-ARP2/3 complex interaction, whereas they play no role in integrin inhibition or LUBAC activation. Consistent with its novel role in ARP2/3 regulation, serine 146 (S146) phosphorylation of SHARPIN promoted lamellopodia formation. Notably, CRISPR-Cas9 mediated knockout of SHARPIN abrogated three-dimensional (3D) invasion of several cancer cell lines. The 3D invasion of cancer cells was rescued by overexpression of the wild-type SHARPIN, but not by SHARPIN S146A mutant, identifying S146 as an invasion promoting phosphorylation switch. Finally, we demonstrate that inhibition of phosphorylation at S146 significantly reduces the in vivo metastasis in the zebrafish model. Collectively, these results demonstrate that SHARPIN S146 phosphorylation constitutes a single functional determinant of cancer cell invasion both in vitro and in vivo.

cancer biology↗

Response of Soil Microbiome Structure to Biological Control Agents (BCAs) in Strawberry Greenhouse

Continuous cropping always leads to severe abiotic and biotic problems, especially the high-intensity land utilization in greenhouses, which causes widespread concern. Effective Microorganisms (EM) and Bacillus subtilis (BS) have been widely used to promote plant growth and increase yields as biological control agents (BCAs). However, their effects on soil microbes are obscure. To regulate the microbial community in continuous cropping strawberry soils, we developed four soil amendments by combining EM and BS with compost. The amplicon sequencing of bacterial and fungal ribosomal markers was applied to study the response of the soil microbiome structure. We noticed a sharp increase in bacterial diversity after the addition of EM-treated high compost and BS-treated low compost, while there was no significant change in fungal diversity among treatments. Interestingly, both the relative abundance and FUNGuild predictions was consistent in revealing that BCAs may inhibit fungal pathogens in soils. Correlation analysis indicated that soil microbial community was indirectly driven by soil properties. Co-occurrence networks demonstrated that BCAs could be microecologically homogeneous through enhancing bacterial network complexity and modularity. Collectively, EM-treated high compost and BS-treated low compost can well regulate the microbial community structure and thus maintain soil health.

microbiology↗

Imaging the Transmembrane and Transendothelial Sodium Gradients in Gliomas

High sodium (Na+) in extracellular (Na+e) and blood (Na+b) compartments and low Na+ in intracellular milieu (Na+i) produce strong transmembrane ({Delta}Na+mem) and weak transendothelial ({Delta}Na+end) gradients respectively, which reflect cell membrane potential (Vm) and blood-brain barrier (BBB) integrity. We developed a sodium (23Na) magnetic resonance spectroscopic imaging (MRSI) method using an intravenously-administered paramagnetic contrast agent to measure {Delta}Na+mem and {Delta}Na+end. In vitro 23Na-MRSI established that the 23Na signal is strongly shifted by the agent compared to biological factors. In vivo 23Na-MRSI showed Na+i remained unshifted and Na+b was more shifted than Na+e, and these together created weakened {Delta}Na+mem and enhanced {Delta}Na+end in rat gliomas. Specifically, RG2 and U87 tumors maintained weakened {Delta}Na+mem (i.e., depolarized Vm) implying an aggressive state for proliferation, and RG2 tumors displayed elevated {Delta}Na+end suggesting altered BBB integrity. 23Na-MRSI will allow explorations of perturbed Na+ homeostasis in vivo for the tumor neurovascular unit.

cancer biology↗

Comparison of in vitro and in planta toxicity of Vip3A for lepidopteran herbivores

Agricultural pest infestation is as old as domestication of food crops and contributes a major share to the cost of crop production. Transgenic production of Vip3A, an insecticidal protein from Bacillus thuringiensis, effectively controls lepidopteran pests. A synthetic vip3A gene was evaluated its efficacy against Spodoptera litura (cotton leafworm), Spodoptera exigua (beet armyworm), Spodoptera frugiperda (fall armyworm), Helicoverpa armigera (cotton bollworm), Helicoverpa zea (corn earworm), Heliothis virescens (tobacco budworm), and Manduca sexta (tobacco hornworm). In artificial diet assays, the Vip3A concentration causing 50% mortality was H. zea > H. virescens > S. exigua > H. armigera > M. sexta > S. frugiperda > S. litura. In contrast, on vip3A transgenic tobacco the order of resistance (time until 50% lethality) was M. sexta > H. virescens > S. litura > H. zea > H. armigera > S. exigua > S. frugiperda. There was no significant correlation between the artificial diet and transgenic tobacco effects. Notably, the two insect species that are best-adapted for growth on tobacco, M. sexta and H. virescens, showed the greatest tolerance of vip3A-transgenic tobacco. This may indicate synergistic effects of Vip3A and endogenous plant defense mechanisms, e.g. nicotine, to which M. sexta and H. virescens would have greater resistance. Together, our results show that artificial diet assays are a poor predictor of Vip3A efficacy in transgenic plants, lepidopteran species vary in their sensitivity to Vip3A in diet-dependent manner, and that host plant adaptation of the targeted herbivores should be considered when designing transgenic plants for pest control.

molecular biology↗

Protein Interactome of the Cancerous Inhibitor of Protein Phosphatase 2A (CIP2A) in Th17 Cells

Cancerous inhibitor of protein phosphatase 2A (CIP2A) is involved in immune response, cancer progression, and in Alzheimers disease. However, an understanding of the mechanistic basis of its function in this wide spectrum of physiological and pathological processes is limited due to its poorly characterized interaction networks. Here we present the first systematic characterization of the CIP2A interactome by affinity-purification mass spectrometry combined with validation by selected reaction monitoring targeted mass spectrometry (SRM-MS) analysis in Th17 cells. In addition to the known regulatory subunit of protein phosphatase PP2A, the catalytic subunit of protein PP2A was found to be interacting with CIP2A. Furthermore, the regulatory (PPP1R18, and PPP1R12A) and catalytic (PPP1CA) subunits of phosphatase PP1 were identified among the top novel CIP2A interactors. Evaluation of the ontologies associated with the proteins in this interactome revealed that they were linked with RNA metabolic processing and splicing, protein traffic, cytoskeleton regulation and ubiquitin-mediated protein degradation processes. Taken together, this network of protein-protein interactions will be important for understanding and further exploring the biological processes and mechanisms regulated by CIP2A both in physiological and pathological conditions.\n\nHighlights{blacksquare} The first characterisation of the CIP2A interactome in Th17 cells.\n{blacksquare}Key interactions were validated by targeted SRM-MS proteomics, western blot and confocal microscopy.\n{blacksquare}Pathway analysis of the interactome revealed interrelationships with proteins across a broad range of processes, in particular associated with mRNA processing.

systems biology↗

Non-Communicable Diseases and their determinants: A Cross-sectional State-Wide STEPS Survey, Haryana, North India

BackgroundRecent studies have documented high variation in epidemiologic transition levels among Indian states with noncommunicable disease epidemic rising swiftly. However, the estimates suffer from non-availability of reliable data for NCDs from sub populations. In order to fill the knowledge gap, the distribution and determinants of NCD risk factors were studied along with awareness, treatment and control of NCDs among the adult population in Haryana, India.\n\nMethodsNCD risk factors survey was conducted among 5078 residents, aged 18-69 years during 2016-17. Behavioural risk factors were assessed using STEPS instrument, administered through an android software (mSTEPS). This was followed by physical measurements using standard protocols. Finally, biological risk factors were determined through the analysis of serum and urine samples.\n\nResultsMales were found to be consuming tobacco and alcohol at higher rates of 38.9% (95% CI: 35.3-42.4) and 18.8% (95% CI: 15.8-21.8). One-tenth (11%) (95% CI: 8.6-13.4) of the respondents did not meet the specified WHO recommendations for physical activity for health. Around 35.2% (95%CI: 32.6-37.7) were overweight or obese. Hypertension and diabetes were prevalent at 26.2% (95% CI: 24.6-27.8) and 15.5% (95% CI: 11.0-20.0). 91.3% (95% CI: 89.3-93.3) of the population had higher salt intake than recommended 5gms per day.\n\nConclusionThe documentation of strikingly high and uniform distribution of different NCDs and their risk factors in state warrants urgent need for evidence based interventions and advocacy of policy measures.

epidemiology↗