Biology subjects

Srinivasan, M.

Publications and source records attributed to Srinivasan, M..

At least 19 recordsLinked to original sources

bioRxiv2026

TRAPPC8 Is an Endogenous Brake on UFMylation That Suppresses Tauopathy

UFMylation, a ubiquitin-like protein modification, drives tau spread through the brain, but what keeps this process in check has remained unclear. We show that TRAPPC8 acts as a natural brake on UFMylation, binding directly to the E1 enzyme UBA5 to dampen pathway activity. In Alzheimer's disease brain tissue, TRAPPC8 is reduced while UFMylation is elevated, suggesting this brake fails as disease progresses. Sustaining UFMylation in human iPSC-derived neurons increased tau aggregation and spread while disrupting lysosomal function and lipid balance. Restoring TRAPPC8-UBA5 binding reversed these defects through the lysosomal protein CLN8, which restored lysosomal function and reduced tau pathology. Notably, expressing just the UBA5-binding region of TRAPPC8 was enough to suppress tau pathology in vivo, marking it as a promising therapeutic target.

neuroscience↗

bioRxiv2026

DNA catenation is essential for Sister Chromatid Cohesion

From S phase until anaphase, sister chromatids remain physically linked to ensure accurate chromosome segregation. This linkage, called sister chromatid cohesion, must withstand the pulling forces generated by the mitotic spindle and is thought to require entrapment of sister DNAs inside the ring-shaped cohesin complex. DNA catenations that arise naturally during replication could also tether sister chromatids, but whether they contribute to cohesion has remained unresolved. Here, using budding yeast, we show that cohesin-mediated sister DNA entrapment alone cannot withstand spindle-generated pulling forces and that robust sister chromatid cohesion requires DNA catenation. Selective removal of DNA catenations causes catastrophic cohesion loss, delays chromosome biorientation and increases chromosome mis-segregation, even when cohesin rings remain intact. Importantly, DNA catenation similarly underpins force-resistant cohesion in metazoan chromosomes. Our findings fundamentally redefine the physical basis of sister chromatid cohesion by establishing DNA catenation as an evolutionarily conserved component of the force-resistant linkage between sister chromatids that enables accurate chromosome segregation.

molecular biology↗

bioRxiv2026

Integrated evaluation of immune system perturbation using structural, functional and cellular immunotoxicity endpoints in rats

Evaluation of unintended immunotoxicity represents an important component of nonclinical safety assessment, as perturbation of immune function may increase susceptibility to infection, impair vaccine responses, and disrupt immune homeostasis. Regulatory guidance, including the ICH S8 Immunotoxicity Guideline, recommends a weight-of-evidence approach in which observations from conventional toxicological endpoints are integrated with functional immune assays to support interpretation of immune system effects. The present study applied an integrated immunotoxicity evaluation framework to examine concordance among structural, functional, and cellular immune endpoints in male Sprague-Dawley rats using a well-characterized immunosuppressive reference compound. Hematological evaluation revealed leukopenia characterized primarily by lymphocyte depletion. Reductions in spleen and thymus weights were accompanied by histopathological evidence of lymphoid depletion in multiple immune tissues, including spleen, thymus, lymph nodes, Peyers patches, and bone marrow. Functional immune competence was assessed through hemagglutination antibody response to sheep red blood cells and delayed-type hypersensitivity assays, both of which demonstrated marked suppression of adaptive immune responses. Flow cytometric immunophenotyping further demonstrated substantial reductions in B-cell populations and decreases in CD4 and CD8 T-cell counts, whereas NK cell populations were comparatively less affected. The concordance of hematological alterations, lymphoid tissue changes, impaired functional immune responses, and lymphocyte subset depletion provides integrated evidence of immune system perturbation. These findings demonstrate that complementary immunotoxicity endpoints collectively support hazard characterization of immune system effects under GLP conditions. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/713556v1_ufig1.gif" ALT="Figure 1"> View larger version (72K): org.highwire.dtl.DTLVardef@10154aaorg.highwire.dtl.DTLVardef@5d78e7org.highwire.dtl.DTLVardef@acaaceorg.highwire.dtl.DTLVardef@1f42c_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2026

Multiomic Spatial Imaging Assay (MSIA) -- A High-plex In Situ Detection Method for mRNAs, Proteins, and Protein-Protein Interactions using Manual And Semi-Automated Workflows

We report Multiomics Spatial Image Analysis (MSIA), a suite of technologies that include streamlined manual and semi-automated workflows to image 100s of RNAs from fresh frozen and formalin-fixed paraffin-embedded (FFPE) samples, contextualize RNAs with select protein markers including imaging synaptic protein interactions, a data analysis pipeline that includes corrections for chromatic aberration, algorithms for image stitching, deep learning models for image analysis (cell segmentation and RNA dot detection using hundreds of RNAscope images) from multiple stain-image cycles and proof of concept for a language model trained on extensive Parkinsons Disease (PD) literature. We used the language model to identify potential new biomarkers that were confirmed in MPTP-treated mouse model of PD. Furthermore, by incorporating more stain-image cycles alongside an additional fluorescent channel and advanced error-correcting decoding schemes, the MSIA workflow demonstrates the scalability to potentially quantify over 1,000 genes.

neuroscience↗

bioRxiv2026

Highly under-actuated dynamic manipulation: Dice stacking is mostly open-loop

Humans ability to grasp and dynamically manipulate objects with their hands is unmatched by current robots. To better understand human dynamic manipulation, we studied dice stacking, a task in which humans form a vertical stack of dice from a set of initially unstacked playing dice using an overturned cup and the surface of a table. This task is high dimensional and under-actuated, so it may superficially seem an incredible feat of state estimation and feedback control, but we show that this task is amenable to open-loop strategies. We simulated a cup with dice oscillated by fixed arm movement patterns using two different computer simulation frameworks with different contact models. These simulations showed that, for a range of arm and wrist movements, the dice naturally stack without any dice state feedback. We verified the predictions of these simulations with a physical robot. Thus, we have added dice stacking to the small list of dynamic manipulation tasks that can be robustly performed open-loop. We speculate that, for highly under-actuated tasks, humans may be biased to learn open-loop strategies over state feedback strategies. Future work could investigate the presence of such a bias in humans and its potential value for reinforcement learning algorithms.

animal behavior and cognition↗

bioRxiv2025

STING_IFN_CH25H lipid axis links innate immune activation to tau pathology

Genetic risk for Alzheimers disease is strongly enriched in pathways governing microglial activation and cholesterol metabolism, yet how these processes converge to drive neurodegeneration remains unclear. Here, we identify the oxysterol 25-hydroxycholesterol (25- HC) as a pathogenic lipid downstream of the cGAS-STING-IFN pathway. In models of tau pathology, interferon signaling induces Cholesterol 25-hydroxylase (CH25H) expression in microglia. Ch25h deletion in female P301S mice suppressed tau aggregation, preserved synapses, prevented brain atrophy, and rescued memory. Mechanistically, loss of CH25H disrupted STING trafficking, attenuated IFN activation, dampened self-perpetuating microglial inflammation. Strikingly, 25-HC directly accelerated tau propagation in human iPSC derived neurons. It also disrupted lysosomal and mitochondrial lipid composition, driving cholesteryl ester accumulation and promoting apoptosis under tau-induced stress. These findings define a STING-IFN-CH25H lipid axis that bridges innate immune activation to tau pathology and toxicity, offering a tractable therapeutic pathway for inflammation-driven neurodegenerative conditions.

neuroscience↗

bioRxiv2025

A metabolite extracted from E. coli suppresses tau aggregation

Tau aggregation is a key pathological feature of neurodegenerative diseases termed tauopathies. Identifying the various cellular factors that function to prevent tau aggregation in cells can generate key insights into how to mitigate diseases associated with protein misfolding. During an investigation into developing purification methods for the protein tau, we observed that isolates of E. coli lysate prevented human tau aggregation in vitro. Fractionation of the lysate was used to further isolate a small molecular weight (MW) inhibitory fraction containing multiple components, as determined by mass spectrometry and NMR. A putative inhibitory component, methylphosphonic acid (MePn), decreased tau amyloid formation when supplemented to in vitro aggregation assays. MePn also blocked the aggregation of expressed tau in live E. coli when supplemented to the culture media. Our findings can be directly applied to optimizing purification of recombinant tau protein and more broadly, highlight the potential of cellular metabolites to directly modulate tau amyloid formation.

biochemistry↗

bioRxiv2025

Global diversity of integrating conjugative elements (ICEs) in Helicobacter pylori and their influence on genome architecture

Integrating conjugative elements (ICEs) are mobile genetic elements conferring a wide range of beneficial functions upon their bacterial hosts. Generally, they can be activated from their integrated states to undergo horizontal gene transfer via conjugation. In the case of the human gastric pathogen Helicobacter pylori, a paradigm for extensive genetic diversity, highly efficient natural transformation and recombination processes may superimpose canonical transfer of its two ICEs termed ICEHptfs3 and ICEHptfs4, and thus shape their composition substantially. Here, as a part of the Helicobacter pylori Genome Project (HpGP) initiative, we have analyzed high-quality genome sequences from 1011 clinical strains with respect to their ICE content and variability. We show that both elements are highly prevalent in all H. pylori populations, but have a strong tendency for gene erosion. ICE sequence variations reflect the population structure and show a clear signature of increased horizontal transfer. A detailed map of ICE integration sites revealed local preferences, but also how recombination processes result in hybrid elements or genome rearrangements. Population-specific differences in ICE cargo genes might reflect distinct requirements in the biological functions provided by these mobile elements.

microbiology↗

bioRxiv2025

The SMC Hinge is a Selective Gate for Obstacle Bypass

DNA loop-extruding SMC complexes play vital roles in genome maintenance and DNA immunity. However, the ability of these ring-shaped DNA motors to navigate large DNA-bound obstacles, such as DNA/RNA polymerases and ribosomes in prokaryotes, has remained unclear. Here, we demonstrate that a bacterial SMC Wadjet complex can efficiently bypass obstacles larger than the SMC coiled coil lumen if they are linked to the extruded DNA by single-stranded DNA (ssDNA). This process is mediated by the selective entrapment of the ssDNA linker within the SMC hinge channel, which acts as an obligate gate--permitting ssDNA passage while excluding double-stranded DNA (dsDNA). By threading the linker through the hinge gate as dsDNA is translocated through the SMC motor, the obstacle can follow a trajectory distinct from its associated dsDNA, remaining outside the SMC ring. This mechanism enables continuous dsDNA entrapment while successfully bypassing obstacles. We show that hinges of diverse SMC complexes including eukaryotic condensin and Smc5/6 also selectively accommodate ssDNA, suggesting that hinge bypass is a conserved feature across SMC proteins. We demonstrate that while the hinge domain is essential for obstacle bypass, it is dispensable for loop extrusion, showing that these functions are independent, provided by separate SMC modules. These findings uncover the long-sought function of the SMC hinge toroid and provide the first mechanistic explanation for how DNA-entrapping SMC complexes can extrude loops on chromosomal DNA densely populated with obstacles. Integrating hinge bypass into the DNA loop extrusion model, we propose that the hinge may also facilitate the passage of RNA and peptide, enabling bypass of transcription-associated ribonucleoprotein complexes and other SMC complexes.

molecular biology↗

bioRxiv2025

Natural variability increases human walking metabolic costs and its implications to simulation-based metabolic estimation

Human walking contains variability due to small intrinsic perturbations arising from sensory or motor noise, or to promote motor learning. We hypothesize that such stride-to-stride variability may increase the metabolic cost of walking over and above a perfectly periodic motion, and that neglecting such variability in simulations may mis-estimate the metabolic cost. Here, we quantify the metabolic estimation errors accrued by neglecting the stride-to-stride variability using human data and a musculoskeletal model by comparing the cost of multiple strides of walking and the cost of a perfectly periodic stride with averaged kinematics and kinetics. We find that using an averaged stride underestimates the cost by about 2.5%, whereas using a random stride may mis-estimate the cost positively or negatively by up to 15%. As a further illustration of the cost increase in a simpler dynamical context, we use a feedback-controlled inverted pendulum walking model to show that increasing the sensory or motor noise increases the overall metabolic cost, as well as the variability of stride-to-stride metabolic costs, as seen with the musculoskeletal simulations. Our work establishes the importance of accounting for stride-to-stride variability when estimating metabolic costs from motion.

biophysics↗

bioRxiv2024

James-Stein estimator improves accuracy and sample efficiency in human kinematic and metabolic data

Human biomechanical data are often accompanied with measurement noise and behavioral variability. Errors due to such noise and variability are usually exaggerated by fewer trials or shorter trial durations, and could be reduced using more trials or longer trial durations. Speeding up such data collection by lowering number of trials or trial duration, while improving the accuracy of statistical estimates, would be of particular interest in wearable robotics applications and when the human population studied is vulnerable (e.g., the elderly). Here, we propose the use of the James-Stein estimator (JSE) to improve statistical estimates with a given amount of data, or reduce the amount of data needed for a given accuracy. The JSE is a shrinkage estimator that produces a uniform reduction in the summed squared errors when compared with the more familiar maximum likelihood estimator (MLE), simple averages, or other least squares regressions. When data from multiple human participants are available, an individual participants JSE can improve upon MLE by incorporating information from all participants, improving overall estimation accuracy on average. Here, we apply the JSE to multiple time-series of kinematic and metabolic data from the following parameter estimation problems: foot placement control during level walking, energy expenditure during circle walking, and energy expenditure during resting. We show that the resulting estimates improve accuracy -- that is, the James-Stein estimates have lower summed squared error from the true value compared with more conventional estimates.

biophysics↗

bioRxiv2024

Childhood brain morphometry in children with persistent stunting and catch-up growth

BackgroundEarly childhood stunting affects around 150 million young children worldwide and leads to suboptimal human potential in later life. However, there is limited data on the effects of early childhood stunting and catch-up growth on brain morphometry. MethodsWe evaluated childhood brain volumes at nine years of age in a community-based birth-cohort follow-up study in Vellore, south India among four groups based on anthropometric assessments at two, five, and nine years namely Never Stunted (NS), Stunted at two years and caught up by five years (S2N5), Stunted at two and five years and caught up by nine years (S2N9), and Always Stunted (AS). T1-weighted magnetic resonance imaging (MRI) images were acquired using a 3T MRI scanner, and brain volumes were quantified using FreeSurfer software. FindingsAmongst 251 children from the overall cohort, 178 children with a mean age of 9.54 were considered for further analysis. The total brain volume, subcortical volume, bilateral cerebellar white matter, and posterior corpus callosum showed a declining trend from NS to AS. Regional cortical brain analysis showed significant lower bilateral lateral occipital volumes, right pallidum, bilateral caudate, and right thalamus volumes between NS and AS. InterpretationTo the best of our knowledge, this first neuroimaging analysis to investigate the effects of persistent childhood stunting and catch-up growth on brain volumetry indicates impairment at different brain levels involving total brain and subcortical volumes, networking/connecting centres (thalamus, basal ganglia, callosum, cerebellum) and visual processing area of lateral occipital cortex.

neuroscience↗

bioRxiv2023

Metabolic cost for isometric force scales nonlinearlyand predicts how humans distribute forces across limbs

Muscles consume metabolic energy for force production and movement. A mathematical model of metabolic energy cost will be useful in predicting instantaneous costs during human exercise and in computing effort-minimizing movements via simulations. Previous in vivo data-derived models usually assumed either zero or linearly increasing cost with force, but a nonlinear relation could have significant metabolic or behavioural implications. Here, we show that metabolic cost scales nonlinearly with joint torque with an exponent of about 1.64, using calorimetric measurements of isometric squats. We then demonstrate that this metabolic nonlinearity is reflected in human behaviour: minimizing this nonlinear cost predicts how humans share forces between limbs in additional experiments involving arms and legs. This shows the utility of the nonlinear energy cost in predictive models and its generalizability across limbs. Finally, we show mathematical evidence that the same nonlinear metabolic objective may underlie force sharing at the muscle level.

biophysics↗

bioRxiv2023

What loss functions do humans optimize when they perform regression and classification

Studying how humans perceive patterns in visually presented data is useful for understanding data-based decision-making and potentially understanding visually mediated sensorimotor control. We conducted experiments to examine how human subjects perform the simplest machine learning or statistical estimation tasks: linear regression and binary classification on 2D scatter plots. We used inverse optimization to infer the loss function humans optimize when they perform these tasks. Minimizing the sum of regression error raised to the power of 1.7 best-described human performing regression on sparse data. Loss functions with lower exponents, which are less sensitive to outliers, were better descriptors for regression tasks performed on less sparse data consisting of more data points. For the classification task, minimizing a logistic loss function was on average a better descriptor of human choices than an exponential loss function applied to only misclassified data. People changed their strategies as data density increased. These results represent overall trends across subjects and trials but there was large inter- and intra-subject variability in human choices. Future work may examine other loss function families and other tasks. Such understanding of human loss functions may inform the design of applications that interact with humans better and imitate humans more effectively.

neuroscience↗

bioRxiv2023

Human force control may trade-off force error with central tendency and recency biases

Understanding how humans control force is useful for understanding human movement behaviors and sensorimotor control. However, it is not well understood how the human nervous system handles different control criteria such as accuracy and energetic cost. We conducted force tracking experiments where participants applied force isometrically while receiving visual force feedback, tracking step changes in target forces. The experiments were designed to disambiguate different plausible objective function components. We found that force tracking error was largely explained by a trade-off between error-reducing tendency and force biases, but we did not need to include an effort-saving tendency. Central tendency bias, which is a shift towards the center of the task distribution, and recency bias, which is a shift towards recent action, were necessary to explain many of our observations. Surprisingly, we did not observe such biases when we removed force requirements for pointing to the target, suggesting that such biases may be task-specific. This study provides insights into the broader field of motor control and human perceptions where behavioral or perceptual biases are involved.

neuroscience↗

bioRxiv2022

Sister chromatid cohesion establishment during DNA replication termination

The cohesin complex tethers sister chromatids together from the moment they are generated in S-phase until their separation in anaphase1,2. This fundamental phenomenon, called sister chromatid cohesion, underpins orderly chromosome segregation. The replisome complex coordinates cohesion establishment with replication of parental DNA3. Cohesion can be established by cohesin complexes bound to DNA before replication4,5, but how replisome interaction with pre-loaded cohesin complexes results in cohesion is not known. Prevailing models suggest cohesion is established by replisome passage through the cohesin ring or by transfer of cohesin behind the replication fork by replisome components5. Unexpectedly, by visualising single replication forks colliding with pre-loaded cohesin complexes, we find that cohesin is pushed by the replisome to where a converging replisome is met. Whilst the converging replisomes are removed during DNA replication termination, cohesin remains on nascent DNA. We demonstrate that these cohesin molecules tether the newly replicated sister DNAs together. Our results support a new model where sister chromatid cohesion is established during DNA replication termination, providing important insight into the molecular mechanism of cohesion establishment.

biophysics↗

bioRxiv2022

A unified peptide array platform for antibody epitope binning, mapping, specificity and predictive off-target binding

Therapeutic antibody efficacy is largely determined by the target epitope. In addition, off-target binding can result in unanticipated side-effects. Therefore, characterization of the epitope and binding specificity are critical in antibody discovery. Epitope binning provides low-resolution of an antibody epitope and is typically performed as a cross-blocking assay to group antibodies into overlapping or non-overlapping bins. Epitope mapping identifies the epitope with high resolution but requires low throughput methods. In addition to binning and mapping, there is a need for a scalable and predictive approach to reveal off-target binding early in antibody discovery to reduce the risk of in vivo side effects. Peptide microarrays are an information-rich platform for antibody characterization. However, the potential of peptide microarrays in early-stage antibody discovery has not been realized because they are not produced at the scale, quality and format needed for reliable high-throughput antibody characterization. A unified, peptide library platform for high-resolution antibody epitope binning, mapping and predictive off-target binding characterization is described here. This platform uses highly scalable array synthesis and photolithography to synthesize more than 3 million addressable peptides. These arrays conform to a microplate format and each synthesis is qualified with mass spectrometry. Using this platform, a scalable approach to early-stage epitope and specificity characterization, with prediction of off-target interaction(s), is demonstrated using a panel of anti-HER2 monoclonal antibodies. This study highlights the prospect of this platform to improve antibody discovery productivity by generating epitope and specificity information much earlier with potentially hundreds of antibody clones.

bioengineering↗

bioRxiv2022

Formation of the clamped state by Scc2 and DNA overcomes the constraints imposed by zipping-up of the SMC coiled coils on cohesin's ATPase

In addition to mediating sister chromatid cohesion, cohesin, by virtue of Loop Extrusion (LE), organises the spatial arrangement of interphase DNA. The latter activity relies on DNA and Scc2 dependent ATP hydrolysis by cohesin. How the impetus from the ATPase cycle translates into reeling of DNA loops into the SMC kleisin rings is still unclear. The SMC coiled coils show several striking structural features like folding and zipping-up, if and how these structural states affect cohesins activity is still unclear. We show here that cohesins loop extruding motor contains an internal constraint that regulates its ATPase activity, zipping-up of the coiled coils impedes ATP hydrolysis by cohesin. We show that integrity of a region where the coiled coils emerge for the SMC hinge domains, SMC wrist, is critical for the zipping up of the coiled coils and the resulting inhibition of cohesins ATPase. Clamping of DNA by Scc2 onto the engaged SMC heads in the presence of ATP leads to unzipping of the coiled coils and permits ATP hydrolysis. Strikingly, irreversible folding of the coiled coils at the elbow region does not lead to any measurable change to the ATPase activity suggesting that recurrent cycles of folding and unfolding of the coiled coils is not necessary for driving continuous ATP hydrolysis by cohesin.

biochemistry↗