Biology subjects

Islam, M.

Publications and source records attributed to Islam, M..

At least 19 recordsLinked to original sources

bioRxiv2026

A quantitative three-dimensional bone mineralisation assay using human dental pulp stem cell spheroids

Matrix mineralisation in three-dimensional (3D) human cell culture is still assessed predominantly by terminal histochemical staining. Alizarin Red S and Von Kossa are destructive, semi-quantitative, and require fixation and dye extraction before a number can be obtained, which precludes longitudinal measurement and makes miniaturised multiwell formats impractical. We describe a scaffold-free assay that renders 3D human bone mineralisation as a continuous, well-level quantity. Primary human dental pulp stem cells (DPSCs) were dispensed by automated liquid handling into 384-well plates, where they formed a single, centrally positioned spheroid per well. Eleven plate geometry and surface-coating combinations were compared, and cell-repellent coating rather than well geometry alone was identified as the determinant of single-aggregate formation. Mineral deposition was measured non-destructively by adding the tetracycline-derived near-infrared probe BoneTag680 directly to the existing culture volume and reading the plate from below, with no spheroid transfer, embedding, sectioning or dye extraction at any point. Spheroids maintained in 10% fetal calf serum (FCS) with osteogenic cocktail were separated from a 1% FCS low-mineralisation condition with an assay window of 13.74 plus-or-minus sign 3.29-fold and a Z-factor of 0.627 plus-or-minus sign 0.119 across four independent plates, with a well-level coefficient of variation of 10.88% compared with 55.81% in a commercial alternative. A DNA content measurement acquired from the same wells after near-infrared acquisition showed no increase in cell number under osteogenic conditions, establishing that the mineral signal is not biomass-driven and providing an internal counter-screen against proliferative and cytotoxic artefacts. All data derive from a single donor; the assay is therefore characterised for technical and within-donor reproducibility, and is presented as a defined quantitative measurement intended as a foundation for bone-anabolic compound screening rather than as a screening-validated platform.

bioengineering↗

bioRxiv2026

Tryptophan Restores Recovery Competence Following Starvation in the Absence of Lysosomal Amino Acid Sensing

How organisms recover from starvation to nutrient-replete physiology remains poorly understood. In C. elegans, we previously observed that transcription factor hlh-30 or a combination of glucose and linoleic acid in its absence are essential for survival with refeeding following starvation, i.e. recovery competence. A forward genetic screen to evaluate mechanisms identified depd-5, which encodes a GATOR1 subunit, loss of which is expected to impair amino acid sensing with unrestrained raga-1 and mTOR activation. Surprisingly, glucose refeeding reduced recovery competence in depd-5(lf, loss-of-function) animals, which was rescued by amino acids, specifically tryptophan. Increasing tryptophan levels in depd-5(lf) worms through supplementation, reduced tryptophan catabolism with tdo-2 ablation and prolonged starvation restored recovery competence. raga-1(gf, gain-of-function) recapitulated whereas raga-1(lf) rescued the impaired recovery competence in starved depd-5(lf) worms. An analogous DEPDC5 mutation in mammalian cells impaired starvation-induced mTOR inactivation. We conclude that tryptophan counters unrestrained mTOR activity to restore recovery competence following starvation.

cell biology↗

bioRxiv2026

Impaired proteostasis is an early feature of the diabetic heart in humans and mice

Diabetes and obesity increase cardiac lipid levels leading to cardiomyopathy and heart failure. We hypothesized that intermittent fasting would reduce cardiac lipid levels. Surprisingly, intermittent fasting increased myocardial triglyceride content, but rescued mortality and attenuated cardiomyopathy in mice overexpressing cardiomyocyte acyl-CoA synthetase 1 (MHC-ACSL1). Lipid overload caused cardiomyocyte accumulation of polyubiquitinated protein aggregates containing desmin, a scaffolding intermediate filament protein, which intermittent fasting prevented. Furthermore, intermittent fasting reversed elevated myocardial C16:0 ceramide content, and knockdown of ceramide synthase CerS5 and CerS6 reduced palmitate-induced protein aggregation, highlighting a role for C16:0 ceramides in this pathology. Conversely, impairing aggrephagy with cardiomyocyte-specific p62 ablation induced heart failure in mice fed a high-fat diet, with paradoxically reduced cardiac lipid content. Crucially, non-failing diabetic human hearts also exhibited protein aggregate pathology. Taken together, these results demonstrate that impaired proteostasis characterizes cardiomyopathy from cardiac lipid overload and identify a promising new therapeutic target for this condition.

molecular biology↗

bioRxiv2026

GuavaVision AI: An Explainable Deep Learning Framework for Automated Classification, Lesion Localization, and Segmentation of Guava Diseases

Guava cultivation is considerably influenced by foliar and fruit diseases whose overlapping symptoms and environmental variability make accurate field-level diagnosis challenging. Numerous studies have been conducted to find efficient methods of diagnosing plant diseases, but most focus on image-level classification and do not include lesion localization or pixel-level segmentation of the images within a single framework of analysis. This study proposes a comprehensive framework for utilizing automated image analysis to classify guava leaf and fruit diseases at the image level, locate lesions, and segment lesions at the pixel level from multiple images of the same type of disease collected from various growing conditions. The dataset was enriched through three augmentation strategies including standard preprocessing, structured augmentation, and GAN-based synthetic image generation, expanding the effective training data to approximately 7,000 images, while a 5-fold cross-validation strategy guided model selection and final performance was assessed on a held-out test set. The experimental evaluation of multiple state-of-the-art Convolutional Neural Networks (CNNs) for the classification of guava leaf and fruit diseases indicated that the model generated using the ResNet50+DenseNet121 model fusion achieved the highest classification accuracy of 98.20%. For lesion detection and segmentation, YOLOv8-seg outperformed Mask R-CNN, achieving mAP@0.5 of 0.907 and 0.889, and mAP@0.5:0.95 of 0.783 and 0.769 for detection and segmentation, respectively, with a balanced precision-recall profile. The techniques of Explainable AI (XAI) were used to increase the transparency of this model by identifying areas in the image that are significant to the actual lesion. The framework was further designed with practical web-based deployment in mind, evaluating both lightweight and high-capacity models to balance computational efficiency against predictive accuracy. From this research, it was concluded that using model fusion, data augmentation, and segmentation-aware lesion detection would provide a solution for managing guava diseases effectively.

bioengineering↗

bioRxiv2026

The PMADS Project: A Longitudinal Multimodal Cohort Study to Understand Risk for Perinatal Mood and Anxiety Disorders

BackgroundPerinatal mood and anxiety disorders (PMADs) are among the most common and consequential complications of pregnancy. The perinatal period is also characterized by profound hormonal fluctuations and large-scale brain plasticity. However, the mechanisms linking these neurobiological changes to psychiatric risk are poorly understood. Prospective, clinically informed studies are needed to identify quantitative biomarkers and clarify pathways linking perinatal neurobiology to PMADs risk. MethodsThis report describes the design of a prospective, longitudinal cohort study integrating multimodal neuroimaging, biofluid sampling, and deep clinical phenotyping to enable precision characterization of neurobiological trajectories of PMADs risk. Twenty-five individuals at elevated risk for PMADs will be recruited prior to conception and followed across six in-person timepoints spanning the menstrual cycle, pregnancy, and early postpartum, with additional remote follow-ups through the first postpartum year. Data collection includes high-resolution structural MRI, functional brain mapping using multi-echo resting-state fMRI, diffusion MRI, arterial spin labeling, ultra-high field MR-based techniques for measuring glutamate (GluCEST and 1HMRS), biofluid sampling, and comprehensive clinical, behavioral, and cognitive assessments. Structured clinical interviews assess categorical diagnoses while dimensional symptom measures capture heterogeneity and transdiagnostic features of perinatal psychopathology. Longitudinal analyses will model nonlinear trajectories of brain and symptom change across the perinatal period as well as evaluate whether preconception network features and menstrual cycle-related brain changes are associated with subsequent perinatal symptom emergence. DiscussionThis cohort study establishes a longitudinal, multimodal framework for investigating neurobiological changes across the transition to pregnancy in individuals at elevated risk for PMADs. By anchoring pregnancy-related brain changes to preconception and menstrual cycle-related variability within the same individuals, this study is designed to evaluate associations between preconception hormone sensitivity, pregnancy-induced neuroplasticity, and PMADs risk. The resulting dataset will provide a deeply phenotyped longitudinal resource for investigating brain-behavior relationships across the perinatal period. Findings are expected to inform future larger-scale studies aimed at advancing mechanistic understanding of PMADs, improving individualized risk stratification, and supporting development of personalized preventive and neuromodulatory interventions.

neuroscience↗

bioRxiv2026

Murine Neutrophil Chemotaxis Following Burn Injury with Poloxamer 188 Treatment in a Microfluidic Platform

This study investigates the effects of Poloxamer 188 (P188) on neutrophil chemotaxis following burn injury in male and female mice using a microfluidic system. Utilizing male and female CD1 mice, we evaluated neutrophil migration towards two chemoattractants, N-formyl-l-methionyl-l-leucyl-l-phenylalanine (fMLP) and Leukotriene B4 (LTB4), and FPR1 and BLT1 G protein-coupled receptors after administering P188. Our findings revealed that P188 significantly increased the migration toward LTB4 in both sexes. Additionally, our findings highlight the upregulation of BLT1 and FPR1 markers due to burn injury in both female and male mice in the Burn vs. Sham groups. These results demonstrate the potential of P188 in modulating neutrophil behavior post-burn injury in therapeutic strategies for inflammation management. This microfluidic platform offers a precise and controlled microenvironment for studying neutrophil chemotaxis post-burn injury with and without P188 treatment.

bioengineering↗

bioRxiv2026

Hair promotion effect of Beta vulgaris L. fruit extracts; physicochemical, and analytical evaluation

Natural products are used frequently for medicinal purposes due to their lower toxicity effect and greater safety than synthetic products. Alopecia is becoming common due to inheritance, hormonal change and environmental factors. The current study evaluates the physicochemical, analytical and hair growth promotion activity of extracts of Beta vulgaris L. Extraction was done by using hexane, chloroform, methanol, ethanol and water in increasing order of their polarity. For the hair growth activity, five groups (positive, negative, untreated, test-group 1 and test-group 2) of albino mice were made and each group has five mice. The hair tonic formulation was applied on their dorsal surface. The analysis revealed that methanolic and ethanolic extracts showed the highest phytochemical content. The average length and diameter were noted. On day 14 and 21 length of different groups were: standard group (7.40{+/-}0.34, 8.15{+/-}0.56), negative group (3.05{+/-}0.65 and 5.65{+/-}0.78), untreated group (3.44{+/-}0.27 and 4.58{+/-}0.61), test group1 5% methanol (5.25{+/-}0.20 and 6.26{+/-}0.10), 10% methanol (5.23{+/-}0.07 and 6.35{+/-}0.33), test group2, 5% ethanol 5.28{+/-}0.50 and 6.30{+/-}0.84, 10% ethanol 5.50{+/-}0.50 and 6.72{+/-}0.75 and the diameter of groups were; standard (3.5{+/-}0.42 and 4{+/-}0.86), negative (1.5{+/-}0.33 and 2{+/-}0.22), untreated (2{+/-}0.34 and 2{+/-}0.24), test group1 5% (2{+/-}0.41 and 2.5{+/-}0.65), 10%(2{+/-}0.65 and 2.5{+/-}0.34), test group2 5%(1.5{+/-}0.67 and 2.5{+/-}0.42), 10% (2{+/-}0.88 and 2.5{+/-}0.54). Both extracts showed significant results, but ethanolic extract is more effective than methanolic. The exact mechanism of hair growth is not known yet, but it might be due to its strong antioxidant and anti-inflammatory effect. hence, this study is useful in treating baldness.

pharmacology and toxicology↗

bioRxiv2025

Metabolic Versatility of Lysinibacillus capsici BCSIR-Raj-01 Underpins Its Multifunctionality in Biocontrol, Bioremediation, and Plant Growth Promotion

Microbial inoculants that integrate plant growth promotion, pathogen suppression, and pollutant degradation are central to sustainable agriculture. Here, we report the genomic and phenotypic characterization of Lysinibacillus capsici BCSIR-Raj-01, an endophyte isolated from citrus leaves in Bangladesh. The 4.62 Mb genome encodes 4,699 coding sequences and displays an open pangenome with loci linked to stress adaptation, xenobiotic degradation, and secondary metabolite biosynthesis. Genome mining revealed complete pathways for indole-3-acetic acid (IAA) production, siderophore biosynthesis, and phosphate metabolism, alongside gene clusters for bacteriocins, lantibiotics, terpenes, and polyketides. Nitrogen cycling genes indicated diazotrophic growth potential and a truncated denitrification pathway. Phenotypic assays validated these predictions: L. capsici BCSIR-Raj-01 solubilized phosphate, produced IAA and siderophores, grew on hydrocarbons, and exhibited diazotrophic activity. Notably, the strain showed potent larvicidal activity against Culex and Anopheles larvae, suggesting ecological roles beyond plant association. Together, these results establish L. capsici BCSIR-Raj-01 as a multifunctional bacterium with potential applications in crop improvement, bioremediation, and biological vector control. IMPORTANCEThe challenges of modern agriculture and environmental sustainability demand microbial solutions that deliver multiple functions. Lysinibacillus species are increasingly recognized for such versatility, but their genomic basis remains poorly resolved. Our study provides the first genome-enabled framework for understanding multifunctionality in L. capsici. By combining whole-genome sequencing with phenotypic validation, we show that BCSIR-Raj-01 harbors biosynthetic clusters, stress adaptation loci, and xenobiotic degradation genes while also expressing experimentally confirmed traits, including phosphate solubilization, IAA and siderophore production, nitrogen fixation, hydrocarbon utilization, and larvicidal activity. This integration of plant growth promotion, biocontrol potential, and pollutant degradation positions L. capsici BCSIR-Raj-01 as a next-generation bioinoculant. Beyond broadening the functional scope of Lysinibacillus, our findings highlight how genome-guided approaches can identify microbes with cross-sectoral applications in agriculture, bioremediation, and vector management.

microbiology↗

bioRxiv2025

A molecular inventory of the faecal microbiomes of 23 marsupial species

Despite the recent expansion of culture-independent analyses of animal faecal microbiomes, many lineages remain understudied. Marsupials represent one such group, where despite their iconic status, direct sequencing-based analyses remain limited. Here we present a metagenomic and metabolomic exploration of the faecal microbiomes of 23 Diprotodontia marsupials, producing a reference set of 3,868 prokaryotic and 12,142 viral metagenome-assembled genomes, the majority (>80%) of which represent novel species. As with other animals, host phylogeny is the primary driver of microbiome composition, including distinct profiles for two eucalyptus folivore specialists (koalas and southern greater gliders), suggesting independent solutions to this challenging diet. Expansion of several bacterial and viral lineages were observed in these and other marsupial hosts that may provide adaptive benefits. Antimicrobial resistance genes were significantly more prevalent in captive than wild animals likely reflecting human interaction. This molecular dataset contributes to our ongoing understanding of animal faecal microbiomes. Impact statementDespite their ecological and evolutionary importance, marsupials remain underrepresented in microbiome research. Here, we present the most extensive faecal microbiome dataset to date for this group, encompassing metagenomic, metabolomic, and proximity ligation data from 23 marsupial species. As in other animals, we find the microbial community structure reflects the host species, and some marsupials carry expanded sets of certain microbial lineages indicative of within-host evolution. This work substantially expands the genomic landscape of host-associated microbes and viruses in a poorly studied mammalian clade. Data summaryRaw read data, prokaryotic MAGs [≥]50% complete with [≤]10% contamination are available via the European Nucleotide Archive under project PRJEB89408. The full set of viral genomes, clustered protein database and metabolite data (raw and processed) are available via https://doi.org/10.48610/14e37e9. Prokaryotic MAGs are also available via https://figshare.com/s/87443d80817f57aadc16.

microbiology↗

bioRxiv2025

Orthogonal and Robust Analytics Enable Reproducible and Scalable Manufacturing of High Purity Extracellular Vesicles Derived from Mesenchymal Stromal Cells

The development of extracellular vesicle (EV) based therapeutics requires robust analytical assays and scalable downstream processing (DSP) strategies to ensure product quality and reproducibility. In this study, we established an analytical toolbox comprising scattering and fluorescence mode nanoparticle tracking analysis (NTA), fluorescence-based flow cytometry (Fl-FC), and multi-detector analytical size exclusion chromatography. Liposomes, selected for their physicochemical similarity to EVs, were used as reference materials to optimize assay parameters, fluorescence labeling conditions, and dynamic range, minimizing artifacts such as photobleaching and masking effects. Using these optimized analytical tools, we designed a scalable DSP workflow for human bone marrow mesenchymal stromal cell (hBM-MSC) derived EVs, incorporating clarification, tangential flow filtration (TFF), ion exchange chromatography (IEX), buffer exchange, and sterile filtration. IEX chromatography resulted in the elution of two cell-secreted populations, with similar scattering signals while eluate 1 showed approximately 30 times higher absorbance signal compared to eluate 2. Transmission electron microscopy revealed that eluate 1 contained non-vesicular extracellular particles (NVEPs), and eluate 2 was enriched in EVs and showed higher expression of positive markers such as CD81 and CD73 using Simple Western. Additionally, the two IEX eluates showed different proteomic and lipidomic profiles. Then the analytical toolbox was utilized to monitor the DSP process in terms of particle recovery and impurity removal throughout the process determining the high purity level of the final EV preparation. Together, these results demonstrate that orthogonal analytics coupled to a scalable DSP yield reproducible MSC-EV preparations while depleting commonly co-isolated NVEPs. This practical framework advances process analytics of MSC-EV manufacturing and supports reporting of identity, purity, and function aligned with existing guidelines in the field. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=91 SRC="FIGDIR/small/672476v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@142ff8aorg.highwire.dtl.DTLVardef@196c0bforg.highwire.dtl.DTLVardef@485c36org.highwire.dtl.DTLVardef@9dff39_HPS_FORMAT_FIGEXP M_FIG C_FIG Liposomes were used as reference materials to optimize single particle analytics as well as multi detector analytical chromatography to assess particle recovery and impurity removal. This optimized analytical toolbox enabled accurate monitoring of downstream processing steps, establishing a robust workflow for reproducible and scalable mesenchymal stromal derived extracellular vesicles bioprocessing.

bioengineering↗

bioRxiv2025

Unbiased recording of clonal potency reveals species-specific regulation of mammalian intestine

The mammalian intestine regenerates rapidly after damage, yet the clonal dynamics and species-specific regulation of different populations remain poorly understood. Here we used synthetic or naturally occurring DNA alterations to reconstruct clonal histories of the mouse and human intestinal epithelium at single-cell resolution. In mice, we uncovered the clonal architecture of different cell types and their roles in regeneration, supporting a hierarchical regenerative response model. We identified a rare embryonic precursor population that persisted in the adult and was crucial for regeneration after irradiation. This population was marked by Tob2, which is required for nuclear transport of Ascl2. A parallel clonal analysis of 65 human colonic biopsies revealed secretory lineage bias and an age-associated decline in clonal diversity in the distal colon. Unlike highly proliferative murine Lgr5+ stem cells, human LGR5+ cells were found largely quiescent, revealing species-specific difference in clonal potency, and suggesting a distinct regulation of intestinal stemness.

genomics↗

bioRxiv2025

Associations between floor material and E. coli contamination in rural Bangladeshi households

Soil floors are common in low-income countries and can harbor contamination from unsafely managed human and animal fecal waste. Soil/dust ingestion directly from floors or indirectly via hands, drinking water and food can significantly contribute to childrens ingestion of fecal organisms. We assessed if finished (e.g., concrete) floors are associated with lower E. coli contamination in the domestic environment in rural Bangladesh. We collected samples from 1864 households over 3.5 years, including stored drinking water, child and caregiver hand rinses, courtyard soil, food, and flies (n=24,118 samples), and enumerated E. coli using IDEXX Quanti-Tray/2000. Controlling for potential confounders (socio-demographics, water/sanitation status, animal ownership), households with finished floors had slightly lower log10-transformed E. coli counts ({Delta}log10= -0.10 (-0.20, 0.00)) and prevalence (prevalence ratio=0.90 (0.83, 0.98)) on child hands than households with soil floors; floor material was not associated with contamination levels in other sample types. Finished floors were associated with lower E. coli contamination of child hands, food and stored drinking water following periods of higher rainfall and temperature, and lower E. coli contamination of child hands in households with more domestic animals. Measures to control enteric infections in low-income countries should test flooring improvements to reduce exposure to fecal contamination.

microbiology↗

bioRxiv2025

Mammary gland metabolism and its relevance to the fetoplacental expression of cytokine signaling in Caveolin-1 null mice

Mice lacking Caveolin-1 (Cav1), a major protein of the lipid raft of plasma membrane, show dysregulated cellular proliferation of mammary gland and an abnormal fetoplacental communication during pregnancy. The aim of this study is to better understand the functional links of mammary gland metabolism with gene expression of the placenta and fetus. Untargeted metabolomics analysis was performed to examine changes in mammary gland metabolism due to the absence of Cav1. Integrative metabolomics and transcriptomics analyses were applied to untangle functional links of metabolic pathways of the mammary gland with the gene expression changes of the placenta and fetus. The findings of this study show that metabolism and gene expression of the mammary gland are significantly impacted due to the loss of Cav1. Genes associated with specific metabolic and signaling pathways show coordinated expression changed in the placenta, mammary gland and fetal brain in Cav1-null mice. The cytokine signaling pathway emerges as a key player of the molecular crosstalk among the mammary gland, placenta and fetal brain. By interrogating the single-nuclei gene expression data of placenta and fetal brain previously generated from Cav1-null mice, the study further reveals that these metabolic and signaling genes are differentially regulated in specific cell types of the placenta and fetal brain. The findings of this study expand our understanding about the role of mammary gland metabolism in the regulation of fetoplacental communication in mammalian pregnancy.

genomics↗

bioRxiv2025

A single-chain antibody-based AID2 system for conditional degradation of GFP-tagged and untagged proteins

Protein knockdown using an improved auxin-inducible degron (AID2) technology has proven to be a powerful tool for studying protein function. The current approach requires the fusion of target proteins with a degron tag, a process typically achieved through CRISPR knock-in. However, knock-in remains challenging in non-model organisms and humans, limiting the broader applicability of AID2. To overcome this limitation, we developed a single-chain antibody AID2 (scAb-AID2) system. This approach employs an adaptor composed of a single-chain antibody fused with a degron, which recognises a target protein and induces rapid degradation in the presence of the inducer 5-Ph-IAA. We demonstrated that scAb-AID2, in combination with an anti-GFP nanobody, degraded GFP-fused proteins in human cells and C. elegans. Furthermore, we showed that endogenous p53 and H/K-RAS were conditionally degraded in cells expressing an adaptor encoding an anti-p53 nanobody and -RAS monobody, respectively, and led to aphidicolin sensitivity in cell culture and growth inhibition in mouse xenografts. This study paves the way for broader application of AID2-based target depletion in model and non-model organisms and for advancing therapeutic strategies.

bioengineering↗

bioRxiv2024

Mitophagy Facilitates Cytosolic Proteostasis to Preserve Cardiac Function

BackgroundProtein quality control (PQC) is critical for maintaining sarcomere structure and function in cardiac myocytes, and mutations in PQC pathway proteins, such as CRYAB (arginine to glycine at position 120, R120G) and BAG3 (proline to lysine at position 209, P209L) induce protein aggregate pathology with cardiomyopathy in humans. Novel observations in yeast and mammalian cells demonstrate mitochondrial uptake of cytosolic protein aggregates. We hypothesized that mitochondrial uptake of cytosolic protein aggregates and their removal by mitophagy, a lysosomal degradative pathway essential for myocardial homeostasis, facilitates cytosolic protein quality control in cardiac myocytes. MethodsMice with inducible cardiac myocyte specific ablation of TRAF2 (TRAF2icKO), which impairs mitophagy, were assessed for protein aggregates with biochemical fractionation and super-resolution imaging in comparison to floxed controls. Induced pluripotent stem cell (iPSC)-derived cardiac myocytes with R120G knock-in to the CRYAB locus were assessed for localization of the CRYAB protein. Transgenic mice expressing R120G CRYAB protein (R120G-TG) were subjected to both TRAF2 gain-of-function (with AAV9-cardiac Troponin T promoter-driven TRAF2 transduction) and TRAF2 loss-of-function (with tamoxifen-inducible ablation of one Traf2 allele) in cardiac myocytes to determine the effect of mitophagy modulation on cardiac structure, function, and protein aggregate pathology. ResultsCardiomyocyte-specific ablation of TRAF2 results accumulation of mitochondrial and cytosolic protein aggregates and DESMIN mis-localization to protein aggregates. Isolated mitochondria take up cardiomyopathy-associated aggregate-prone cytosolic chaperone proteins, namely arginine to glycine (R120G) CRYAB mutant and proline to lysine (P209L) BAG3 mutant. R120G-CRYAB mutant protein increasingly localizes to mitochondria in human and mouse cardiomyocytes. R120G-TG mice demonstrate upregulation of TRAF2 in the mitochondrial fraction with increased mitophagy as compared with wild type. Adult-onset inducible haplo-insufficiency of TRAF2 resulted in accelerated mortality, impaired left ventricular systolic function and increased protein aggregates in R120G-TG mice as compared with controls. Conversely, AAV9-mediated TRAF2 transduction in R120G-TG mice reduced mortality and attenuated left ventricular systolic dysfunction, with reduced protein aggregates and restoration of normal localization of DESMIN, a cytosolic scaffolding protein chaperoned by CRYAB, as compared with control AAV9-GFP group. ConclusionsTRAF2-mediated mitophagy in cardiac myocytes facilitates removal of cytosolic protein aggregates and can be stimulated to ameliorate proteotoxic cardiomyopathy.

cell biology↗

bioRxiv2024

Prevalence of Key Spike Protein Mutations and Their Limited Effect on COVID-19 Clinical Manifestations in Sylhet, Bangladesh

SARS-CoV-2 is the virus responsible for the COVID-19 pandemic, which has spread rapidly around the world and had a significant impact on public health and the economy worldwide. This study investigated the correlation between SARS-CoV-2 spike protein mutations, clinical outcomes and patient demographics in the Sylhet region of Bangladesh. We looked at the full genome sequences of 37 SARS-CoV-2 samples that were collected between January and June 2020. Specifically, we looked at five major spike protein mutations: D614G, A570D, D1118H, A222V, and P681R. The D614G mutation was the most prevalent (94.6%), followed by A570D and D1118H (both 32.4%), A222V (29.7%), and P681R (13.5%). Despite their high prevalence, we found no statistically significant associations between these mutations and clinical outcomes or demographic variables, except for possible trends for the P681R mutation. We found that age played a decisive role in recovery from COVID-19, with older patients exhibiting slower recovery rates. In terms of predictors of outcome, gender differences were observed: clinical symptoms and viral genetic mutations were more influential for men, while age and disease progression were more important for women. Common nucleotide substitutions (A23403G, C3037T, and C14408T) associated with European strains were identified, suggesting possible routes of transmission. This study contributes to our understanding of the genetics, clinical manifestations and epidemiology of SARS-CoV-2 in the Sylhet region and emphasizes the need for continuous genomic surveillance and adaptive public health strategies.

microbiology↗

bioRxiv2024

Phosphorylation of CRYAB Induces a Condensatopathy to Worsen Post-Myocardial Infarction Left Ventricular Remodeling.

Protein aggregates are emerging therapeutic targets in rare monogenic causes of cardiomyopathy and amyloid heart disease, but their role in more prevalent heart failure syndromes remains mechanistically unexamined. We observed mis-localization of desmin and sarcomeric proteins to aggregates in human myocardium with ischemic cardiomyopathy and in mouse hearts with post-myocardial infarction ventricular remodeling, mimicking findings of autosomal-dominant cardiomyopathy induced by R120G mutation in the cognate chaperone protein, CRYAB. In both syndromes, we demonstrate increased partitioning of CRYAB phosphorylated on serine-59 to NP40-insoluble aggregate-rich biochemical fraction. While CRYAB undergoes phase separation to form condensates, the phospho-mimetic mutation of serine-59 to aspartate (S59D) in CRYAB mimics R120G-CRYAB mutants with reduced condensate fluidity, formation of protein aggregates and increased cell death. Conversely, changing serine to alanine (phosphorylation-deficient mutation) at position 59 (S59A) restored condensate fluidity, and reduced both R120G-CRYAB aggregates and cell death. In mice, S59D CRYAB knock-in was sufficient to induce desmin mis-localization and myocardial protein aggregates, while S59A CRYAB knock-in rescued left ventricular systolic dysfunction post-myocardial infarction and preserved desmin localization with reduced myocardial protein aggregates. 25-Hydroxycholesterol attenuated CRYAB serine-59 phosphorylation and rescued post-myocardial infarction adverse remodeling. Thus, targeting CRYAB phosphorylation-induced condensatopathy is an attractive strategy to counter ischemic cardiomyopathy.

cell biology↗

bioRxiv2024

Highly accurate metagenome-assembled genomes from human gut microbiota using long-read assembly, binning, and consolidation methods

Long-read metagenomic sequencing is a powerful approach for cataloging the microbial diversity present in complex microbiomes, including the human gut microbiome. We performed a deep-sequencing experiment using PacBio HiFi reads to obtain metagenome-assembled genomes (MAGs) from a pooled human gut microbiome. We performed long-read metagenome assembly using two methods (hifiasm-meta, metMDBG), used improved bioinformatic and proximity ligation binning strategies to cluster contigs and identify MAGs, and developed a novel framework to compare and consolidate MAGs (pb-MAG-mirror). We found proximity ligation binning yielded more MAGs than bioinformatic binning, but our novel comparison framework resulted in higher MAG yields than either binning strategy individually. In total, from 255 Gbp of total HiFi data we produced 595 total MAGs (including 175 high-quality MAGs) using hifiasm-meta, and 547 total MAGs (including 277 high-quality MAGs) with metaMDBG. Hifiasm-meta assembled almost twice as many strain-level MAGs as metaMDBG (246 vs. 156), but both assembly methods produced up to five strains for a species. Approximately 85% of the MAGs were assigned to known species, but we recovered >35 high-quality MAGs that represent uncultured diversity. Based on strict similarity scores, we found 125 MAGs were unequivocally shared across the assembly methods at the strain level, representing [~]22% of the total MAGs recovered per method. Finally, we detected more total viral sequences in the metaMDBG assembly versus the hifiasm-meta assembly ([~]6,700 vs. [~]4,500). Overall, we find the use of HiFi sequencing, improved metagenome assembly methods, and complementary binning strategies is highly effective for rapidly cataloging microbial genomes in complex microbiomes.

microbiology↗