Biology subjects

Kumar, M.

Publications and source records attributed to Kumar, M..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Unlocking Antiviral Potentials of Traditional Plants: A Multi-Method Computational Study against Human Metapneumovirus (HMPV)

Human metapneumovirus (HMPV) remains a critical challenge in respiratory healthcare, particularly due to the lack of targeted antiviral therapies and vaccines. This study employs an integrative computational framework to identify and evaluate the antiviral potential of nature-based compounds derived from traditional medicinal plants. A suite of advanced methodologies, including virtual screening, molecular docking, molecular dynamics (MD) simulations, density functional theory (DFT) calculations, pharmacophore modeling, and ADMET profiling, was utilized to comprehensively analyze candidate compounds. Among the tested compounds, Glycyrrhizin exhibited exceptional properties, with a binding energy of -65.4 kcal/mol, eight stabilizing hydrogen bonds, and remarkable dynamic stability (RMSD 1.3 [A]). Similarly, Withaferin A demonstrated a binding energy of -63.7 kcal/mol and high pharmacokinetic potential. Quantum-level analyses revealed favorable electronic properties, while ADMET profiling confirmed the compounds safety and drug-like characteristics. These findings underscore the potential of traditional phytochemicals to serve as lead candidates in antiviral drug development. This research bridges the gap between traditional medicine and modern computational techniques, paving the way for innovative and efficient therapeutic strategies against HMPV.

bioinformatics↗

bioRxiv2025

Exploring FDA-Approved Antiviral Drugs for Human Metapneumovirus Treatment: Integrative Computational Insights

This study leverages advanced computational methodologies to identify potential antiviral therapies targeting human metapneumovirus (HMPV), focusing on FDA-approved antiviral drugs and control compounds. A comprehensive computational framework, encompassing virtual screening, molecular docking, molecular dynamics (MD) simulations, density functional theory (DFT) analysis, and ADMET profiling, was employed. Key findings highlight Remdesivir and Peramivir as the most promising candidates, with superior binding energies (-9.5 kcal/mol and - 9.2 kcal/mol, respectively), stable interaction profiles, and robust pharmacological properties. Molecular dynamics revealed exceptional stability for Remdesivir, with the lowest RMSD (0.20 nm), and pharmacophore analysis emphasized its strong hydrogen bonding and hydrophobic interactions. ADMET profiling confirmed their high bioavailability (85% {+/-} 3 for Remdesivir) and low toxicity, positioning these drugs for repurposing against HMPV. This integrative study underscores the potential of computational tools in streamlining drug discovery and advancing therapeutic interventions.

bioinformatics↗

bioRxiv2025

Repurposing Metal-Based Therapeutics for Human Metapneumovirus (HMPV): An Integrative Computational Approach

Human metapneumovirus (HMPV) poses a significant global health challenge, with limited therapeutic options available. This study employs a comprehensive computational framework to repurpose metal-based drugs as potential HMPV inhibitors. A library of compounds was systematically evaluated using virtual screening, high-precision molecular docking, molecular dynamics (MD) simulations, density functional theory (DFT) calculations, molecular electrostatic potential (MESP) mapping, and pharmacophore modeling. Key candidates, including Auranofin, Silver Sulfadiazine, and Gallium Nitrate, demonstrated high binding affinities ({Delta}Gbinding: -68.5 to -62.7 kcal/mol) and favorable stability metrics (RMSD: 2.1-2.4 [A]). ADME-toxicity (ADMET) profiling highlighted Auranofins robust bioavailability (80%) and extended half-life (8.5 hours), while Ribavirin and Favipiravir emerged as safe controls with minimal toxicity. Quantum chemical analyses reinforced the compounds electronic stability and reactivity. This integrative study provides a promising avenue for repurposing existing therapeutics, bridging computational insights with translational potential to combat HMPV.

bioinformatics↗

bioRxiv2025

Improved Functional Classification of Hydrolases through Pairwise Structural Similarity of Reaction Cores

We report a systematic pipeline is for extracting the catalytically relevant reactive site in addition to the surrounding allosterically linked residue shells around the reaction site of the most diverse enzyme class - hydrolases, with known experimental structures. We first successfully extract 40196 such hydrolase reaction cores (RC) and collates them into a publicly accessible reaction core collection (RC-Hydrolase). We perform 128M pairwise shape comparison across RC-Hydrolase using a three-dimensional search engine and present 155,329 pair instances clustering them by 60% or higher similarities in a publicly available, visually interactive dataset. Robustness of defined RCs is shown to successfully capture experimentally known function-enhancing mutations distal to the active site in PETases. Allowing comparisons of enzyme reaction centers across functional spaces (ligands bound, EC classification numbers, and expression hosts) enables identification of enzyme backbones which can be minimally mutated to accommodate more than one type of catalytic activity thereby aiding rational design of multifunctional enzymes. We also demonstrate how such versatile enzyme backbones could be leveraged by the latest diffusion-based protein design models to design bespoke libraries of small molecule inhibitors, and structurally stable multifunctional enzyme pockets. With only sporadic successes in multifunctional enzyme design thus far, we provide strong structural priors for machine-learning-guided advanced enzyme engineering in the future.

bioinformatics↗

bioRxiv2025

GPR15LG binds CXCR4 and synergistically modulates CXCL12-induced cell signaling and migration

GPR15LG, a chemokine-like ligand for the G-protein coupled receptor 15 (GPR15), is abundantly expressed in the gastrointestinal mucosa and inflamed skin. Emerging evidence suggests its involvement in inflammatory disorders and cancers. This study investigates the effects of GPR15LG on the signaling and downstream functions of C-X-C chemokine receptor type 4 (CXCR4), which plays a critical role in immune cell trafficking and cancer metastasis. The results demonstrate that GPR15LG binds to the orthosteric site of CXCR4, modulating downstream signaling in a context-dependent manner. Specifically, GPR15LG enhances CXCL12-mediated CXCR4 signaling synergistically, promoting wound healing and cell migration across various cell types, including CD4+ T cells and cancer cells. These findings underscore the role of GPR15LG in inflammation and metastasis, offering potential therapeutic avenues for CXCR4-mediated diseases. TeaserGPR15LG binds CXCR4 thereby modulating CXCL12/CXCR4 signaling and immune and cancer cell trafficking.

cell biology↗

bioRxiv2025

Endogenous gene tagging with FnCas9 to track and sort neural lineages from 3D cortical organoids

Neural lineage tracing, or molecular dissection of lineage-specific brain cell types, is used in many labs to learn how neurons grow and mature. However, these studies depend on the growth and characterization of pure cultures, which takes a long time because of biochemical or fluorescence-based isolation through cell surface markers that overlap. These lineage-specific cells, however, can be efficiently sorted using endogenously expressed, fluorescently labeled marker genes. The labeled cell lines can be used not only to differentiate and purify different types of neurons but also to study the long-term development of neural lineages in two- and three-dimensional development models. In this study, we used an orthogonal Cas protein to generate human embryonic stem cell (hESC) lines with genetically labeled fluorescent barcodes for discrete neural lineages. We use these lines to successfully demonstrate spatial and temporal tracing of DCX-positive neuroblasts and immature neuronal cells within 2D neural cultures and 3D cortical organoids derived from human embryonic stem cells. This allowed the purification of endogenously tagged live neural cells from heterogeneous cortical organoids across multiple stages of development.

neuroscience↗

bioRxiv2025

Harnessing Computational Insights to Identify Potent Inhibitors for Human Metapneumovirus (HMPV): A Synergistic Approach with Natural Compounds

Human metapneumovirus (HMPV), a leading cause of acute lower respiratory tract infections, has emerged as a global health challenge due to its high prevalence, particularly among children, the elderly, and immunocompromised individuals. Despite its significant impact, no targeted antivirals or vaccines are available. This study employs a comprehensive computational pipeline to identify and evaluate potential inhibitors of the HMPV matrix protein (PDB: 5WB0). Natural compounds such as epigallocatechingallate (EGCG), rutin, and quercetin, along with control drugs, were screened for their therapeutic potential.Virtual screening identified EGCG (-9.1 kcal/mol), rutin (-9.0 kcal/mol), and quercetin (-8.8 kcal/mol) as top binders, surpassing standard drugs like ribavirin (-8.9 kcal/mol). Molecular docking revealed stable binding interactions, including hydrogen bonding with residues Arg143 and Glu186. Molecular dynamics (MD) simulations over a 1000 ns trajectory confirmed the stability of these complexes, with EGCG displaying the lowest RMSD (2.1 [A]) and consistent hydrogen bonding throughout the simulation. Density Functional Theory (DFT) calculations highlighted favorable electronic properties, with EGCG showing a low band gap (3.29 eV) and high dipole moment (3.12 D), indicative of strong reactivity and binding potential. ADMET profiling revealed excellent oral bioavailability for EGCG (84%) and quercetin (88%), with minimal toxicity risks. The Molecular Electrostatic Potential (MESP) mapping identified highly reactive regions on the molecular surface, correlating with nucleophilic and electrophilic binding capabilities. The findings position EGCG, rutin, and quercetin as promising candidates for HMPV therapy, providing a strong foundation for further experimental validation and preclinical development.

bioinformatics↗

bioRxiv2024

DIS3L2 is essential for neural crest survival by modulating Akt signaling

DIS3 like 3-5 exoribonuclease 2 (DIS3L2), an exoribonuclease is known to preferentially degrade uridylated RNA substrates, miRNAs, and ncRNAs. Recent reports show that DIS3L2 also plays a key role in cell proliferation and tumor growth. Mutations in DIS3L2 are associated with congenital disorders such as Perlman syndrome, yet the developmental functions of DIS3L2 remain unknown. We report the developmental role of dis3l2 in neural crest specification, patterning, and survival in the zebrafish embryo. Dis3l2 morphants exhibited reduced expression of neural crest specifier genes coupled with extensive apoptosis in the neural tissue. Our study demonstrates that DIS3L2 regulates neuronal apoptosis and progenitor functions through the Akt -GSK3{beta} signaling pathway. Additionally, we show that DIS3L2 is essential for early mitoses in the zebrafish blastula and plays a key role in maintaining spindle length at metaphase, chromosome congression, spindle pole integrity, and cytokinesis. In summary, we identify new functions of exoribonuclease DIS3L2 in cell fate specification, neural progenitor survival, and mitosis during embryogenesis which form the underlying basis of DIS3L2-associated overgrowth Perlman syndrome. Plain English summaryDIS3 like 3-5 exoribonuclease 2 (DIS3L2) degrades mRNAs and various RNA substrates in the eukaryotic cells. DIS3L2 mutations are associated with congenital overgrowth syndromes like Perlman syndrome and Wilms tumor. The role of DIS3L2 in regulating the embryonic processes remains poorly understood. Our study delineates the developmental functions of DIS3L2 in cell fate determination, survival, and proliferation during vertebrate embryogenesis using zebrafish embryos as a model. We show that DIS3L2 plays a key role in neural crest survival and patterning by modulating Akt-GSK{beta} signaling. We also report unique molecular functions of DIS3L2 in mitotic fidelity and cytokinesis during embryonic mitoses. Our study provides novel insights into the molecular functions of DIS3L2 in regulating neuronal apoptosis during embryonic brain morphogenesis and associated CNS disorders.

developmental biology↗

bioRxiv2024

Heterologous immunization strategy developed broadly reactive human monoclonal antibodies against the BK virus

BK polyomavirus (BKV) causes polyomavirus-associated nephropathy (BKV-nephropathy) and polyomavirus-associated hemorrhagic cystitis (BKV-HC) following kidney transplantation and allogeneic hematopoietic stem cell transplantation (HSCT). BKV strains consist of four distinct genotypes (BKV-I, - II, -III, and -IV) with more than 80% of individuals seropositive for the BKV-I genotype, and lower prevalences of infection or co-infection with the other genotypes. BKV-nephropathy occurs widely in immunosuppressed transplant recipients, with the recommended treatment including reduction of immunosuppressive drugs. High serum titers of BKV-neutralizing antibodies and treatment with BKV-neutralizing intravenous immunoglobulin (IVIG) are associated with reduced levels of BKV-DNAemia in kidney transplant recipients, suggesting anti-BKV antibodies can limit viral load. Thus, we set out to generate broadly neutralizing human monoclonal antibodies (mAbs) against the viral protein 1 (VP1) major capsid protein of BKV genotypes I-IV using VelocImmune(R) transgenic mice that encode for human immunoglobulins. Hybridoma clones from VelocImmune(R) mice immunized with combinations of BKV I-IV VP1 and respective genotypes of BKV pseudoviruses (BK-PsV) were screened using a high-throughput binding assay against BKV-I VP1 expressed in HEK-293 cells. The VP1-binding hybridoma clones were then assessed for neutralization with BK-PsV consisting of respective VP1 proteins from BKV-I, -II, -III, or -IV on the virion surface. Overall, thirty-six broadly cross-neutralizing mAbs against BKV-I, -II, -III, and -IV -were identified. Twenty of the cross-reactive immunoglobulins were subjected to nucleotide sequencing resulting in six clonotype families with fourteen genetically distinct immunoglobulins. Several of the most effective mAbs were fully humanized with the IgG1 Fc domain and broad neutralization of BK-PsV-I, II, III, and IV genotypes with IC50s ranging from [~]7-200 pM. Thus, these cross-neutralizing mAbs represent potential biologics to developed into BKV therapeutics.

microbiology↗

bioRxiv2024

Facilitating Gene Editing in Human Lymphoma Cells Using Murine Ecotropic γ-Retroviruses

Genetic modifications using CRISPR-Cas9 have revolutionized cancer research and other pre-clinical studies. Exceptionally, these efficient tools are inadequate in a few disease models and cell lines due to the aberrant differentiation states and the accumulation of excessive somatic mutations that compromise the robustness of viral gene delivery and stable transduction. A couple of B lymphoma cell lines fall into this category where lentiviral transfection becomes inefficient and exhibits variable efficiency. Additionally, lentiviral delivery requires high biosafety levels. To address this challenge, we have developed a two-step strategy that supports CRISPR-Cas9 through lentivirus and murine ecotropic {gamma}-retrovirus. By engineering B lymphoma cell lines to express Cas9 and mCat-1, a specific receptor for ecotropic retroviruses, we enable efficient and safe gene editing through ecotropic {gamma}-retrovirus. We demonstrate the efficacy of this method by generating IgM-deficient B lymphoma cell lines. This innovative approach simplifies protocols, enhances accessibility, and paves the way for standardized gene manipulation of B cell lymphoma models for molecular cell biology research.

molecular biology↗

bioRxiv2024

Proteome allocation of the microbiome reveals how diet and metabolic dysbiosis impact disease

The gut microbiome plays a critical role in human health, spurring extensive research into host-microbe interactions using multi-omic technologies. Although these tools offer valuable insights, they often fall short in capturing the complexity of microbial interactions and assigning causality to disease onset, progression, and treatment. Proteome allocation is intertwined with microbial interactions, yet there is little mechanistic knowledge. Here, we deploy models of metabolism and gene expression (ME-models) that predict proteome allocation. Despite their potential, their deployment has been limited by the laborious reconstruction process. To address this, we reconstructed 495 ME-models for human gut microbes using an automated pipeline. By integrating ME-models with multi-omics data from patients with inflammatory bowel disease (IBD), we identified taxa responsible for variations in amino acids, short-chain fatty acids, and pH in the gut of IBD patients. Thus, this approach provides a mechanistic understanding and paves the way for new intervention strategies.

systems biology↗

bioRxiv2024

Developmental functions of rapgef1b in neural crest specification and presomitic mesoderm patterning

RAPGEF1, a guanine nucleotide exchange factor, regulates signaling and cytoskeletal dynamics in mammalian cells, yet its role in development remains unclear as Rapgef1 null mouse embryos do not survive beyond implantation. We demonstrate that zebrafish rapgef1 is maternally expressed, and its paralogs, rapgef1a and rapgef1b, exhibit tissue and developmental stage-specific splicing. Disruption of rapgef1b caused brain and somite defects, impaired cranial neural crest specification, and microcephaly-like phenotypes, uncovering its previously uncharacterized functions in morphogenesis and tissue patterning. Transcriptomic analyses and differential gene expression provide fresh insights into the developmental functions of rapgef1b in presomitic mesoderm and somitogenesis by modulating the Wnt/{beta} catenin signaling. Rapgef1b deficient embryos also showed spindle pole disorganization and chromosome mis-congression, linking Rapgef1 to centrosome-mediated mitotic fidelity. Together, our findings identify Rapgef1b as a key regulator of neural crest development, mesodermal morphogenesis, and early mitoses, highlighting its tissue-specific functions during vertebrate embryogenesis. TeaserIn this study, we show that rapgef1b is essential for shaping the embryonic brain, somites, and body axis by regulating gene expression, cell division, survival, and differentiation. Our findings reveal a new dimension of signaling-mediated cell fate specification during early vertebrate development.

developmental biology↗

bioRxiv2024

A TORC1-PHR1 signaling axis regulates phosphorus starvation and immunity signaling network in Arabidopsis

The Target of Rapamycin Complex 1 (TORC1) is a crucial eukaryotic kinase that modulates growth in response to nutrient availability. Phosphorus (P) is an essential macronutrient, and its deficiency induces extensive reprogramming of growth and defense strategies in plants. This process involves Phosphate Starvation Response 1 (PHR1), a master regulator of the Phosphate Starvation Response (PSR). In this study, we identify a novel, non-canonical role for TORC1 in regulating P starvation responses in Arabidopsis. We demonstrate that P limitation activates TORC1, leading to the stabilization of PHR1. Inhibition of TORC1 increased sensitivity to P starvation, accompanied by disruption of starvation-induced transcriptional reprogramming. Additionally, our results reveal that the TORC1-PHR1 signaling axis plays a crucial role in reprogramming the expression of genes involved in the plant immune signaling network. This regulation is critical for the symbiotic association with the endophytic fungus Piriformospora indica under P starvation. These findings underscore the significant role of the TORC1-PHR1 module in orchestrating the PSR and highlight the evolutionary adaptation of TORC1 signaling pathways in plants.

plant biology↗

bioRxiv2024

In vivo imaging of T-cell coregulator B7-H4 reveals protumor macrophage status in prostate cancer

BackgroundB7-H4 is a cell surface ligand overexpressed by tumors to inhibit T cell functions and evade the immune system. B7-H4 is minimally expressed in normal tissues but is highly expressed by various cancer cells and tumor-associated macrophages (TAM). Despite its importance as an immune checkpoint inhibitor, no imaging techniques specifically targeting B7-H4 have been established. To close this gap, we sought to assess the ability of a monoclonal antibody (mAb) based immunoPET radiotracer to visualize B7-H4 in human and murine prostate cancer models. MethodsAnti-B7-H4 mAb clone 2H9 was functionally characterized for binding to the human and mouse B7-H4 protein. The antibody was conjugated with chelator p-SCN-Bn-Deferoxamine (DFO) and labeled with radioisotope Zirconium-89 (89Zr) to obtain immunoPET tracer 89Zr-2H9-mAb. The biolayer interferometry method was used to test the binding kinetics of DFO-2H9-mAb compared to that of parental 2H9 mAb. A group of six athymic nude mice with human DU145 prostate tumor xenograft underwent MicroPET imaging after tail vein injection of [~]150{micro}Ci 89Zr-2H9-mAb or non-binding 89Zr-Isotype-mAb. Next, immunocompetent C57BL/6J mice with TRAMP-C2 tumors each were injected with either PBS (n=8), cold 2H9 mAb (10mg/kg) to block B7-H4 (n=6), or chlodronate liposome (15mg/kg) to cause total macrophage depletion (n=6), followed by 89Zr-2H9-mAb MicroPET imaging. An ex vivo biodistribution assay was performed after 144 hr post radiotracer injection. Tumor radiotracer binding, quantified as a percentage injected dose per gram (%ID/g), was compared between different experimental groups using two-way ANOVA with Bonferroni or Tukey corrections. ResultsImmunoconjugation yielded a 2.59 {+/-} 0.08 chelator-to-antibody ratio, and the binding of DFO conjugated 2H9-mAb was similar to that of parental 2H9 mAb, with unaffected affinity in targeting B7-H4 protein moiety. The radiochemical purity of 89Zr-2H9-mAb tracer was yielded >95% with an average specific activity of 5{micro}Ci/{micro}g antibody. DU145 tumor xenografts demonstrated significantly stronger radiotracer binding at 24, 48, 72, 96, and 120 hr than the non-binding isotype control group. In TRAMP-C2 tumor xenografts, the radiotracer binding in B7-H4 blocked tumors was significantly lower than in the non-blocked PBS-injected group. Macrophage depletion resulted in a significant decrease in tumor binding compared to the control group. 89Zr-2H9-mAb could efficiently distinguish tumors with high sensitivity, showing a high correlation between PET imaging and bio-distribution. More importantly, the immunohistochemistry of the harvested tumor revealed no significant difference between the three groups, as discernible through in vivo PET imaging. ConclusionThis study highlights the potential of B7-H4 immunoPET imaging for monitoring immunotherapy response. With the emerging potential of B7-H4 blocking as an immunotherapeutic, immunoPET imaging could be readily expanded to patient stratification and therapy monitoring. B7-H4 imaging could augment our understanding of B7-H4 dynamics in response to various therapeutic interventions in clinical trials. The new B7-H4 immunoPET probe is, in principle, clinically translatable.

immunology↗

bioRxiv2024

FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models

Genome-scale metabolic models (GEMs) and other constraint-based models (CBMs) play a pivotal role in understanding biological phenotypes and advancing research in areas like metabolic engineering, human disease modelling, drug discovery, and personalized medicine. Despite their growing application, a significant challenge remains in ensuring the reproducibility of GEMs, primarily due to inconsistent reporting and inadequate model documentation of model results. Addressing this gap, we introduce FROG analysis, a community-driven initiative aimed at standardizing reproducibility assessments of CBMs and GEMs. The FROG framework encompasses four key analyses--Flux variability, Reaction deletion, Objective function, and Gene deletion--to produce standardized, numerically reproducible FROG reports. These reports serve as reference datasets, enabling model evaluators, curators, and independent researchers to verify the reproducibility of GEMs systematically. BioModels, a leading repository of systems biology models, has integrated FROG analysis into its curation workflow, enhancing the reproducibility and reusability of submitted GEMs. In our study evaluating 65 GEM submissions from the community, approximately 40% reproduced without intervention, 28% requiring minor adjustments, and 32% needing input from authors. The standardization introduced by FROG analysis facilitated the detection and resolution of issues, ultimately leading to the successful reproduction of all models. By establishing a standardized and comprehensive approach to evaluating GEM reproducibility, FROG analysis significantly contributes to making CBMs and GEMs more transparent, reusable, and reliable for the broader scientific community.

systems biology↗

bioRxiv2024

Insights from Molecular Docking and Dynamics Simulations of P2RX7-????Syn Complex

Alpha-synucleinopathies, characterized by extracellular alpha-synuclein (Syn) accumulation and aggregation, have been linked to neurological disorders including Parkinsons disease (PD) and multiple system atrophy (MSA). Syn interacts with membrane proteins, phospholipids, and cholesterol, leading to membrane damage and inflammation. This interaction heightens the likelihood of Syn engaging with P2RX7, a non-selective cationic transmembrane receptor that is primarily overexpressed in immune and neural cells. Activation of P2RX7 by Syn is implicated in neuronal degeneration, potentially causing pore dilation and increased inflammation. However, the precise molecular mechanisms and binding sites for this interaction, as well as the conformational dynamics of P2RX7 in response to Syn, remain unclear. We attempted to elucidate the molecular mechanisms and binding sites for P2RX7-Syn interaction, by integrating the data curation, molecular docking, and molecular dynamics (MD) simulations coupled with structural analyses. We elucidated interactions between P2RX7 and the N-terminal domain (NTD) of Syn using cryo-EM structures of P2RX7 in both ATP-bound and unbound states and assessed how Syn influences P2RX7structural and functional dynamics. Initially, the analyses revealed that Syn interactomes are mainly involved in regulating mitochondrial homeostasis, while P2RX7 interactors are linked to receptor internalization and calcium transport. Molecular docking with six tools identified that Syn-NTD fragments preferentially bind to the proximal region of P2RX7 transmembrane domain. Microsecond all atom MD simulations in a POPS lipid bilayer showed significant atomic fluctuations, particularly in the head region, lower body, and large loop of P2RX7 cytoplasmic domain. Secondary structure analysis indicated unfolding in regions related to pore dilation and receptor desensitization. Further by contact-based and solvent accessibility analyses, along with protein structure network (PSN) studies, we identified crucial residues involved in Syn-P2RX7 interactions. This insight deepens our understanding of how Syn and P2RX7 interact, offering a detailed atomic view of the structural and functional changes that occur during these interactions. This understanding could advance our grasp of neurodegenerative diseases and be vital for devising future preventive and therapeutic strategies. Author summaryNeural homeostasis is crucial for neuron survival and function, with protein-protein interactions, particularly between Syn and P2RX7, playing a vital role. Accumulation of Syn can worsen neuronal damage through its interaction with P2RX7. Traditional biological experiments struggle with time-scale limitations, but advances in computational methods--like molecular dynamics (MD) simulations and protein structure network (PSN) analysis--allow detailed atomic-level study of these interactions. This study used these computational tools to explore the dynamics between Syn and P2RX7, aiming to uncover structural and functional changes relevant to protein interactions and neural damage. The findings contribute to understanding the dynamics of P2RX7-Syn interactions.

bioinformatics↗

bioRxiv2024

Cellulose synthesis in Arabidopsis by heterologous expression of lower plants CESA proteins

Cellulose is the most abundant component of plant cell walls where it plays a pivotal role in regulating plant cell size and shape. In addition, as a component of the woody secondary cell walls, cellulose represents an abundant renewable resource to produce materials and chemicals. In higher plants, cellulose is synthesised at the plasma membrane by a hexameric protein complex, known as the rosette, that is able to synthesise 18 glucose chains that bond together to form a microfibril. While this rosette structure is highly conserved, significant variation exists in the structure and physical properties of cellulose found in different cell types and synthesised by different species. In this study, we surveyed the ability of the catalytic subunits of the cellulose synthase complex (CESA proteins) from a range of lower plant species to synthesise cellulose in the Arabidopsis secondary cell walls. Several lower plant CESA proteins are able to function in higher plants in conjunction Arabidopsis CESAs. Additionally, two moss CESA proteins synthesised cellulose in absence of Arabidopsis CESAs but with reduced crystallinity, indicating that it is the structure of CESA proteins themselves and not the cellular environment that determines the properties of the cellulose synthesised.

plant biology↗

bioRxiv2024

Primary bovine white blood cells support dissemination of Lumpy Skin Disease Virus while suppressing viral replication

Lumpy skin disease (LSD) is a severe infectious, emerging transboundary disease of cattle, caused by a Pox family DNA virus. Lumpy skin disease virus (LSDV) infection is associated with a febrile response followed by emergence of widespread dermal nodules. In addition to the skin, LSDV resides in multiple internal organs and can be isolated from the blood of infected cattle. LSDV is suggested to be mechanically transmitted by biting arthropods. Live attenuated vaccines are commonly used to control disease and its spread. We have characterized the tropism, replication, and dissemination of a LSDV field isolate and of an attenuated vaccine strain using in vitro systems. To follow virus infection and dissemination in living cells, we have generated recombinant viruses expressing green fluorescent protein (GFP) under a synthetic viral promoter. Recombinant, GFP-expressing, LSDVs demonstrated similar replication kinetics to their corresponding parental LSDV strains in a bovine kidney cell line (MDBK). We further demonstrated that LSDV-GFP productively replicated in a bovine macrophage cell line and in primary bovine foreskin cells with no apparent differences between the field isolate and the vaccine strain. When bovine peripheral blood mononuclear cells (PBMCs) were infected with either LSDV recombinant strain, we observed specific viral driven GFP fluorescence as well as significant viral gene expression. However, infected PBMCs failed to support substantial viral DNA replication and release of infectious progeny. Subsequent analysis of the anti-viral response revealed that heat treated (HT) LSDV induced the expression of interferon- stimulated genes (ISGs) in PBMCs, but this response was suppressed by infectious viruses. Finally, we show that despite failed replication, LSDV infected PBMCs transmitted the virus to recipient co-cultured MDBK cells and produced infectious foci, suggesting a potential role of PBMCs in LSDV dissemination. HighlightsO_LIVirulent and attenuated LSDV productively replicated in bovine kidney and bovine macrophage cell lines as well as in primary fibroblasts. C_LIO_LIAdherent white blood cells were susceptible to LSDV field and attenuated vaccine infection. C_LIO_LILSDV showed active viral transcription in PBMCs yet no significant viral genome replication or production of infectious progeny. C_LIO_LIPBMCs infected with heat-treated LSDV but not with fully infectious viruses upregulated ISGs RNA. C_LIO_LIPBMCs transmitted and disseminated LSDV to contacting permissive cells. C_LI

microbiology↗