Biology subjects

Ray, D.

Publications and source records attributed to Ray, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Generative AI Models Reveal Dynamic Views of Aging (DyViA) Phenotypes in Healthy Individuals

Background and objectivesIn recent years, the need to develop analytical strategies for healthy aging has assumed great importance. In this study, we introduce DyViA, a generative artificial intelligence (genAI) platform that can construct personalized trajectories capable of predicting the plausible progression of selected phenotypes with advancing age. Research design and methodsDyViA presents a suite of deep learning models covering two major GenAI approaches: DyViA-Diff, a new diffusion model; and DyViA-mGAN, an improved version of a recent Generative Adversarial Network model. It demonstrated the dynamic progression of femoral neck bone mineral density (BMD) using data from a longitudinal cohort study of women in the U.S. of age 65 years or above. ResultsUsing very few initial measurements, DyViA generated individual-specific continuous trajectories of BMD, with a corresponding region of acceptable predictions, from 66 to 89 years. The results were subjected to rigorous quality-control and comparative analysis across multiple methods. While DyViA-Diff is the superior model with more coherent and accurate predictions, DyViA-mGAN allows for encoding population- and individual-level effects with a better control. Discussion and implicationsGiven the prevalence of osteoporosis in the aging population, the main impact of DyViAs genAI-driven contribution in the form of personalized, plausible models of BMD progression with age lies in the systematic yet rigorous transition from otherwise static models of inference about a clearly dynamic phenomenon to a continuous one. The foresight offered by DyViAs outputs empowers an individual by conferring a certain degree of strategic preparedness in the course of aging.

bioinformatics↗

bioRxiv2026

HEALTHY AGING AS INFORMATION DIVERGENCE IN THE MULTIPLEX BRAIN

AO_SCPLOWBSTRACTC_SCPLOWUnderstanding the co-evolution of the human brains structural scaffold and functional traffic across the adult lifespan remains a fundamental challenge in neuroscience. While age-related degradation in grey matter and functional activation is well-documented, the joint trajectory of the structural (SC) and functional (FC) connectomes is often overlooked due to the lack of an integrative framework. Here, we model the brain as a multiplex network to quantify the information-theoretic interdependencies between these two layers in a cross-sectional cohort of 589 healthy individuals (ages 18-88) from the Cambridge Centre for Ageing and Neuroscience (Cam-CAN) dataset. Using Jensen-Shannon Divergence and relative entropy metrics, we identify a fundamental organizing principle of healthy aging characterized by: a progressive information divergence where functional dynamics increasingly "untether" from their underlying structural constraints. Our results reveal that this decoupling follows a robust linear trajectory, yet is highly spatially hetero-geneous. Meso-scale community analysis using the Multiplex Map Equation identifies subcortical hubs--specifically the putamen, pallidum, caudate, and thalamus--as the primary epicenters of age-related SC-FC divergence. This topological shift toward functional independence in subcortical "switchboards" provides a mechanistic connectomic signature for the well-documented decline in fluid intelligence and motor adaptation that accompanies aging. In striking contrast, the limbic core (hippocampus and entorhinal cortex) exhibits remarkable stability across the lifespan, suggesting a biological imperative to preserve high-fidelity memory circuits amidst global communicative rewiring. By framing healthy aging as a systematic subcortical untethering alongside limbic resilience, our work provides a powerful new multiplex baseline to distinguish normative cognitive decline from the early topological signals of neurodegenerative disease. Significance StatementHealthy aging involves a fundamental reorganization of the brains information architecture. By modeling the brain as a multiplex network and leveraging information-theoretic measures, we demonstrate that adult lifespan development is characterized by a progressive "untethering" of functional dynamics from their underlying structural constraints. This decoupling is driven by a striking geometric paradox within subcortical hubs: while physical structural scaffolds undergo severe network constriction and isolation, their functional boundaries expand and blur in a state of neural de-differentiation. This architectural mismatch is mediated by a synchronized prefrontal-to-limbic pathway shift that operates collinearly with chronological age and mirrors the selective decline of fluid intelligence and motor adaptation that accompanies aging. Our work establishes a rigorous multiplex framework that moves beyond descriptive accounts of neural tissue loss to provide a normative baseline for distinguishing healthy brain aging from neurodegeneration.

neuroscience↗

bioRxiv2026

Hydroxychloroquine alters the cytoskeleton to impair cell migration

Hydroxychloroquine (HCQ), a clinically relevant quinoline derivative, impairs both collective and individual cell migration by disrupting actin and vimentin cytoskeletal dynamics during wound healing. In scratch assays with HeLa cells, HCQ treatment significantly reduces wound closure rates and inhibits bursts of coordinated migration, as well as single-cell motility. Quantitative imaging reveals that HCQ diminishes actin filament density at the wound edge and induces reorganization of the vimentin network, resulting in smaller nuclei and compromised structural connectivity. Particle tracking micro-rheology demonstrates that HCQ softens the cytoplasm and decreases cellular mechanical heterogeneity. In vitro spectroscopic studies show that HCQ binds cooperatively to actin with micromolar affinity, perturbing its secondary structure, reducing filament polymerisation rates, and impairs interactions between actin and actin binding proteins (ABPs). HCQ also significantly suppresses lamellipodial protrusive activity, indicating a link between cytoskeletal remodelling and impaired cell migration. Collectively, these findings establish that HCQ disrupts essential mechanisms for directed migration by modulating the cytoskeleton and cell mechanics. This multifaceted impairment may underlie therapeutic potential of HCQ as an anticancer agent by restricting cellular invasive capacity and remodelling required for tumour progression.

cell biology↗

bioRxiv2026

DNA Damage Driven Viability Loss and Transcriptional Reprogramming in Chinese Hamster Ovary Cell Perfusion Culture

Intensified perfusion cultures promise higher yields and consistent product quality, yet extended runs frequently stall due to declining Chinese hamster ovary (CHO) cell viability at high cell density. Here, we identify DNA damage accumulation as a central, previously underappreciated driver of this limitation. Using two antibody-expressing CHO cell lines operated at a control and high cell density in perfusion bioreactors, we combined time-resolved transcriptomics with molecular, biophysical and super-resolution imaging analyses. We observed a progressive, global downregulation of DNA damage response (DDR) pathways accompanied by a time-dependent accumulation of DNA lesions. Notably, {gamma}H2AX signalling declined despite DNA damage, indicating impaired damage sensing and repair. Concomitantly, RNA polymerase II protein levels and transcriptional hub organisation were markedly reduced, consistent with widespread transcriptional dysfunction preceding loss of viability. An extended 21-day perfusion run confirmed continued viability decline beyond day 14, supporting a cumulative damage model. Comparison with HEK293 cells revealed substantially more efficient DNA repair, underscoring an intrinsically attenuated DDR in CHO cells. Together, these findings demonstrate that unrepaired DNA damage fundamentally constrains perfusion culture longevity, exposing limits of CHO genomic plasticity and highlighting DDR pathways as promising targets for host cell engineering to enhance perfusion performance.

bioengineering↗

bioRxiv2025

Automated generation of personalized trajectories of aging phenotypes with DyViA-GAN

With a general increase in human lifespan, the need for technological advances to develop strategies for healthy aging has assumed great importance. In the present study, our goal is to predict the progression of selected aging phenotypes in a given healthy individual as one continues aging past 65 years. Therefore, we developed a novel framework called Dynamic Views of Aging with conditional Generative Adversarial Networks (or DyViA-GAN) which is capable of predicting the plausible personalized trajectories of a selected aging phenotype conditioned on the available measurements of the phenotype at a few initial time instances, and additional covariates. Given the prevalence of osteoporosis in the aging population, we selected femoral neck Bone Mineral Density (BMD) of a healthy individual as the phenotype of interest, and baseline individual Body Mass Index (BMI) as covariate. We trained DyViA-GAN on a publicly available longitudinal dataset of a large cohort of mostly white women in the United States of age 65 years or above. Thus, it generated, for each individual, continuous phenotype trajectories, along with a corresponding region of acceptable predictions, for an age range of 66 to 89 years, for eight different combinations both with and without involving the covariate. The prediction results were subjected to rigorous quality-control and multiple comparative analyses. Our results clearly demonstrate the potential of generative deep learning frameworks in healthspan research.

bioinformatics↗

bioRxiv2025

The 18S rRNA methyltransferase, BUD23, is required for appropriate lipid and mitochondrial metabolism

Efficient energy metabolism is essential for health and its dysregulation drives cardiometabolic disease. Delivery of regulatory control through translation and ribosome function is emerging as important. Here, we identify the rRNA methyltransferase BUD23 as a potent regulator of cellular and systemic energy homeostasis. Adipocyte-specific deletion of BUD23 in mice regulates lipid and mitochondrial metabolism resulting in a pronounced lean phenotype and resistance to diet-induced obesity. Mechanistically, BUD23 modulates translation initiation and efficiency of mRNAs with specific features - including short 5 UTR length and GC-rich post-initiation codon usage - characteristic of mitochondrial and lipogenic proteins. Genetic analyses and Mendelian randomisation support a role for BUD23 in human cardiometabolic traits and disease burden. Together, our findings uncover a conserved translational control mechanism that regulates energy state, from cellular metabolism through to human cardiometabolic health.

cell biology↗

bioRxiv2025

The cause-effect conundrum of local-scale site and soil factors in acute oak decline (AOD)

Background and aimsAcute oak decline (AOD), a decline syndrome affecting mature oaks, involves bacterial pathogens which likely act as opportunists under host stress. Trees displaying symptoms (bleeding cankers) appear in localized clusters, not whole stands. This study investigates the potential involvement of local-scale factors, in interaction with large-scale environmental drivers, in influencing onset and progression of AOD. MethodsAOD-symptomatic (n=30) and asymptomatic trees (n=30) across three UK oak woodlands were assessed for tree characteristics, their surrounding context, and soil properties. ResultsTree health status was linked to significant differences in soil and tree properties across sites. Symptomatic trees exhibited greater loss of crown density, lower local stand (0-20 m) basal area and shallower depth to gleying. Significant differences in soil properties included lower concentrations of Olsen P, total N, and exchangeable Mg in symptomatic trees, alongside higher exchangeable Fe, especially at 40-50 cm depth. Depth to gleying and exchangeable Fe were identified as the most influential predictors of AOD. ConclusionsAOD symptomatic trees may experience seasonal soil water saturation closer to the surface compared to asymptomatic trees, resulting in a higher proportion of their roots being exposed to an anoxic, iron-reducing environment. This study is the first to report such an association between gleying depth, likely seasonal water saturation, and symptom status for AOD. It is unclear whether water balance and associated soil nutrient variations are predisposing factors or consequences of declining tree health, though the identified local-scale factors likely contribute to AOD. A feedback loop is conceptualised where declining tree health worsens soil conditions, creating a negative cycle that accelerates tree decline.

ecology↗

bioRxiv2025

Dual Probe Ligation In Situ Hybridization with Rolling-Circle Amplification for High-Plex Spatial Transcriptomics

New biological insights are increasingly dependent upon a deeper understanding of tissue architectures. Critical to such studies are spatial transcriptomics technologies, especially those amenable to analysis of the most widely available human tissue type, formalin-fixed and paraffin-embedded (FFPE) clinical specimens. Here we build on our previous oligonucleotide probe ligation-based approach to accurately analyze FFPE mRNA, which suffers from variable levels of degradation. Ligation In Situ Hybridization followed by rolling circle amplification (LISH-LocknRoll or LISH-LnR), provides a streamlined method to detect the spatial location of specific mRNA isoforms within FFPE tissue architectures. Iterative fluorescent probe hybridization and imaging enables highly multiplexed spatial transcriptomic studies, as demonstrated herein for fixed specimens from inclusion body myositis patients and pediatric rhabdomyosarcoma patients. We additionally demonstrate a system of molecular rheostats that can be used to fine tune the performance of the LISH-LnR assay. Combined with LISH-seq and LISH-QC, the LISH-LnR methodology provides a powerful approach to spatial transcriptomics.

molecular biology↗

bioRxiv2024

At-RS31 orchestrates hierarchical cross-regulation of splicing factors and integrates alternative splicing with TOR-ABA pathways

O_LIAlternative splicing is essential for plants, enabling a single gene to produce multiple transcript variants to boost functional diversity and fine-tune responses to environmental and developmental cues. At-RS31, a plant-specific splicing factor in the Serine/Arginine (SR)-rich protein family, responds to light and the Target of Rapamycin (TOR) signaling pathway, yet its downstream targets and regulatory impact remain unknown. C_LIO_LITo identify At-RS31 targets, we applied individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP) and RNAcompete assays. Transcriptomic analyses of At-RS31 mutant and overexpressing plants further revealed its effects on alternative splicing. C_LIO_LIiCLIP identified 4,034 At-RS31 binding sites across 1,421 genes, enriched in CU-rich and CAGA RNA motifs. Comparative iCLIP and RNAcompete data indicate that the RS domain of At-RS31 may influence its binding specificity in planta, underscoring the value of combining in vivo and in vitro approaches. Transcriptomic analysis showed that At-RS31 modulates diverse splicing events, particularly intron retention and exitron splicing, and influences other splicing modulators, acting as a hierarchical regulator. C_LIO_LIBy regulating stress-response genes and genes in both TOR and abscisic acid (ABA) signaling pathways, At-RS31 may help integrate these signals, balancing plant growth with environmental adaptability through alternative splicing. C_LI

plant biology↗

bioRxiv2024

Reconstructing the sequence specificities of RNA-binding proteins across eukaryotes

RNA-binding proteins (RBPs) are key regulators of gene expression. Here, we introduce EuPRI (Eukaryotic Protein-RNA Interactions) - a freely available resource of RNA motifs for 34,736 RBPs from 690 eukaryotes. EuPRI includes in vitro binding data for 504 RBPs, including newly collected RNAcompete data for 174 RBPs, along with thousands of reconstructed motifs. We reconstruct these motifs with a new computational platform -- Joint Protein-Ligand Embedding (JPLE) -- which can detect distant homology relationships and map specificity-determining peptides. EuPRI quadruples the number of known RBP motifs, expanding the motif repertoire across all major eukaryotic clades, and assigning motifs to the majority of human RBPs. EuPRI drastically improves knowledge of RBP motifs in flowering plants. For example, it increases the number of Arabidopsis thaliana RBP motifs 7-fold, from 14 to 105. EuPRI also has broad utility for inferring post-transcriptional function and evolutionary relationships. We demonstrate this by predicting a role for 12 Arabidopsis thaliana RBPs in RNA stability and identifying rapid and recent evolution of post-transcriptional regulatory networks in worms and plants. In contrast, the vertebrate RNA motif set has remained relatively stable after its drastic expansion between the metazoan and vertebrate ancestors. EuPRI represents a powerful resource for the study of gene regulation across eukaryotes.

genomics↗

bioRxiv2024

The dynamic crosstalk between cytoskeletal filaments regulates the cytoplasmic mechanics across the apicobasal axis

The cytoplasm exhibits viscoelastic properties, displaying both solid and liquid-like behavior, and can actively regulate its mechanical attributes. The cytoskeleton is a major regulator among the numerous factors influencing cytoplasmic mechanics. We explore the interdependence of various cytoskeletal filaments and the impact of their density on cytoplasmic viscoelasticity. The heterogeneous distribution of these filaments give rise to polarised mechanical properties of the cytoplasm along the apicobasal axis. Actin filament (F-actin) disassembly softens the basal cytoplasm while stiffening the mid-cytoplasm due to increased vimentin filament assembly. Disruption of microtubules (MT) or depletion of vimentin softens both the basal and mid-cytoplasm. Cyto D treatment results in localised increase of vimentin assembly in the mid cytoplasm which is dependent on the cytolinker plectin. Nocodazole treatment has a negligible effect on F-actin distribution but significantly alters vimentins spatial arrangement. We demonstrate that Cyto D treatment upregulates vimentin expression via ROS-mediated activation of NF-{kappa}B. This manuscript investigates how different cytoskeletal filaments influence the rheological characteristics of various cytoplasmic regions.

cell biology↗

bioRxiv2024

The functional anatomy of nociception: Effective Connectivity in Chronic Pain and Placebo Responders

There is growing recognition of cortical involvement in nociception. The present study is motivated by predictive coding formulations of pain perception that stress the importance of top-down and bottom-up information flow in the brain. It compares forward and backward effective connectivity - estimated from resting-state fMRI - between chronic osteoarthritic patients and healthy control subjects. Additionally, it assesses differences in effective connectivity between placebo responders and non-responders and asks whether these differences can be used to predict pain perception and placebo response. To assess hierarchical processing in nociception, we defined two primary cortical regions: primary somatosensory cortex (SSC) and posterior insula (PI) (primary interoceptive cortex) and lateral frontal pole (FP1), a terminal relay station of the pain processing pathways. The directed (effective) connectivity within and between these regions were estimated using spectral dynamic causal modeling (DCM). 56 osteoarthritis patients and 18 healthy controls were included in the analysis. Within the patient group, effective connectivity was compared between placebo responders and non-responders. In osteoarthritic patients, contra control group, forward connectivity from SSC to FP1 and from PI to FP1 was enhanced in the left hemisphere. Backward connections from FP1 to SSC were more inhibitory. Intrinsic (i.e., inhibitory recurrent or self-connectivity) of left FP1 increased. In placebo responders compared to non-responders, forward connections from bilateral SSC to PI, left SSC to FP1, left PI to left FP1 were more inhibitory. In addition, self-connections of bilateral PI and top-down connections from right FP1 to right SSC were disinhibited; whereas self-connections of right FP1 became increasingly inhibitory. We confirmed the robustness of these results in a leave-one-out cross-validation analysis of (out-of-sample) effect sizes. Overall, effective extrinsic and intrinsic effective connectivity among higher and lower cortical regions involved in pain processing emerges as a promising and quantifiable candidate marker of nociception and placebo response. The significance of these findings for clinical practice and neuroscience are discussed in relation to predictive processing accounts of placebo effects and chronic pain.

neuroscience↗

bioRxiv2023

CoFrEE: An Application to Estimate DNA Copy Number from Genome-wide RNA Expression Data

We introduce CoFrEE, a simple python-based approach to extracting copy number data from expression values that works with either RNAseq or array-based expression data. CoFrEE works best in tumor cohorts that include a subset of non-tumor tissues and is applied to processed (RSEM, RPKM or TPM) expression, rather than raw data. Experiments with real public data suggest CoFrEE can provide copy number estimations comparable to existing RNAseq-based approaches, with the advantage of also being applicable to the multitude of older expression-array cohorts.

bioinformatics↗

bioRxiv2023

Conditional Generative Learning for Medical Image Imputation

Image imputation refers to the task of generating a type of medical image given images of another type. This task becomes challenging when the difference between the available images, and the image to be imputed is large. In this manuscript, one such application, derived from the dynamic contrast enhanced computed tomography (CECT) imaging of the kidneys, is considered: given an incomplete sequence of three CECT images, we are required to the impute the missing image. This task is posed as one of probabilistic inference and a generative algorithm to generate samples of the imputed image, conditioned on the available images, is developed, trained, and tested. The output of this algorithm is the "best guess" of the imputed image, and a pixel-wise image of variance in the imputation. It is demonstrated that this best guess is more accurate than those generated by other, deterministic deep-learning based algorithms, including ones which utilize additional information and more complex loss terms. It is also shown the pixel-wise variance image, which quantifies the confidence in the reconstruction, can be used to determine whether the result of the imputation meets a specified accuracy threshold and is therefore appropriate for a downstream task.

cancer biology↗

bioRxiv2022

Viability of carcass removal as an option for offsetting the incidental take of golden eagles (Aquila chrysaetos) at wind energy facilities

As wind energy expands to achieve the United States net zero emission goals, compensatory mitigation will be required to offset negative impacts to birds and bats. The golden eagle (Aquila chrysaetos) is particularly susceptible to collision with wind turbines but only one option for offsetting mortalities has been approved by the U.S. Fish and Wildlife Service despite many sources of anthropogenic-caused mortality. Here, we update a previously developed vehicle-collision model with empirical data and integrate a resource equivalency analysis so that removal of road-killed game animals can be used as mitigation to offset incidental mortality. We parameterized the golden eagle behavior parameters using camera-traps placed at roadside carcasses. We quantified the effects of different carcass-removal schemes based on vehicle and carcass characteristics observed for the state of Wyoming. Our model results indicate that while eagles saved per carcass removed depends on removal interval and vehicle traffic volume, carcass removal is a viable mitigation strategy; up to seven eagles could be saved per year in some counties. While some uncertainty remains about the precise credit received from each carcass removed, delaying the inclusion of additional mitigation methods prevents opportunities for conservation action. An adaptive management program could be a way forward where management and monitoring are combined to further improve estimates of mitigation credit.

ecology↗

bioRxiv2022

A Suite of Advanced Tutorials for the WESTPA 2.0 Rare-Events Sampling Software

We present six advanced tutorials instructing users in the best practices of using key new features and plugins/extensions of the WESTPA 2.0 software package, which consists of major upgrades for enabling applications of the weighted ensemble (WE) path sampling strategy to even larger systems and/or slower processes. The tutorials demonstrate the use of the following key features: (i) a generalized resampler module for the creation of "binless" schemes, (ii) a minimal adaptive binning scheme for more efficient surmounting of free energy barriers, (iii) streamlined handling of large simulation datasets using an HDF5 framework, (iv) two different schemes for more efficient rate-constant estimation, (v) a Python API for simplified analysis of WE simulations, and (vi) plugins/extensions for Markovian Weighted Ensemble Milestoning and WE rule-based modeling at the system biology level. Applications of the tutorials range from atomistic to residue-level to non-spatial models, and include complex processes such as protein folding and the membrane permeability of a drug-like molecule. Users are expected to already have significant experience with running conventional molecular dynamics simulations and completed the previous suite of WESTPA tutorials.

biophysics↗

bioRxiv2022

Genome-Wide Large-Scale Multi-Trait Analysis Characterizes Global Patterns of Pleiotropy and Unique Trait-Specific Variants

Genome-wide association studies (GWAS) have found widespread evidence of pleiotropy, but characterization of global patterns of pleiotropy remain highly incomplete due to insufficient power of current approaches. We develop fastASSET, an extension of the method ASSET, to allow computationally efficient detection of variant-level pleiotropic association across a large number of traits. We analyze GWAS summary statistics of 116 complex traits of diverse types collected from the NIH GRASP repository and a number of other large GWAS consortia. We identify a total of 2,293 independent loci at the genome-wide significance level and found that the lead variants in nearly all of these loci ([~]99%) to be associated with to two or more (median = 6) traits. Further, the estimated degree of pleiotropy for the detected variants strongly predicted their degree of pleiotropy across a much larger number of traits (K=4,114) in the UK Biobank Study. Follow-up analyses of 21 unique trait-specific variants suggest that they are often linked to the expression in trait-related tissues for a small number of genes, some of which are well known to be involved in relevant biological processes. Our findings provide deeper insight into the nature of complex trait pleiotropy and leads to, for the first time, identification of highly unique trait-specific susceptibility variants.

genetics↗

bioRxiv2022

Force Field Dependent DNA Breathing Dynamics: A Case Study of Hoogsteen Base Pairing in A6-DNA

The Hoogsteen (HG) base pairing (bp) conformation, commonly observed in damaged and mutated DNA helices, facilitates DNA repair and DNA recognition. The free energy difference between HG and Watson-Crick (WC) base pairs has been computed in previous studies. However, the mechanism of the conformational transition is not well understood. A detailed understanding of the process of WC to HG base pair transition can provide deeper understanding of DNA repair and recognition. In an earlier study, we explored the free energy landscape for this process using extensive computer simulation with the CHARMM36 force field. In this work, we study the impact of force field models in describing the WC to HG base pairing transition using meta-eABF enhanced sampling, quasi-harmonic entropy calculation, and non-bonded energy analysis. The secondary structures of both base pairing forms and the topology of the free energy landscapes were consistent over different force field models, although the relative free energy, entropy and the interaction energies tend to vary. The relative stability of the WC and HG conformations is dictated by a delicate balance between the enthalpic stabilization and the reduced entropy of the structurally rigid HG structure. These findings highlight the impact that subtleties in force field models can have on accurately modeling DNA base pair dynamics and should stimulate further computational investigations into other dynamically important motions in DNA. Graphical TOC Entry O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/490579v2_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@1580f16org.highwire.dtl.DTLVardef@4688b6org.highwire.dtl.DTLVardef@b97962org.highwire.dtl.DTLVardef@d028e5_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗