Biology subjects

Mondal, A.

Publications and source records attributed to Mondal, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Decoding the molecular cues regulating the transition of Influenza virus polymerase from transcriptase to replicase.

Influenza virus polymerase (FluPol) dynamically transitions between distinct conformational states to coordinate viral gene transcription and genome replication. While vRNP-associated monomeric FluPol supports transcription, ANP32-dependent asymmetric and ANP32-independent symmetric polymerase dimers mediate genome and antigenome (vRNA/cRNA) replication. How FluPol coordinates these distinct functional states to maintain the transcription-replication balance remains poorly understood. Here, we identify and characterize interdomain interactions within PB2 that govern the stability of the replication-competent conformation of FluPol. Specifically, a highly conserved salt bridge between PB2 Mid-E282 and NLS-K752 stabilizes the replicase conformation, while the charge state of residue 627 (E or K) dictates ANP32 engagement, together coordinating polymerase dimerization and replication activity. Strikingly, bat influenza A viruses H17N10 and H18N11 harbor unconventional serine substitutions at both positions, compromising polymerase dimerization, ANP32 interaction, and vRNA/cRNA replication. Remarkably, introducing these bat-signature substitutions (E282S/K627S) into human H1N1 polymerase results in phosphorylation at both positions in human cells. These findings suggest that phosphorylation can partially compensate for the loss of negative charge at these residues, revealing a phosphomimetic adaptation mechanism that modulates polymerase conformational dynamics and function. Collectively, our study reveals how a conserved interdomain interaction within PB2 regulates conformational transitions and transcription-replication balance of FluPol, which might have been driven by phosphomimetic adaptations during the course of a diverse range of influenza virus evolution.

microbiology↗

bioRxiv2026

Influenza virus Non Structural protein 1 (NS1) Chaperones Nucleoprotein (NP) Oligomerization to Coordinate Ribonucleoprotein Assembly and Genome Replication

Influenza virus nucleoprotein (NP) co-transcriptionally enwraps viral genomic/antigenomic RNAs to assemble viral ribonucleoprotein complexes (RNPs), while the non-structural protein-1 (NS1) is classically recognized as an antagonist of host antiviral responses. Although NP-NS1 interaction has long been reported, the molecular basis of this protein-protein interaction and its relevance in the virus life cycle remain elusive. Here, we define the NP-NS1 interaction interface and uncover a noncanonical role of NS1 in regulating RNP assembly and viral genome replication. Using integrated biochemical, biophysical, and structural analyses, we demonstrate that the RNA-binding domain (RBD) of NS1 directly engages the NP tail-loop, conferring high affinity for monomeric NP. Functional assays reveal that a cytoplasm-restricted NS1 variant acts as an NP-specific chaperone by stabilizing monomeric NP through sequestration of its intrinsically flexible tail-loop and by scaffolding NP-NP interactions. During influenza virus infection, phosphorylation at the homotypic interface restricts NP in a replication-competent monomeric state. Cytoplasmic NS1 recruits these phosphorylated monomeric NPs into assembling RNPs, thereby facilitating viral genome replication and virus propagation. Collectively, our findings establish NS1 as a selective cytoplasmic chaperone of NP and reveal a novel regulatory axis governing influenza virus RNP biogenesis and replication.

molecular biology↗

bioRxiv2026

The NMR Exchange Format (NEF): Specification and Applications

The NMR Exchange Format (NEF) is a community-driven standard for representing NMR experimental data in a consistent, interoperable, and machine-readable form. Built on the STAR syntax, NEF provides a structured framework for storing and exchanging chemical shifts, peak lists, various types of structural restraints, and related metadata, thus allowing for data exchange across software platforms. By enabling direct, lossless transfer of information, NEF simplifies multi-software workflows, improves reproducibility, and supports FAIR (Findable, Accessible, Interoperable, Reusable) data principles. We describe the NEF specification, its current implementation across commonly used NMR software packages, and its application in areas including biomolecular structure determination, metabolomics, and ligand screening. Testing demonstrates that NEF can be used to exchange complete datasets between programs without loss of information or functionality. We also outline recent developments and future directions, such as inclusion of NMR relaxation data and support for non-standard residue topologies. NEFs growing adoption highlights its potential as a unifying standard for NMR data, enabling more efficient, transparent and collaborative research.

biochemistry↗

bioRxiv2026

Hyperosmolar stress promotes the release of small extracellular vesicles containing metabolic proteins from corneal epithelial cells

PurposeHyperosmolar stress (HOS) is a major contributor to corneal epithelial cell damage in dry eye disease. We have previously shown that HOS damages mitochondria and impairs cell metabolism in corneal epithelial cells. Small extracellular vesicles (sEVs) are cell-derived lipid envelopes that are present in all body fluids, including tears. Prior studies suggest that sEV release and composition may be linked with changes in cell metabolism. In this study, we tested the effects of HOS on sEV release and composition, and found that sEV cargo may reflect early, underlying changes in dry eye disease. MethodsTelomerase-immortalized human corneal epithelial (hTCEpi) cells were treated with 450 mOsm NaCl for five days to induce chronic HOS. sEVs were isolated using differential centrifugation followed by iodixanol density gradient flotation. Particle number was determined using Nanoparticle Tracking Analysis (NTA). Mass spectrometry was used to assess the sEV proteome, and selected proteins were validated by immunoblot. Proteome pathways were analyzed using KEGG and CORUM. ResultsPathway analysis revealed an increase in metabolic proteins and proteasome components in sEV cargo released from hTCEpi cells exposed to HOS. These proteins were increased more than fourfold in HOS-sEVs. Examination of proteins involved in the endosomal pathway and NTA further confirmed an increase in HOS-sEV release. ConclusionOur findings suggest a potential mechanism whereby corneal epithelial cells exposed to HOS retain proteins involved in maintaining tissue integrity, while simultaneously releasing unneeded proteins involved in cell metabolism. The presence of metabolic proteins in sEVs may serve as early indicators of dry eye disease.

cell biology↗

bioRxiv2026

Organization of core mitochondrial replication components into multiphasic condensates

Genomes are organized across several hierarchical levels. Intracellular phase transitions compartmentalize many genomic processes, including transcription and DNA repair. However, little is known regarding how phase transitions contribute to replication, in which long strands of double- and single-stranded DNA need to be coordinated. Here, we investigated the molecular interactions driving the condensation of core mitochondrial replication components into mt-nucleoids. Complex phase behavior emerged among purified mt-replication components: each nucleic acid colocalized with its cognate architectural protein within multiphasic condensates. Using single-molecule experiments, we found that formation of ssDNA increased the partitioning of its cognate protein mtSSB within the condensate, consistent with the preferential localization of mtSSB to replicating mt-nucleoids. To develop mechanistic insights, we built a minimalistic coarse-grained model of mt-replication components that showed how interactions between binary pairs dictate their assembly within condensates. The multiphasic organization of mt-nucleoids has implications for how replication can be spontaneously organized in cells. HighlightsO_LIComplex co-phase behavior of TFAM-mtDNA depends on their affinity and DNA length C_LIO_LIMt-replication architectural proteins segregate ssDNA and dsDNA within condensates C_LIO_LImtSSB selectively partitions into actively replicating nucleoids in vivo C_LIO_LIExposure of ssDNA promotes mtSSB partitioning into TFAM-mtDNA condensates C_LI

biophysics↗

bioRxiv2026

Cytosolic interaction with RNA-helicase DDX39A titrates viral RNA G-quadruplex mediated α-Synuclein amyloidogenesis

Amyloid aggregates of -Synuclein are hallmark of Parkinsons Disease (PD) and related neurodegenerative diseases. -Synuclein, being an non-canonical RNA-binding protein (RBP), associates with other RBPs within cytosolic RNA-protein granules to modulate mRNA-stability. Conversely, mRNA G-quadruplexes (rG4s) expedite -Synuclein amyloidogenesis. However, spatiotemporal control on -Synuclein amyloidogenesis by other RBPs remains unexplored. Here, we report that RNA-dependent cytosolic interaction with DEAD-box RNA-helicase DDX39A decelerates -Synuclein amyloidogenesis. Viral infections transiently elevate rG4s in cytoplasm. Perturbing interactions between Synuclein and DDX39A using viral rG4s from H1N1-influenza and SARS-CoV-2 genomes expedites intracellular amyloidogenesis. Conversely, DDX39A overexpression alleviates -Synuclein amyloidogenesis in mouse primary neurons triggered by SARS-CoV-2 infection. We demonstrate that while DDX39A unwinds viral rG4s to mitigate -Synuclein sol-gel transition, its reciprocal cooperative phase separation with -Synuclein enhances the helicases rG4-unwinding activity. We propose that accelerated -Synuclein amyloidogenesis represents a trade-off within this RNA-protein interaction equilibrium, contributing to the viral etiology of PD.

biochemistry↗

bioRxiv2025

Loop Plasticity Drives Paralog-Specific Recognition in BET ET Domains

The bromodomain and extraterminal domain (BET) family of proteins recognizes diverse peptide motifs via their conserved ET domains, yet exhibits paralog-specific binding preferences with unclear structural origins. Here, we use extensive molecular dynamics simulations and ensemble-based analyses to investigate how two known pep-tide epitope binders - one from the host regulatory protein NSD3 and one from the murine leukemia virus integrase - interact with the ET domains of BRD3 and BRD4. Our results reveal that differences in peptide recognition are not driven by large conformational changes, but by subtle variations in loop dynamics and local secondary structure. Two divergent residues (positions 35 and 36) in the flexible loop connecting helices 2 and 3 shape the conformational ensemble of each paralog by modulating the formation of flanking helices (1 and 2), which in turn control the opening of the peptide-binding cavity. These intrinsic dynamical differences influence the number and stability of accessible binding modes, with BRD3 showing greater plasticity and weaker binding, particularly for NSD3. Our findings support a model in which local sequence variation tunes conformational selection and induced fit mechanisms, offering a structural rationale for paralog-specific targeting of BET proteins. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/687848v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@1215f22org.highwire.dtl.DTLVardef@1ecd6b0org.highwire.dtl.DTLVardef@2d45eorg.highwire.dtl.DTLVardef@1c473a2_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

Environmental Regulation of Toxin Production in Bacillus anthracis

Pathogenic Bacillus anthracis strains carry two plasmids - pX01, which encodes a tripartite protein exotoxin complex (PA, LF, and EF); and pX02, which encodes a poly-D-gamma-glutamic acid capsule. A multidomain transcription factor, AtxA, regulates the expression of these virulence genes. AtxA has two DNA-binding Helix-Turn-Helix (HTH) domains, two phosphoenolpyruvate:carbohydrate phosphotransferase system regulatory domains (PRD1 and PRD2), and a putative EIIB domain (a component of PTS sugar transport EII-complexes). Previous studies showed that glucose and CO2 increase AtxA-dependent toxin gene transcription, along with histidine phosphorylation of PRD1 and PRD2. Our transcriptional profiling of virulence factors, PA secretion, and fluorescent reporter strain analyses confirms a synergistic effect of glucose and CO2 on AtxA-dependent toxin production. Deletion of AtxA ({Delta}atxA) significantly reduced glucose uptake in bacteria, suggesting that AtxA may act within the glucose-PTS system. Mutation analysis of the EIIB domain of AtxA identified the cysteine at position 402 as essential for the transcriptional activity of AtxA. Deletion of glucose PTS permease PtsG ({Delta}ptsG) significantly reduced the expression of PA, LF, and EF. Loss of PtsG also caused attenuation in a mouse model of infection. Intracellular imaging using FLIM confirms a physical interaction of PtsG and AtxA through EIIB domain of AtxA. Using phosphomimetic and phosphoablative mutants of AtxA, we confirmed that the physical interaction of PtsG and AtxA is essential for AtxA activity. Finally, the synergy between glucose and CO2 was targeted by deleting pyruvate carboxylase Pyc ({Delta}pyc), which regulates anaplerosis. This deletion confirms that Pyc stimulates the level of phosphoenolpyruvate (PEP) and increases the phosphorelay in glucose-PTS to enhance AtxA activity. Therefore, we propose that a histidine-phosphorelay from PEP regulates AtxA via PTS enzymatic activity, impacting AtxA activity through physical interaction of AtxA and PtsG. Finally, we propose AtxA as an integral component of the glucose-PTS, where transcriptional activity of AtxA is regulated by environmental signals including glucose and CO2.

molecular biology↗

bioRxiv2025

Domain Compatibility and Linker Design Dictate the Success of Chimeric Cellulase Engineering

Efficient conversion of lignocellulosic biomass into fermentable sugars remains a major challenge due to individual cellulases limited synergy and catalytic efficiency. Engineering chimeric enzymes provides a promising strategy to streamline biomass hydrolysis by combining complementary catalytic activities in a single protein, thereby enhancing efficiency and lowering process costs. In this study, we constructed chimeric cellulases by fusing a thermophilic GH1 {beta}-glucosidase (TsBG) with endoglucanases from the GH5 (BsEG2) or GH9 (BlEG) families through flexible peptide linkers. Constructs containing BsEG2 exhibited a pronounced loss of {beta}-glucosidase activity and reduced endoglucanase activity, whereas substitution with the full-length BlEG restored dual functionality under identical design conditions. The optimized chimera (BlEG+(G4S)2+TsBG) demonstrated enhanced catalytic performance, with a 4.8-fold lower Km, a 1.7-fold higher Vmax, and an increased kcat (from 1088 to 1454 s-1). The chimera also exhibited enhanced stability, retaining [~]10 % higher activity under elevated cellobiose (up to 300 mM) and >90 % specific activity in 2.5 M NaCl. Molecular dynamics simulations further revealed that activity loss in non-optimized constructs arose from C-terminal structural instability and steric clashes, underscoring the critical role of domain orientation and linker flexibility in chimera design. These findings establish a chimeric cellulase that integrates endoglucanase and {beta}-glucosidase activities in a single polypeptide, offering a robust and cost-effective biocatalyst for lignocellulosic biomass conversion.

biochemistry↗

bioRxiv2025

A lipid plug affects K2P6.1(TWIK-2) function

Lipids are integral to ion channel function yet delineating mechanisms by which they affect function remains challenging. Within the K2P family of leak potassium channels1-3, observation of tubular densities interpreted as alkyl chains occupying lateral fenestrations linking the pore and bilayer4-8 raised the possibility that lipid access from the bilayer acts as a regulatory mechanism4-7. Here, we present cryo-electron microscopy (cryo-EM) structures of the human leak potassium channel K2P6.1 (TWIK2)9-11 and mutants in nanodisc and detergent environments that reveal an unusual conformation in the first selectivity filter (SF1) and a pair of two-chain lipids within the channel cavity (denoted the lipid plug). The chains of each plug lipid occupy separate binding sites that laterally extend to the bilayer from the channel cavity. One, the upper leg, matches the previously identified alkyl chain binding site4-8,12. The second, the lower leg, occupies a fenestration common with K2P1.1 (TWIK1)13. Together, they demonstrate a bidentate means to coordinate each plug lipid that offers a reinterpretation of previous observations. Structures of a K2P6.1 (TWIK2) mutant that directs the channel to the plasma membrane14 and an R257A mutant that increases function yield plugged and unplugged forms. Notably, the R257A plugged form shows a change in lipid plug position, indicating a key role for this residue in lipid binding. Together, our data suggest that occupation of the central cavity by the lipid plug serves as a mechanism to render the TWIK channels inactive and points to the importance of lipid plug removal to create an ion permeable pore. Such a mechanism could provide a potent way for limiting the leak function of K2Ps based on cellular location or other contextual factors.

biophysics↗

bioRxiv2025

Sexually-dimorphic neurons in the Drosophila whole-brain connectome

Sexual dimorphisms in the brain arise from differences in cell number, morphology, and connectivity, and underlie sex-specific behaviors. In Drosophila, these differences are largely governed by the transcription factors Fruitless (Fru) and Doublesex (Dsx), expressed in neurons implicated in reproductive and social behaviors. However, how these neurons are integrated into the connectome to drive different behaviors in different sexes remains unclear. Here, we identify 98 putative Fru- or Dsx-expressing cell types ([~]1700 neurons) in the female whole-brain connectome by matching electron microscopy reconstructions to light microscopy images. We then analyze their connectivity within the whole-brain network. Fru/Dsx neurons are strongly interconnected, but are not part of a private network. We measure distances to the sensory periphery to examine multisensory interactions, and map connections to descending neurons that drive behavior. We further cluster Fru/Dsx neurons based on whole-brain connectivity, and uncover functional groupings. We analyze a subset of strongly connected Fru/Dsx neurons to make functional predictions, and test some of these with experiments. Together, this work provides a brain-wide framework for understanding the organization of sexually dimorphic circuits and establishes a resource for dissecting the neural basis of social and sexual behaviors.

neuroscience↗

bioRxiv2025

Multiphasic Organization and Differential Dynamics of Proteins Within Protein-DNA Biomolecular Condensates

Biomolecular condensates formed through liquid-liquid phase separation are increasingly recognized as critical regulators of genome organization and gene expression. While the role of proteins in driving phase separation is well-established, how DNA modulates the structure and dynamics of protein-DNA condensates remains less well understood. Here, we employ a minimalist coarse-grained model to investigate the interplay between homotypic protein-protein and heterotypic protein-DNA interactions in governing condensate formation, composition, and internal dynamics. Our simulations reveal that DNA chain length and flexibility critically influence condensate morphology, leading to the emergence of multiphasic and core-shell organizations under strong heterotypic interactions. We find that DNA recruitment into the condensate significantly alters protein mobility, giving rise to differential dynamics of proteins within the condensate. By analyzing the distribution profiles of protein displacements, we identify up to five distinct diffusion modes, including proteins bound to DNA, confined within the dense phase, or freely diffusing. These results provide a mechanistic framework for interpreting spatially heterogeneous protein dynamics observed in chromatin condensates and emphasize the direct role of DNA in tuning condensate properties. Our findings provide new insights into how biophysical parameters may control the functional architecture of protein-DNA condensates in biological systems. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=158 SRC="FIGDIR/small/658691v1_ufig1.gif" ALT="Figure 1"> View larger version (73K): org.highwire.dtl.DTLVardef@108a818org.highwire.dtl.DTLVardef@153f9a1org.highwire.dtl.DTLVardef@29f220org.highwire.dtl.DTLVardef@1d74d6e_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

A High-Throughput, Flow Cytometry Approach to Measure Phase Behavior and Exchange in Biomolecular Condensates

Biomolecular condensates are essential for cellular organization, yet their formation dynamics and molecular content exchange properties remain poorly understood. In this study, we developed a high-throughput flow cytometry approach to quantify condensate formation, molecular colocalization, and dynamic exchange. Using self-interacting NPM1 condensates as a model system, we benchmarked the use of flow cytometry to broadly characterize their phase behavior across various protein concentrations and salt conditions. We further demonstrated that flow cytometry can assess the colocalization of macromolecules - including antibodies, lipids, small-molecule drugs, and RNAs, within NPM1 condensates. Importantly, we established the first assay to track real-time molecular exchange between preformed condensates and newly added, orthogonally tagged protein. This revealed that condensate aging significantly reduces molecular dynamisms, likely due to altered biophysical properties with time. Compared to conventional imaging techniques, which often require immobilized samples and complex experimental setups, our solution-based approach enables rapid, quantitative analysis of condensate behavior at the single-droplet level. This work provides a powerful framework for studying biomolecular condensates with enhanced precision and scalability, offering new insights into their dynamic properties and molecular interactions.

biophysics↗

bioRxiv2025

Influenza virus recruits PKCa-MEK1-ERK2 complex to regulate nuclear export of viral ribonucleoproteins and promote virus replication.

Host kinases had long been implicated in regulating various steps of influenza virus replication cycle. Previous studies showed that the protein kinase C (PKC) activated mitogen activated protein kinase (MEK)/ extracellular signal-regulated kinase (ERK) cascade promotes nuclear export of viral ribonucleoprotein complexes (RNPs), by triggering phosphorylation of viral nucleoprotein (NP), the major constituent of RNPs. But, the molecular mechanism by which PKC coordinates with specific members of the MAPK pathway to regulate NP phosphorylation remained obscure. Additionally, the molecular interactions of these kinases with NP and the spatiotemporal dynamics of such interactions have never been investigated. Here we unravel the existence of a tripartite PKC-MEK1-ERK2 complex that associates with influenza virus NP and mediates its phosphorylation during the course of infection. Using an analogue sensitive kinase, we show that ERK2 can directly phosphorylate NP at specific serine-threonine residues, which promote vRNP nuclear export and are indispensable for virus propagation. PKC not only activates the MAP kinase, but acts as a scaffold for mediating stable interactions between MEK1, ERK2 and NP, thereby forming an NP associated multi-kinase complex that facilitate its phosphorylation. This multiprotein complex localizes in the nucleus early during infection but into cytoplasm at later stages and overexpression of a dominant negative PKC blocks this complex formation, NP phosphorylation, vRNP export and progeny virus production. These data not only unravel a complex network of virus-host interactions supporting different influenza A and B virus replication, but also shade light upon an unexplored avenue of PKC mediated regulation MAPK pathway. SignificanceThe substrate specificity of kinases is the key for precise regulation of various signaling cascades and can be governed by direct kinase-substrate interaction or indirect interaction mediated through scaffolding or anchoring proteins. This study shows how influenza virus exploit a well-known cellular kinase, PKC, as a scaffold protein to activate and recruit other cellular kinases, MEK1 and ERK2, upon viral replication machinery, RNPs. This RNP associated multi-kinase complex facilitates ERK2 mediated phosphorylation of viral NP protein, which regulates RNP nuclear export and ultimately the production of new virion particles. This work elucidates an unconventional mechanism of kinase-substrate interaction which is critical for influenza virus replication and hence paves the way towards the development of novel host directed anti-influenza therapy.

molecular biology↗

bioRxiv2025

Monoclonal antibody to Filarial serpin Wb123 impedes the urokinase plasminogen activator receptor-mediated Alternative activation of macrophages

Macrophages play a multifaceted role in mounting an immune response against pathogens through phagocytosis, antigen presentation and cytokine production. Activated macrophages are critical for the initiation, maintenance, and resolution of inflammation. They can either be classically activated (Th1 response), which promotes inflammation or alternatively activated (Th2 response), which resolves inflammation. The alternate activation of macrophages, along with diminished T cell response, is thought to be an important immune evasion strategy employed by the filarial parasites. However, the mechanism behind filaria-induced alternate activation remains unclear. In this study, by using in-silico approach we identified filarial serpins which are highly expressed in the infective L3 larval stages. We characterized the filarial serine protease inhibitor, Wb123 and established its role in alternate activation. We observed that Wb123 impairs nitric oxide (NO) and reactive oxygen species (ROS) expression, which plays a crucial role in mounting a strong immune response. Surprisingly, we also observed elevated IL6 expression and phosphorylation of STAT3, indicating IL-6-dependent alternate activation. Our findings indicate that the urokinase plasminogen activator receptor (uPAR) is essential for Wb123-induced alternate activation. Furthermore, we demonstrated that the monoclonal antibody MAbG8 impedes the Wb123-induced alternate activation, as shown by reduced CD163 expression along with increased ROS and uPA expression in response to lipopolysaccharide (LPS) and interferon-gamma (IFN-{gamma}). Overall, our study identifies the filarial serpin Wb123 and highlights its potent role in alternative activation. This interaction reveals, for the first time a mechanism exploited by filarial parasites to evade a strong pro-inflammatory immune response.

cell biology↗

bioRxiv2025

Multitask deep learning for the emulation and calibration of an agent-based malaria transmission model

Agent-based models of malaria transmission are useful tools for understanding disease dynamics and planning interventions, but they can be computationally intensive to calibrate. We present a multitask deep learning approach for emulating and calibrating a complex agent-based model of malaria transmission. Our neural network emulator was trained on a large suite of simulations from the EMOD malaria model, an agent-based model of malaria transmission dynamics, capturing relationships between immunological parameters and epidemiological outcomes such as age-stratified incidence and prevalence across eight sub-Saharan African study sites. We then use the trained emulator in conjunction with parameter estimation techniques to calibrate the underlying model to reference data. Taken together, this analysis shows the potential of machine learning-guided emulator design for complex scientific processes and their comparison to field data. Author summaryMathematical models can help understand and design interventions for infectious diseases such as malaria, but they can be complex and time-consuming to work with. In this study, we developed a machine learning approach to create a fast and accurate emulator for a detailed malaria transmission model. Our emulator can quickly predict various disease outcomes based on different immune system parameters. We trained it using a large set of simulations created using the EMOD malaria model and tested it against real-world data from multiple African countries. The emulator not only matches the original models predictions closely, but can also be used to efficiently find the best parameter values to match field observations. We hope that this work can serve as a demonstration of machine learning tools to link complex models of disease transmission to field data.

bioinformatics↗

bioRxiv2024

Sex-specific attenuation of photoreceptor degeneration by reserpine in a rhodopsin P23H rat model of autosomal dominant retinitis pigmentosa

Inherited retinal degenerations (IRDs) constitute a group of clinically and genetically diverse vision-impairing disorders. Retinitis pigmentosa (RP), the most common form of IRD, is characterized by gradual dysfunction and degeneration of rod photoreceptors, followed by the loss of cone photoreceptors. Recently, we identified reserpine as a lead molecule for maintaining rod survival in mouse and human retinal organoids as well as in the rd16 mouse, which phenocopy Leber congenital amaurosis caused by mutations in the cilia-centrosomal gene CEP290 (Chen et al., 2023). Here, we show the therapeutic potential of reserpine in a rhodopsin P23H rat model of autosomal dominant RP. At postnatal day (P) 68, when males and females are analyzed together, the reserpine-treated rats exhibit higher rod-derived scotopic b-wave amplitudes compared to the controls with little or no change in scotopic a-wave or cone-derived photopic b-wave. Interestingly, the reserpine-treated female rats display enhanced scotopic a- and b-waves and photopic b-wave responses at P68, along with a better contrast threshold and increased outer nuclear layer thickness. The female rats demonstrate better preservation of both rod and cone photoreceptors following reserpine treatment. Retinal transcriptome analysis reveals sex-specific responses to reserpine, with significant upregulation of phototransduction genes and proteostasis-related pathways, and notably, genes associated with stress response. This study builds upon our previously reported results reaffirming the potential of reserpine for gene-agnostic treatment of IRDs and emphasizes the importance of biological sex in retinal disease research and therapy development.

neuroscience↗

bioRxiv2024

Identification of novel thiazole derivatives as flaviviral protease inhibitors against DENV and JEV

Flaviviruses are the causative agents of viral hemorrhagic fever (VHF) globally and have demonstrated the capacity to result in fatal outcomes if not managed effectively. Among different types of flaviviruses, dengue (DENV) and Japanese encephalitis (JEV) are the most common in tropical and subtropical countries. Given the scarcity of effective vaccines against flaviviral infections, small molecule agents that target crucial viral proteins emerge as the sole feasible option. This study outlines the synthesis of novel thiazole compounds as flavivirus NS2B-NS3 protease inhibitor and characterization of their antiviral activity against DENV and JEV. We synthesized a heterocyclic template derived from a substrate-based retrotripeptide dengue protease inhibitor, leading to forty-eight thiazole derivatives. Two compounds demonstrated significant inhibition of dengue virus protease activity in vitro. Comprehensive characterization of these two compounds was conducted through biochemical assay which revealed an uncompetitive mode of inhibition. Subsequent cell-based assays using Dengue and Japanese encephalitis viruses as representatives Flaviviruses imparted the potential of these compounds to block viral RNA synthesis, and viral replication. Finally time-course experiments unveiled that the two compounds impeded the accumulation of viral genomic RNA primarily at later stages of infection, aligning with their capacity to hinder NS2B-NS3 protease activity, polyprotein processing and viral genomic RNA replication. Together our work presents the development and validation of flavivirus protease inhibitors with therapeutic potential against Dengue and Japanese encephalitis virus.

microbiology↗