Biology subjects

Malik, H.

Publications and source records attributed to Malik, H..

10 recordsLinked to original sources

bioRxiv2026

Cross-Continental Analysis of Vampire Bat Betaherpesvirus Reveals Limited Interference Among Strains and Local Geographic Spread

Desmodus rotundus Betaherpesvirus (DrBHV) is a candidate vector for a transmissible vaccine targeting the circulation of rabies virus within its vampire bat reservoir. Studies assessing the potential for DrBHV as a vector have not considered its geographic range, potential for transboundary spread or how the diversity of wildtype DrBHV in natural bat populations might impede the spread of a modified vaccine strain. Here, by sequencing DrBHVs from vampire bats spanning 15 regions across 7 rabies-affected countries in Latin America and the Caribbean, we characterise the continent-scale distribution of DrBHV diversity and demonstrate widespread and apparently unconstrained co-infection. DrBHV occurred in all regions, forming a monophyletic clade consistent with a single introduction to vampire bats or host-virus co-speciation rather than frequent host switching. Phylogeographic analyses revealed cross-boundary spread that was predicted by geographic proximity. We identified 50 putative DrBHV strains and 79% of DrBHV-infected bats harboured multiple strains. No strains were over- or under-represented in co-infection and co-infections occurred proportionately to local strain prevalence. Whether strains circulated in given populations was predominantly driven by the geographic proximity of other populations containing that strain. The evolutionary relatedness of strains constrained neither rates of co-infection within individuals nor whether strains co-circulated within regions, suggesting vaccine vectors might be locally sourced rather than requiring imported, divergent strains to ameliorate interference. These results support the viability of DrBHV-vectored vaccines for mitigating rabies virus across Latin America and the Caribbean, despite widespread circulation of wildtype viruses.

genomics↗

bioRxiv2026

TLR5 drives metabolic dysfunction-associated steatohepatitis through lipid- and flagellin-induced hepatocyte injury signalling

Liver fibrosis is a strong predictor of clinical outcomes in metabolic dysfunction-associated steatohepatitis (MASH). Fibrosis is a consequence of persistent liver cell injury and inflammation in which Toll-like receptors (TLRs) play a key initiating role. Here we test the hypothesis that TLR5 is involved in the development of MASH and fibrosis using a combination of clinical data from multiple independent patient cohorts, single cell liver transcriptomics and human in vitro and ex vivo models. Hepatic TLR5 expression, but not TLR2 or TLR4, is associated with liver fibrosis and mortality. Plasma levels of TLR5s cognate ligand flagellin are increased in MASH with advanced fibrosis and fall with liver disease improvement. Mechanistically, we identify two parallel TLR5-mediated routes to hepatocyte injury: one elicited by flagellin and the other indirectly by lipid injury. Furthermore, hepatocyte TLR5 inhibition abrogates paracrine activation of hepatic stellate cells to suppress collagen production. This is also seen ex vivo in patient-derived precision-cut liver slices where TLR5 inhibition significantly reduces lipid-induced collagen deposition. These findings reveal a new role for TLR5 signalling, specifically in the development of advanced MASH fibrosis and may offer a novel disease-specific therapeutic approach.

molecular biology↗

bioRxiv2025

The Drosophila PDGF/VEGF signaling pathway regulates host immunometabolism in response to parasitoid infection

Mounting an immune response requires energy, but how that energy is reallocated at the organismal level remains poorly understood. In Drosophila melanogaster, infection by a parasitoid wasp triggers a systemic metabolic switch known as immunometabolism which is characterized by a shift in metabolic activity and the redistribution of resources away from organismal development and toward the production of a cellular immune response. We identify the PDGF/VEGF (PVF) signaling pathway as a key initiator of this immunometabolic switch. Genetic manipulation of PVF signaling alters infection outcomes, modulates systemic metabolite profiles, and reveals a direct trade-off between immune function and development. Our findings establish the Drosophila-parasitoid wasp system as a genetically tractable model for understanding the molecular basis of immunometabolism.

biochemistry↗

bioRxiv2025

Understanding bottlenecks in the microbial production of partially acetylated chitooligosaccharides

Chitooligosaccharides (COS) are versatile biomolecules with applications across food, pharmaceutical, and cosmetic industries. Expanding the COS portfolio, particularly with partially acetylated COS (paCOS) of defined degree and pattern of acetylation, is essential to unlocking their full potential. This study investigates the co-expression of chitin deacetylases (CDAs) with a chitooligosaccharide synthase (CHS) RhNodC in E. coli for in vivo paCOS production. While this approach shows promise, it is hampered by reduced overall (pa)COS yields and incomplete conversion of fully acetylated COS to paCOS. Our findings reveal that RhNodC and CDAs co-localize, suggesting potential interactions that influence production efficiency. Additionally, CDA expression induces significant stress responses, including upregulation of ibpA and cpxP promoters linked to inclusion body formation and membrane stress, respectively. This is accompanied by pronounced cellular elongation, further indicating cellular distress. These bottlenecks highlight the need for deeper exploration of RhNodC-CDA interactions and stress mitigation strategies to optimize scalable in vivo paCOS production. Highlights- Co-expression of rhizobial NodC and chitin deacetylases reduces chitooligosaccharide yield. - Conversion of COS into paCOS remains incomplete upon co-expression. - Upregulation of stress responses suggests protein misfolding and membrane stress. - NodC and chitin deacetylases possibly co-localize and affect cellular localization. - Chitin deacetylase expression causes cell elongation up to 30 micrometers. - Further study needed on rhizobial NodC-chitin deacetylase and substrate interactions.

synthetic biology↗

bioRxiv2024

One Health assessment of poultry and cattle farms as reservoirs for ESBL-producing Escherichia coli

BACKGROUNDUnregulated use of antibiotics in animal food production leads to the emergence of multidrug resistant bacteria, notably extended-spectrum beta-lactamases producing Escherichia coli (ESBL E. coli). ESBLs severely limit treatment options and pose a significant threat to public health. Investigating the potential role of livestock and poultry farms in harboring ESBL E. coli is crucial, given the prevalence of ESBL E. coli in humans, animals, and the environment, following the One Health framework. OBJECTIVESThe aim of this study was to assess and compare the potential contribution of cattle and poultry farms along with their respective human handlers to the emergence and spread of ESBL E. coli following One Health approach. METHODSTwenty cattle and twenty poultry farms were surveyed in Ludhiana, India to determine antibiotic usage, prevalent diseases in the farms. Animal faeces/poultry droppings, handler hand swabs, and stool samples were examined for the presence of ESBL E. coli. The isolates were examined for their susceptibility to 16 antibiotics and for the presence of selected antimicrobial resistance genes, including ESBL genes. Generalized linear mixed models were applied to investigate variations in the prevalence of ESBL E. coli associated with farm animal species, farm practices, and farm biosecurity measures. RESULTSOur findings revealed a higher prevalence of ESBL E. coli in poultry farms (53.75%) than in cattle farms (40.72%) and overall lower prevalence (12%) in human handlers. Of the total isolates, 86.52% were multidrug resistant, and 93.91% showed a high multiple antibiotic resistance (MAR) index (>0.2). Isolates from poultry farms exhibited a higher level of resistance with 97% of isolates exhibiting multidrug resistance, 100% isolates with MAR index of more than 0.2, and 90.70% carrying the blaCTXM gene. CONCLUSIONOur findings highlight cattle and poultry farms as potential reservoirs for multidrug-resistant and ESBL E. coli, contributing to the rising environmental burden of antibiotic resistance genes. This emphasizes the urgency of limiting antibiotic use in animal farming, especially in poultry production, to address the escalating problem of antibiotic resistance and protect both animal and human health.

microbiology↗

bioRxiv2024

A Machine Learning Framework to Identify the Correlates of Disease Severity in Acute Arbovirus Infection

Most viral diseases display a variable clinical outcome due to differences in virus strain virulence and/or individual host susceptibility to infection. Understanding the biological mechanisms differentiating a viral infection displaying severe clinical manifestations from its milder forms can provide the intellectual framework toward therapies and early prognostic markers. This is especially true in arbovirus infections, where most clinical cases are present as mild febrile illness. Here, we used a naturally occurring vector-borne viral disease of ruminants, bluetongue, as an experimental system to uncover the fundamental mechanisms of virus-host interactions resulting in distinct clinical outcomes. As with most viral diseases, clinical symptoms in bluetongue can vary dramatically. We reproduced experimentally distinct clinical forms of bluetongue infection in sheep using three bluetongue virus (BTV) strains (BTV-1IT2006, BTV-1IT2013 and BTV-8FRA2017). Infected animals displayed clinical signs varying from clinically unapparent, to mild and severe disease. We collected and integrated clinical, haematological, virological, and histopathological data resulting in the analyses of 332 individual parameters from each infected and uninfected control animal. We subsequently used machine learning to identify the key viral and host processes associated with disease pathogenesis. We identified five different fundamental processes affecting the severity of bluetongue: (i) virus load and replication in target organs, (ii) modulation of the host type-I IFN response, (iii) pro-inflammatory responses, (iv) vascular damage, and (v) immunosuppression. Overall, our study using an agnostic machine learning approach, can be used to prioritise the different pathogenetic mechanisms affecting the disease outcome of an arbovirus infection.

microbiology↗

bioRxiv2022

Cardiac MAO-A inhibition protects against catecholamine-induced ventricular arrhythmias via enhanced diastolic calcium control

BackgroundPeople with clinical depression exhibit increased risk for cardiac arrhythmias that could be related to differences in catecholamine metabolism. Emerging studies have implicated a pathophysiologic role for monoamine oxidase (MAO-A), which catalyzes catecholamine metabolism in the heart. MAO-A is the pharmacological target of some classes of anti-depressants. Here, we investigated the relationship between MAO-A activity and arrhythmogenesis. Methods & ResultsTriNetX database analysis of adult patients with depression (n=11,533) revealed that MAO inhibitor (MAOI) treatment is associated with significantly lower risk of arrhythmias compared with selective serotonin reuptake inhibitor (SSRI) treatment (16.7% vs 18.6%, p=0.0002). To determine a mechanistic link between MAO activity and arrhythmia, we utilized a genetically modified mouse model with cardiomyocyte-specific MAO-A deficiency (cMAO-Adef). Compared with wild-type (WT) mice, cMAO-Adef mice had a significant reduction in the incidence (38.9% vs. 77.8%, p=0.0409) and duration (55.33 {+/-} 26.21s vs.163.1 {+/-} 56.38s, p=0.0360) of catecholamine stress-induced ventricular tachyarrhythmias (VT). Reduced VT risk and duration were associated with altered cardiomyocyte Ca2+ handling in the cMAO-Adef hearts, including a marked increase in Ca2+ reuptake rate, decreased diastolic Ca2+ levels, decreased SR Ca2+ load and reduced Ca2+ spark activity following catecholamine stimulation relative to WT. Further analysis of molecular mechanisms revealed that altered Ca2+ handling in the cMAO-Adef hearts was related to decreased catecholamine-induced phosphorylation of Ca2+/calmodulin-dependent kinase II (CaMKII) and ryanodine receptor 2 (RyR2), and increased phosphorylation of phospholamban (PLB). ConclusionsThese findings suggest that MAO-A inhibition in cardiomyocytes mitigates arrhythmogenesis via enhanced Ca2+ reuptake that lowers diastolic Ca2+ levels thereby diminishing arrhythmic triggers following catecholamine stimulation. Thus, cardiac MAO-A represents a potential target for antiarrhythmic therapy.

physiology↗

bioRxiv2022

Anthropogenic disturbance impacts gut microbiome homeostasis in a Malagasy primate

Increasing anthropogenic disturbances in Madagascar are exerting constrains on endemic Malagasy lemurs and their habitats, with possible effects on their health and survival. An important component of health is the gut microbiome, which might be disrupted by various stressors associated with environmental change. We have studied the gut microbiome of grey-brown mouse lemurs (Microcebus griseorufus), one of the smallest Malagasy primates and an important model of the convergent evolution of diseases. We sampled two sites: one situated in a national park and the other consisting of a more disturbed site around human settlement. We found that more intense anthropogenic disturbances indeed disrupted the gut microbiome of this lemur species with a marked reduction in its diversity and led to a shift in microbial community composition. Interestingly, we noted a decrease in beneficial bacteria together with a slight increase in disease-associated bacteria and alterations in microbial metabolic functions. Because of the crucial services provided by the microbiome to host health and in disease, such negative alterations in the gut microbiome of the lemur from anthropogenically disturbed habitat might impact the health of mouse lemurs, rendering them susceptible to diseases and ultimately affecting their survival in the shrinking biodiversity seen in Madagascar. Gut microbiome analyses might thus serve as an early warning signal for pending threats to lemur populations.

microbiology↗

bioRxiv2020

Structural analysis of RIG-I-like receptors reveals ancient rules of engagement between diverse RNA helicases and TRIM ubiquitin ligases

RNA helicases and ubiquitin E3 ligases mediate many critical functions within cells, but their actions have been studied largely in distinct biological contexts. Here, we uncover evolutionarily conserved rules of engagement between RNA helicases and tripartite motif (TRIM) E3 ligases that lead to their functional coordination in vertebrate innate immunity. Using cryo-electron microscopy and biochemistry, we show that RIG-I-like receptors (RLRs), viral RNA receptors with helicase domains, interact with their cognate TRIM/TRIM-like E3 ligases through similar epitopes in the helicase domains. Their interactions are avidity-driven, restricting the actions of TRIM/TRIM-like proteins and consequent immune activation to RLR multimers. Mass-spectrometry and phylogeny-guided biochemical analyses further reveal that similar rules of engagement apply to diverse RNA helicases and TRIM/TRIM-like proteins. Our analyses thus reveal not only conserved substrates for TRIM proteins but also unexpectedly deep evolutionary connections between TRIM proteins and RNA helicases, thereby linking ubiquitin and RNA biology throughout animal evolution.

biochemistry↗

bioRxiv2018

Scarless gene tagging of transcriptionally silent genes in hiPSCs to visualize cardiomyocyte sarcomeres in live cells

We describe a multi-step CRISPR/Cas9 gene editing method to create endogenously tagged GFP-fusions of transcriptionally silent genes in human induced pluripotent stem cells (hiPSCs), allowing visualization of proteins that are only expressed upon differentiation. To do this, we designed a donor template containing the monomeric EGFP (mEGFP) fusion tag and an mCherry selection cassette delivered in tandem to a target locus via homology directed repair (HDR). mCherry expression was driven by a constitutive promoter and served as a drug-free, excisable selection marker. Following selection, the mCherry cassette was excised with Cas9, creating an mEGFP-fusion with the target gene. We achieved scarless excision by using repetitive sequences to guide microhomology-mediated end joining (MMEJ) and introduce linker sequences between the mEGFP tag and the target gene. Using this strategy, we successfully tagged genes encoding the cardiomyocyte sarcomeric proteins troponin I (TNNI1), alpha-actinin (ACTN2), titin (TTN), myosin light chain 2a (MYL7), and myosin light chain 2v (MYL2) with mEGFP in undifferentiated hiPSCs. This methodology provides a general strategy for scarlessly introducing tags to transcriptionally silent loci in hiPSCs.

cell biology↗