Biology subjects

Ghosh, R.

Publications and source records attributed to Ghosh, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Biomechanical effects of load-carrying in adolescent idiopathic scoliosis: a subject-specific musculoskeletal modelling study

Load carrying is a common activity during adolescence, yet its biomechanical consequences for the structurally asymmetric spine in adolescent idiopathic scoliosis (AIS) remain poorly understood. This study investigated how load magnitude, carrying height, and side of application influence spinal loading and paraspinal muscle forces in AIS. A subject-specific musculoskeletal model of a 16-year-old female with a 59{degrees} right-convex thoracic curve was used to simulate bilateral and unilateral load carrying at the hand, chest, and above-shoulder levels, with loads corresponding to 5%, 10%, and 15% of body weight. Intervertebral compressive and lateral forces and erector spinae (ES) and multifidus (MF) muscle forces were evaluated. Spinal loading increased progressively with load magnitude and carrying height. At 15% body weight, compressive forces at the curve apex increased from 511-566 N at hand level to 721-831 N above the shoulder. Unilateral carrying produced distinct side-dependent responses: convex-side carrying generated greater compressive forces, whereas concave-side carrying generated greater lateral forces, which were concentrated around the curve apex. Paraspinal muscles also exhibited muscle-specific responses. ES forces primarily reflected the imposed external asymmetry, with unilateral carrying eliciting predominantly contralateral recruitment, whereas MF maintained a characteristic convex-side dominance concentrated around the curve apex. These findings demonstrate that load carrying in AIS produces a coupled biomechanical response governed by both the external loading configuration and the pre-existing structural asymmetry of the spine, highlighting the importance of considering loading direction and muscular adaptation alongside load magnitude when evaluating everyday carrying activities in AIS.

bioengineering↗

bioRxiv2026

Transcriptomic profiling of normal and glaucomatous trabecular meshwork cells in a tissue-like soft ECM environment

Purpose. Trabecular meshwork (TM) dysfunction contributes to the elevated intraocular pressure in primary open-angle glaucoma. To better understand the molecular signature distinguishing glaucomatous from normal TM cells, we interrogated their genome-wide transcriptomic differences in a tissue-like soft extracellular matrix (ECM) microenvironment. Methods. Primary human glaucomatous and normal TM cell strains (N = 5 each) from three independent laboratories were plated on bioengineered collagen type I/hyaluronic acid/elastin-like polypeptide ECM hydrogels in 10% FBS media for 4-5 days, then serum-free media for 2 days. Cell-laden hydrogels were homogenized in TRIzol for RNA isolation, quality assessment, and library preparation, followed by paired-end 100-bp Illumina sequencing. Differential expression was assessed using DESeq2, including glaucoma status, originating laboratory, and donor age/sex in the model. Differentially expressed genes (DEGs) were defined as p < 0.05 and |fold change| [≥] 2, followed by Gene Ontology (GO) enrichment and QIAGEN Ingenuity Pathway Analysis (IPA). Results. In total, 588 DEGs distinguished the glaucomatous from the normal TM transcriptome (393 up-regulated in glaucomatous TM; 195 up-regulated in normal TM, i.e., down-regulated in glaucomatous TM). GO and IPA causal analyses revealed three coordinated disease programs: (i) TGF-{beta}/Wnt-driven ECM remodeling and fibrosis, (ii) NF-{kappa}B-associated inflammation, and (iii) a hypoxia/metabolic-stress program linked to p300/CREBBP chromatin co-activation. Conclusions. These data define a transcriptomic signature of glaucomatous TM cells when cultured in a soft physiologic ECM microenvironment, independent of the originating laboratory, with three mechanistic axes (ECM/fibrosis, inflammation, hypoxia/metabolism), and nominate p300 (encoded by EP300) as a candidate upstream node integrating these programs.

cell biology↗

bioRxiv2026

Petal photosynthesis and dynamic alterations of carbon metabolism orchestrate floral maturation in Gardenia carinata

During maturation, flowers exhibit complex and finely-coordinated metabolic events facilitating various physiological changes that occur in a short time-span. The floral carbon metabolism underpins a metabolic frame, which provides energy and metabolites to drive the life-processes in flowers. However, studies on floral maturation in the past mostly focused on specialized metabolism or certain metabolite classes of central carbon metabolism. This study aims to provide a detailed insight into the dynamics of floral carbon metabolism and its role in flower maturation; it also addresses a long-standing question on the role of petal photosynthesis in floral maturation. In this report, time-course metabolomic studies were integrated with various physiological, enzymological, histochemical and ultrastructural findings to present a multi-layered investigation on the maturation physiology of Gardenia carinata flowers. This integrated approach revealed the characteristic metabolic features of different floral maturation stages, and also highlighted the metabolic rearrangements that allow each stage to establish their characteristic metabolic state. The photosynthetic bud stages showed metabolism inclined toward active growth and carbon reserve accumulation. A shift to energy-rich metabolism was observed as the flowers unfurled, probably to support energy-demanding events such as flower opening and changes in specialized metabolism. Our study further demonstrates the mechanisms underlining the transition from autotrophic to heterotrophic metabolism during maturation, which also reflects the plasticity in source-sink dynamics of flowers. We envisage that this study could provide a springboard for elucidating the roles of individual metabolites and enzymes in regulating floral maturation.

plant biology↗

bioRxiv2026

Influence of trunk posture on spinal loading and paraspinal muscle forces in adolescent idiopathic scoliosis: a subject-specific musculoskeletal modelling study

Adolescent idiopathic scoliosis (AIS) alters spinal geometry and may influence the biomechanical response of the spine during functional postures. However, posture-dependent changes in spinal loading and paraspinal muscle forces in AIS remain poorly understood. This study investigated the effects of trunk posture on intervertebral loading and paraspinal muscle forces using a subject-specific musculoskeletal model of an adolescent with AIS. The spinal deformity was reconstructed from biplanar radiographs and incorporated into a full-body musculoskeletal model. Flexion, extension, lateral bending, and axial rotation were simulated at three incremental magnitudes, with motion distributed across the thoracolumbar spine. Intervertebral compressive and lateral forces around the curve apex and forces in the erector spinae (ES) and multifidus (MF) muscles were evaluated. Trunk flexion produced the greatest compressive loading, reaching 337 N at the curve apex and 372 N two levels below the apex at 30{degrees} flexion. Lateral bending produced pronounced direction-dependent loading: concave-side bending increased lateral forces, whereas convex-side bending increased compressive forces. Axial rotation produced similar but smaller direction-dependent changes. Paraspinal muscle forces were consistently asymmetric, with concave-side dominance of the ES and convex-side dominance of the MF. Flexion and convex-sided movements generally produced greater muscle imbalance, while increasing posture magnitude amplified spinal loading and muscle forces. These findings demonstrate that trunk posture, movement direction, and magnitude substantially influence the biomechanical environment of the scoliotic spine and should be considered when evaluating spinal mechanics in AIS.

bioengineering↗

bioRxiv2026

Prediction of compressive strength of vertebral body with metastatic lesions based on quantitative computed tomography-based subject-specific finite element models

Pathologic vertebral fractures are a major complication in metastatic spine disease. However, current clinical scores, such as Spinal Instability Neoplastic Score (SINS), show limited predictive capability, particularly within the indeterminate range where most clinical uncertainty lies. This study aimed to develop and evaluate quantitative computed tomography (qCT)-based subject-specific finite element (SSFE) models to predict vertebral strength in presence of different metastatic lesion types. Twelve ex vivo human spine segments, each containing one metastatic (n=12) and one adjacent control vertebra (n=12), were scanned using qCT and calibrated using a calibration phantom. Homogenised nonlinear finite element models were developed with spatially heterogeneous, isotropic, density-dependent material properties and loaded under uniaxial compression corresponding to 1.9% apparent strain. Ultimate failure load, stiffness, and strain distributions were compared between metastatic and control vertebrae. Predicted failure load ranged from 0.2 kN to 6.2 kN (mean. {+/-} standard deviation: 1.8 {+/-} 1.6 kN metastatic; 1.7 {+/-} 1.5 kN control), with no statistically significant difference between groups (p > 0.05). Normalised failure load varied widely, reflecting lesion-specific mechanical heterogeneity. Lytic lesions generally weakened vertebrae, whereas mixed and blastic lesions occasionally enhanced strength, likely due to localised sclerosis or reactive bone formation. High compressive axial strains (greater than 0.019) were frequently concentrated near the endplates, particularly in lytic vertebrae. qCT-derived bone mineral density strongly correlated with failure load (R{superscript 2} = 0.74-0.77). These findings highlight the complexity of metastatic vertebral mechanics and demonstrate that qCT-based SSFE modelling provides a quantitative framework for assessing fracture risk, complementing conventional imaging-based tools.

bioengineering↗

bioRxiv2026

Morph-specific plasticity drives divergent host-shift and acclimation strategies in aphids

Understanding how organisms cope with environmental change is central to eco-evolutionary theory, yet a key unresolved challenge is distinguishing anticipatory plasticity, where phenotypes are pre-configured using predictive cues, from responsive plasticity, where phenotypes are adjusted after environmental exposure. Empirically testing these strategies is challenging because phenotypes measured after environmental transitions integrate both prior cue-dependent state configuration and post-exposure adjustment, obscuring when plastic responses are initiated. Systems with predictable environmental transitions and discrete life-history stages provide a powerful opportunity to resolve this challenge. Here, we use host-alternating aphids to test how plasticity strategies are organized across morphs experiencing the same seasonal host shift but facing different ecological constraints. We quantified fitness, transcriptomic responses, and host chemical landscapes across three morphs transferred among secondary hosts differing in phloem composition. Migratory spring morphs maintained uniformly high survival and showed minimal transcriptional change, consistent with anticipatory plasticity mediated by pre-configured metabolic and detoxification programs. In contrast, summer morphs exhibited host-dependent survival costs and extensive regulatory remodeling, indicating responsive plasticity. By integrating fitness, transcriptomics, and metabolomics, we show that predictable environmental transitions can favor the evolution and partitioning of plasticity strategies across life-history stages. More broadly, our results provide mechanistic evidence linking environmental predictability, regulatory architecture, and the evolution of plastic responses to heterogeneous environments.

evolutionary biology↗

bioRxiv2026

In-Depth Characterization of Stem Cell Potency and Genotoxicity for Clinical-Scale Ex Vivo CRISPR/Cas9 Gene Editing

Translating CRISPR/Cas9-based homology-directed repair (HDR) strategies into clinical application remains a major challenge due to limited standardization, concerns over safety, and efficacy issues. Here, we present a comprehensive and clinically compliant preclinical framework for the ex vivo correction of Wiskott-Aldrich Syndrome (WAS) using a CRISPR/Cas9-AAV6 platform targeting hematopoietic stem and progenitor cells (HSPCs). In this study, we established a clinical-compatible platform enabling large-scale manufacturing while preserving HSPC viability, stemness, and multilineage functionality. To overcome low HSPC long-term engraftment, we fine-tuned AAV dosing and transiently modulated p53 signalling, achieving significantly improved in vivo correction and repopulation. Importantly, we implemented a multi-tiered genotoxicity assessment strategy, integrating in silico, genome-wide, and orthogonal assays, revealing a largely favorable safety profile with minimal off-target risks and no signs of clonal dominance or transformation. Longitudinal in vivo safety monitoring revealed donor specific rare off-target events and structural variants. This highlights the crucial importance of patient monitoring after transplantation, further emphasized by the identification of a de novo chromosomal rearrangements that could be detected exclusively following cell engraftment in mice. This work offers a robust and adaptable roadmap for future HDR-based gene editing platforms, establishing critical benchmarks for efficacy, safety, and regulatory readiness in the development of advanced therapeutic medicinal products.

molecular biology↗

bioRxiv2025

Brain defence by the extracellular matrix protein Cochlin

The vertebrate brain is protected from infection by tight barriers. However, several barrier structures, including circumventricular organs, can be breached by pathogens. Here, we show that Cochlin, an extracellular matrix-binding protein with anti-bacterial properties, is produced in barrier structures and contributes to immune defence. Transcriptome analysis and in situ hybridisation indicate that cochlin is expressed in the pineal gland, area postrema, choroid plexus and discrete regions of the meninges of zebrafish, mice and humans. The protein is present in the cerebrospinal fluid, and on the surface of ventricle and meninges. Cochlin expression increases in the brain of infected animals and patients, and delivery of recombinant Cochlin reduces bacterial load in zebrafish infected with Mycobacterium marinum. Mutation of cochlin inhibits clearance of bacteria from the brain of zebrafish, and this is reversed by supplying the LCCL domain of Cochlin. Barrier tissues thus contribute to brain defence by secreting Cochlin.

immunology↗

bioRxiv2025

Affinity-Based Interactome Mapping of Inositol Pyrophosphates Reveals 4/6-PP-InsP5-Binding Proteins in Plants

Inositol pyrophosphates (PP-InsPs) are central regulators of eukaryotic signaling events. While certain PP-InsP isomers have been conclusively linked to the regulation of phosphate homeostasis through interaction with SPX domain containing proteins in plants, the functions of the recently discovered isomer 4/6-PP-InsP5 remain largely unknown. Here, we employed two complementary affinity-based strategies - a matrix approach and a photoaffinity probe - to systematically identify 4/6-PP-InsP5-binding proteins in Arabidopsis thaliana. The two methods yielded partially overlapping protein sets, with photoaffinity enrichment likely capturing additional transient and/or weak interactions. Moreover, competition experiments with different isomers were applied to obtain information about potential isomer-specific interactions. As a proof-of-concept, one candidate interactor (FHA domain-containing protein AtFHA2) was shown to bind 4-PP-InsP5 in vitro with substantially higher affinity than InsP6. Thus, besides the SPX domain, FHA domain containing proteins, of which 18 exist in Arabidopsis, are potentially regulated by inositol pyrophosphates. More generally, our findings reveal a diverse protein network associated with 4/6-PP-InsP5 and establish a versatile platform for dissecting its biological roles in plants and other organisms.

biochemistry↗

bioRxiv2025

A Common PD-Risk GBA1 Variant Disrupts LIMP2 Interaction, Impairs Glucocerebrosidase Function, and Drives Lysosomal and Mitochondrial Dysfunction

Variants in GBA1 cause Gaucher disease (GD), a lysosomal storage disorder, and represent the most common genetic risk factor for Parkinsons disease (PD). While some GBA1 variants are associated with both GD and PD, several coding mutations, including E326K, specifically confer risk for developing PD. It is established that GD-linked variants in {beta}-glucocerebrosidase (GCase), the enzyme encoded by GBA1, are loss-of-function, but it remains unclear whether variants solely associated with PD similarly reduce GCase activity. The mechanisms by which some of these variants impact GCase activity and PD-associated pathways, including lysosomal and mitochondrial function, are also poorly defined. Here, we show that the PD-linked E326K variant significantly reduces lysosomal GCase activity by impairing its delivery to lysosomes via altered interactions with its receptor, LIMP2. Biophysical and structural characterization of this variant, both alone and in complex with LIMP2, reveals a dimeric organization that appears to result from the loss of a key salt bridge between E326 and R329. Restoration of this salt bridge through the introduction of a negatively charged side chain at position 329 promotes monomeric organization and interaction with LIMP2 in cells. GBA1-p.E326K cell models show greater deficits in PD-linked pathways compared to more severe loss of GCase function, including secondary lysosomal lipid storage and mitochondrial dysfunction. We confirm the E326K variant impacts GCase pathway activity in relevant CNS cell types, including iPSC-derived microglia, and in biofluids from heterozygous GBA1-p.E326K variant carriers. Together, our data provide key insights into the nature of GCase dysfunction in GBA1-PD and can inform the development of GCase-targeted therapeutic strategies to treat PD.

cell biology↗

bioRxiv2025

Influence of simplifications on FE modelling of mandible and TMJ implants

End-stage temporomandibular joint (TMJ) disorders often necessitate joint replacement to restore bilateral mastication. Patient-specific TMJ implants typically rely on detailed in silico modelling derived from subject-specific computed tomography (CT) scans of the mandible. However, generating highly detailed finite element (FE) models is computationally expensive. Although structural simplifications of the mandible are known to influence mechanical behaviour, their quantitative impact on TMJ implant evaluation has not been systematically investigated. This study examines the influence of three modelling simplifications on stress-strain predictions in intact and implanted mandibles: (i) a detailed segmented mandible with tissue-specific material properties (Model 1), (ii) a simplified mandible comprising cortical bone only (Model 2), and (iii) a further simplified mandible excluding dental crowns (Model 3). Both narrow and standard TMJ implants were analysed under osseointegrated and non-osseointegrated conditions, resulting in fifteen FE models. Physiological clenching activities were simulated. Compared with the detailed model, simplified models showed reductions of up to 50% in maximum principal strain in bone and up to 44% in von Mises stress in TMJ implants, while preserving spatial stress-strain trends. These findings indicate that simplified models may be suitable for preliminary implant design, whereas detailed FE modelling remains essential for final pre-clinical evaluation.

bioengineering↗

bioRxiv2025

Identifying non-coding variant effects at scale via machine learning models of cis-regulatory reporter assays

The inability to interpret the functional impact of non-coding variants has been a major impediment in the promise of precision medicine. While high-throughput experimental approaches such as Massively Parallel Reporter Assays (MPRAs) have made major progress in identifying causal variants and their underlying molecular mechanisms, these tools cannot exhaustively measure variant effects genome-wide. Here we present MPAC, an ensemble of machine-learning models trained on MPRA data that provides accurate and scalable prediction of the cis-regulatory impact of non-coding variants. Using MPAC we predict allelic effects for 575M single nucleotide variants (SNVs) across diverse applications, including complex trait genetics, clinical and tumor sequencing, evolutionary analyses, and saturation mutagenesis. We find MPAC predictions match the performance of empirical MPRAs in identifying causal complex trait-associated alleles. We demonstrate the utility of MPAC by applying it to ClinVar, identifying non-coding pathogenic variation with higher accuracy than other sequence-to-function models. We also nominate 1,892 candidate non-coding cancer drivers by predicting the functional effects of somatic SNVs in the COSMIC database. Next, we evaluate population-level genetic variation by predicting effects for all 514M non-coding SNVs in gnomAD, quantifying the relationship between regulatory function and evolutionary constraint. Finally, we generate prospective functional maps using in-silico saturation mutagenesis across 18,658 human promoters, observing widespread selection against variants predicted to disrupt promoter activity. Collectively, this study establishes the value of non-coding functional predictions and provides a comprehensive, publicly available resource for variant interpretation.

genomics↗

bioRxiv2025

Deconvolution of Sample Identity in Single-Cell RNA Sequencing via Genome Imputation

BackgroundDroplet based single-cell RNA sequencing (scRNA-seq) is a powerful tool for measuring RNA abundance profiles at cell-specific resolution. Droplet-based barcoding technology allows sample multiplexing, thereby facilitating high-scale of single cell sequencing. The resulting processing complexity, sample contamination and the underlying chemistries can all contribute to cell mis-labelling and consequent spurious cell-to-sample assignment. Approaches for barcode-free de-multiplexing which leverage natural genetic variation have been developed, but generally require an external source of genotype information. ResultsWe propose a novel method to exploit genome imputation and clustering to assign cells to inferred donor groups in the absence of a priori genetic information. Using tumor-derived single-cell RNA-sequencing (scRNA-seq) data, our workflow successfully assigned individual cells to donor-of-origin with high concordance. ConclusionsThis imputation-clustering approach represents a quality-assessment and quality-control strategy for barcode-free single cell donor-origin deconvolution with the capacity to resolve cases of sample cross-contamination.

bioinformatics↗

bioRxiv2024

Stability of the polarization agent AsymPolPOK in intact and lysed mammalian cells

Dynamic nuclear polarization (DNP) solid-state NMR enables detection of proteins at endogenous concentrations in cells through sensitivity enhancement from nitroxide biradical polarization agents. AsymPolPOK, a novel water-soluble asymmetric nitroxide biradical, offers superior sensitivity and faster build-up times compared to existing agents like AMUPol. Here, we characterize AsymPolPOK in mammalian HEK293 cells, examining its cellular distribution, reduction kinetics, and DNP performance. We demonstrate that electroporation achieves uniform cellular delivery of AsymPolPOK, including nuclear permeation, with no cytotoxicity at millimolar concentrations. However, the cellular environment rapidly reduces AsymPolPOK to its monoradical form, with one nitroxide center showing greater reduction resistance than the other. While AsymPolPOK maintains high DNP enhancements and short build-up times in lysates, its performance in intact cells depends critically on delivery method and exposure time to cellular constituents. Electroporation yields higher, more uniform enhancements compared to incubation, but prolonged exposure to the cellular environment diminishes DNP performance in both cases. These findings establish the potential of AsymPolPOK as a polarization agent for in-cell DNP NMR while highlighting the need for developing more bio-resistant polarization agents to further advance cellular structural biology studies.

biophysics↗

bioRxiv2024

The wheat VIH2-3B, a functional PPIP5K controls the localization of fasciclin-like arabinogalactan protein

Inositol pyrophosphates (PP-InsPs) are important signalling molecules that participate in multiple physiological processes across a wide range of eukaryotes. Metabolic pathway kinases (VIP1/VIHs) leading to the production of PP-InsPs are now well characterized in yeast and plants. Previously, the wheat (Triticum aestivum L.) inositol pyrophosphate kinase (TaVIH2) was shown to encode a catalytic active kinase domain. Heterologous expression of TaVIH2 in Arabidopsis thaliana was shown to enhance drought tolerance by modulating the cell composition. In this study, we attempted to identify the interacting protein targets of wheat VIH2-3B using a yeast two-hybrid (Y2H) cDNA library screen, which led to the identification of 52 putative interactors that are primarily involved in cell wall-related functions. Notably, fasciclin-like arabinogalactan protein (FLA7), a glycosylphosphatidyl inositol (GPI)-anchored protein, emerged as the most frequently interacting partner. Further analysis using pulldown assays validated the interaction between TaVIH2-3B and TaFLA7 in vivo. Using the reporter fusion studies, we observed the localization of TaFLA7 to be a plasma membrane and this localization of the TaFLA7 was perturbed in the yeast vip1{Delta} strain. The expression of TaVIH2-3B bearing PPIP5K enzymatic activity in yeast mutants rescued the level of IP8 and restore the localisation of the TaFLA7 to the membrane. Expression analysis of TaFLA7 revealed a differential expression response to drought in wheat shoot tissues. TaFLA7 was also found to be highly expressed during grain development, particularly in the endosperm and seed coat during grain maturation. Taken together, these findings highlight the potential role of TaVIH2 in cell wall remodelling and stress response pathways, offering new insights into the functional roles of VIH proteins in plants.

plant biology↗

bioRxiv2024

Insights into the triggering factors and determination mechanisms of host alternation in aphids

The bird cherry-oat aphid Rhopalosiphum padi, is one of the ten percent of aphids that are host alternating. The annual life cycle of R. padi entails an obligatory migration between a primary woody host, Prunus padus (Rosaceae), where sexual reproduction occurs, and many secondary hosts of the Poaceae family, where successive generations reproduce parthenogenetically. Migration between the two types of host plants is achieved by specialized migrant morphs. Very little is known about the cues that trigger migrant development, host alternation establishment and the underlying mechanisms. In this study, we aimed to elucidate the key steps involved in migrant induction and determination of host alternation, and to shed light on these intricate processes. We showed that a specific stage of leaf maturity triggers the development into a migrant morph when presented to R. padi at the first or second larval instar stages. We also demonstrated the gradual establishment of acclimation to the secondary hosts that precedes the migration step. Finally, we showed that the switch to feeding on the alternative hosts is irreversible once emigrants have reached adulthood. These results not only allowed us to define the critical periods of the leaf stage associated with morph induction and determination, but also to pinpoint the emigrants developmental stages when acclimation to secondary hosts begins. These novel insights of these critical periods will facilitate the investigation of molecular changes associated with host alternation in aphids.

ecology↗

bioRxiv2024

Biomechanical Evaluation of Temporomandibular Joint Implants Under Complete Mastication Cycle

To ensure the long-term success of temporomandibular joint (TMJ) implants, it is imperative to understand their biomechanical performances. This study aims to compare the biomechanical performance of two stock implants (narrow and standard) under unilateral and bilateral clenching during both osseointegrated and non-osseointegrated conditions. Finite element models of a human mandible were developed from QCT data, with the left TMJ being replaced by the implants. Six clenching tasks were simulated to evaluate stress and strain distributions in the mandible and implants. Ipsilateral clenching produced higher mandibular strains, while contralateral clenching generated larger implant stresses. Furthermore, intercuspal biting was found to have produced the highest strain (1750-1880 {micro}{varepsilon}) and stress ([~]17 MPa) in the mandible. Osseointegration reduced stresses (up to 0.14 MPa) and strains (up to 30 {micro}{varepsilon}) in mandible as well as stresses in mandibular components (up to 48 MPa) and screws (up to 71 MPa). However, during non-osseointegrated conditions, stresses in cortical bone were higher for standard TMJ implant as compared to narrow implant. This suggests possible preference of narrow implant over standard ones.

bioengineering↗

bioRxiv2024

Burkholderia cenocepacia epigenetic regulator M.BceJIV simultaneously engages two DNA recognition sequences for methylation

Burkholderia cenocepacia is an opportunistic and infective bacterium containing an orphan DNA methyltransferase (M.BceJIV) with roles in regulating gene expression and motility of the bacterium. M.BceJIV recognizes a GTWWAC motif (where W can be an adenine or a thymine) and methylates the N6 of the adenine at the fifth base position (GTWWAC). Here, we present a high-resolution crystal structure of M.BceJIV/DNA/sinefungin ternary complex and allied biochemical, computational, and thermodynamic analyses. Remarkably, the structure shows not one, but two DNA substrates bound to the M.BceJIV dimer, wherein each monomer contributes to the recognition of two recognition sequences. This unexpected mode of DNA binding and methylation has not been observed previously and sets a new precedent for a DNA methyltransferase. We also show that methylation at two recognition sequences occurs independently, and that GTWWAC motifs are enriched in intergenic regions of a strain of B. cenocepacias genome. We further computationally assess the interactions underlying the affinities of different ligands (SAM, SAH, and sinefungin) for M.BceJIV, as a step towards developing selective inhibitors for limiting B. cenocepacia infection.

biophysics↗