Biology subjects

Mak, J.

Publications and source records attributed to Mak, J..

13 recordsLinked to original sources

bioRxiv2026

Molecular basis of cooperative assembly of the Ndc80-Ska kinetochore complex on microtubules

Successful chromosome segregation depends on robust kinetochore-microtubule attachments. The outer kinetochore load-bearers Ndc80 and Ska complexes functionally cooperate, but the molecular basis of their interaction remains elusive. Here, we combine cryo-EM and functional investigations of Ndc80:Ska on microtubules. Ndc80 forms longitudinal arrays along single protofilaments using two modules. The HEC1 N-terminal tail stabilizes interactions between microtubule-binding heads regulated by Aurora B. The HEC1 loop, away from microtubules, organizes Ndc80 coiled-coils into stacks matching the periodicity of tubulin subunits. SkaC binds to a previously unknown interface of Ndc80 as well as to microtubules, simultaneously stapling tubulin dimers longitudinally and neighboring protofilaments laterally. Our work demonstrates how several weak interactions of a small number of individual complexes are harnessed to generate a robust and regulated kinetochore coupler.

molecular biology↗

bioRxiv2026

SARS-CoV-2 spike protein-associated sialoglycoconjugates induce nanoscale filipodia to facilitate micro-size platelet clotting

COVID-19 disease is associated with thrombosis, but the pathogenic mechanism remains unclear. Here, we investigate how SARS-CoV-2 spike protein causes platelet activation and aggregation. Our three-dimensional ultrastructural analyses showed that invaginated platelet structures, open canalicular system (OCS), expanded upon activation, trapping viral particles in the process. Binding with platelet OCS concealed SAR-CoV-2 spike-coated particles from virion detection in platelet-depleted blood plasma. Both SARS-CoV-2 spike coated-particles and recombinant spikes specifically induced platelet aggregation with nanoscale filipodia extensions, with the terminal sialic acids of the SARS-CoV-2 spike protein-associated sialoglycoconjugates being the key determinant in platelet activation. Our work illustrates that virus-associated sialic acids, not proteins, are functionally responsible for SARS-CoV-2 induced thrombotic events, providing a mechanistic insight on how glycosylation contributes to disease severity in COVID-19. This study lays the foundation for the development of glycan-modified vaccines with reduced risks of thrombosis.

molecular biology↗

bioRxiv2026

Calcium-phosphate bridge is a novel phosphorylation switch that stabilises protein-complexes during HIV assembly

Calcium (Ca2+) and phosphate (PO43-) are fundamental-element and -chemical group in biology. Specifically, the chemistry of both Ca2+ signalling and phosphorylation switch are independent mechanisms regulating a broad spectrum of biological processes. It is, however, not appreciated that a normal function of phospho-mimic amino acids (aspartate/glutamate) is to interact with Ca2+ at the atomic level. Here, we leveraged HIV-Ca2+ biology in primary cells to describe an unknown layer of regulatory processes via Ca2+-phosphate (PO43-) bridge to support protein complex formation. We identified novel HIV phosphorylation sites overlapping Ca2+ binding domains through phospho-proteomics. Integrating primary cells, molecular virology, structural biology, biophysical and ultrastructural analyses, we presented multiple examples of Ca2+-PO43- bridges that support HIV assembly and function. These include Ca2+-PO43- bridges: (i) stabilising Pr55Gag-Pr160GagPol complex for virus function; (ii) mediating p6Pol dimerization to support virion maturation; and (iii) modulating viral complex formation to package both viral enzymatic- and cellular-proteins. As the convergent enrichment of these signatured calcium-phosphorylation domains occurs across a wide range of viral and cellular proteins, we propose Ca2+-PO43- bridge to be a general principle for Ca2+-coordinated phosphorylation switch to regulate biological processes.

cell biology↗

bioRxiv2025

Mapping the Causal Roles of Non-Primary Motor Areas in Human Reach Planning and Execution

Non-primary motor areas, including the dorsal premotor cortex (PMd), ventral premotor cortex (PMv), and posterior parietal cortex (PPC), are involved in movement planning, but their precise contributions remain unclear. We used functional magnetic resonance imaging (fMRI), transcranial magnetic stimulation (TMS), and kinematic assessments to explore how these areas influence reaching performance in neurologically intact adults. Participants performed a reaching task using the KINARM exoskeleton robot. Brief TMS pulse trains were initiated before movement onset to perturb cortical activity at subthreshold and suprathreshold intensities targeting bilateral PMd, PMv, and PPC. Subthreshold stimulation of contralateral PMd and PMv reduced reach efficiency and smoothness, while suprathreshold stimulation of contralateral PPC increased deviation error and reduced smoothness. Among ipsilateral targets, PMd showed consistent TMS-induced effects, and was the only target where resting-state connectivity predicted behavioral response. Stronger interhemispheric connectivity in the primary motor cortex and weaker interhemispheric PPC connectivity were associated with greater reductions in straightness and smoothness during subthreshold ipsilateral PMd stimulation. These findings show that perturbation of premotor and parietal areas during early movement execution alters reach trajectories, and differences in network organization explain variability in behavioral response. Identifying contributions of cortical areas and connectivity patterns may help personalize interventions after stroke. This study was registered at ClinicalTrials.gov under ID NCT04286516.

bioengineering↗

bioRxiv2025

Inhibited oligodendrogenesis, but not repeated mild traumatic brain injury, impairs attention in adult mice

Attention problems are among the most common long-lasting cognitive symptoms of mild traumatic brain injury (mTBI) and as attention is fundamental to many aspects of cognition, the effects of attentional impairment can be broad. The brains white matter is particularly vulnerable to damage during mTBI. Damage to oligodendrocytes and myelin contributes to cognitive deficits following injury and myelin plasticity is a potential mechanism for functional recovery. The aim of this work was to assess attentional impairment following mTBI in mice and evaluate the role of newly generated oligodendrocytes in recovery. This study used the Myrf conditional knockout mouse model, in which the Myrf gene, required for oligodendrocyte precursor cell (OPC) differentiation into mature myelinating oligodendrocytes, is deleted from OPCs following tamoxifen injection, thereby halting oligodendrogenesis. Mice were trained on the 5-Choice Serial Reaction Time (5-CSRT) task before receiving tamoxifen followed by three mTBI or sham procedures. Attention was probed on the 5-CSRT with decreasing stimulus durations at four time points following injury out to 12 weeks. While no attentional impairment was observed in mice with mTBI, OPC-MyrfKO mice showed lower choice accuracy ({beta} = -2.85%, p = 0.03) and more omitted trials ({beta} = 4.09%, p = 0.02) across injury groups, time points and stimulus durations, suggesting that active oligodendrogenesis is required for sustained attention. These results suggest that this mouse model of mTBI was not severe enough to impact attention as measured by the 5-CSRT task, however myelin plasticity in adulthood may contribute to attention and complex task performance. Significance StatementAttention deficits are common after mild traumatic brain injury (mTBI), yet therapeutic targets remain unclear. This study investigated the role of adult myelin plasticity in cognitive recovery by using a mouse model that blocks new myelin formation. While mild injury alone did not impair attention, mice unable to generate new myelin showed reduced response accuracy. These findings suggest that adult oligodendrogenesis supports attention. Understanding how myelin plasticity influences behaviour could reveal new targets for enhancing recovery after brain injury, highlighting the importance of supporting myelin health in therapeutic strategies.

neuroscience↗

bioRxiv2025

Longitudinal Stability of Mood-Related Resting-State Networks in Youth with Symptomatic Bipolar-I/II Disorder

Bipolar disorder (BD) is characterized by temporal instability of mood and energy, but the neural correlates of this instability are poorly understood. In previous cross-sectional studies, mood state in BD has been associated with differential functional connectivity (FC) amongst several subcortical regions and ventromedial prefrontal cortex. Here, we assess whether BD is associated with longitudinal instability within this mood-related network of interest (NOI). Young people with BD-I/II were scanned 4-6 times and healthy controls (HC) were scanned 4 times over 9 months. Following preprocessing of 20-minute resting-state scans, we assessed across-scan correlation of FC, focusing on FC between regions previously associated with BD mood state. Utilizing Bayesian models, we assessed the relationship between diagnostic group and within-person, across-scan correlation, adjusting for motion, time-of-day, and inter-scan interval; prediction intervals (PI) are reported. In a sample of 16 youth (11 BD, 5 HC; 16.3-23.3 years old) with 70 scans (50 BD, 20 HC), across-scan NOI stability was higher within-than between-person (0.70 vs. 0.54; p<.0001). BD (vs. HC) within-person scan-pairs showed lower NOI stability (mean -0.109; 95% PI -0.181, -0.038), distinguishing BD vs. HC with excellent accuracy (AUC=0.95). NOI instability was more pronounced with manic symptoms (mean -0.012; 95% PI -0.023, -0.0002) and in BD-II (vs. BD-I; mean -0.071; 90% PI -0.136, -0.007). Results persisted after accounting for medications, comorbidity, and sleep/arousal measures. Within this pilot sample, BD is characterized by less within-person stability of a mood-related NOI. While preliminary, these results highlight a possible role for precision imaging approaches to elucidate neural mechanisms underlying BD.

neuroscience↗

bioRxiv2023

A primordial TFEB-TGFβ signaling axis systemically regulates diapause and stem cell longevity

Fasting/refeeding enhances animal health and lifespan across taxa. C. elegans can endure months of fasting in adult reproductive diapause (ARD) and upon refeeding, regenerate and reproduce. hlh-30/TFEB is an ARD master regulator whose mutants live mere days in ARD and dont recover with refeeding. Here we find that downregulation of TGF{beta} signaling bypasses hlh-30 collapse, and restores recovery, germline stem cell proliferation and reproductive competence. Upon fasting, HLH-30/TFEB(+) downregulates TGF{beta} in sensory neurons, to inhibit Notch and promote reproductive quiescence in the germline. Upon refeeding, these pathways are upregulated to activate stem cells and promote reproduction. hlh-30 loss induces a senescent-like DNA damage, immune and growth metabolic signature reversed by inhibiting TGF{beta} signaling. TFEBs role is conserved in mammalian diapause models, including mouse embryonic and human cancer diapause. Thus, TFEB-TGF{beta} axis relays systemic signals matching nutrient supply with growth signaling, to regulate stem cell longevity, senescence and regeneration across species.

cell biology↗

bioRxiv2022

Quantification of membrane binding and diffusion using Fluorescence Correlation Spectroscopy diffusion laws

Many transient processes in cells arise from the binding of cytosolic proteins to membranes. Quantifying this membrane binding and its associated diffusion in the living cell is therefore of primary importance. Dynamic photonic microscopies, e.g. single/multiple particle tracking, fluorescence recovery after photobleaching and fluorescence correlation spectroscopy (FCS) enable noninvasive measurement of molecular mobility in living cells and their plasma membranes. However, FCS with a single beam waist is of limited applicability with complex, non Brownian, motions. Recently, the development of FCS diffusion laws methods has given access to the characterization of these complex motions, although none of them is applicable to the membrane binding case at the moment. In this study, we combined computer simulations and FCS experiments to propose an FCS diffusion law for membrane binding. First, we generated computer simulations of spot-variation FCS (svFCS) measurements for a membrane binding process combined to 2D and 3D diffusion at the membrane and in the bulk/cytosol, respectively. Then, using these simulations as a learning set, we derived an empirical diffusion law with three free parameters: the apparent binding constant KDapp, the diffusion coefficient on the membrane D2D and the diffusion coefficient in the bulk/cytosol, D3D. Finally, we monitored, using svFCS, the dynamics of retroviral Gag proteins and associated mutants during their binding to supported lipid bilayers of different lipid composition or at plasma membranes of living cells and we quantified KDapp and D2D in these conditions using our empirical diffusion law. Based on these experiments and numerical simulations, we conclude that this new approach enables correct estimation of membrane partitioning and membrane diffusion properties (KDapp and D2D) for peripheral membrane molecules.

biophysics↗

bioRxiv2021

piCRISPR: Physically Informed Features Improve Deep Learning Models for CRISPR/Cas9 Off-Target Cleavage Prediction

CRISPR/Cas programmable nuclease systems have become ubiquitous in the field of gene editing. With progressing development, applications in in vivo therapeutic gene editing are increasingly within reach, yet limited by possible adverse side effects from unwanted edits. Recent years have thus seen continuous development of off-target prediction algorithms trained on in vitro cleavage assay data gained from immortalised cell lines. It has been shown that in contrast to experimental epigenetic features, computed physically informed features are so far underutilised despite bearing considerably larger correlation with cleavage activity. Here, we implement state-of-the-art deep learning algorithms and feature encodings for off-target prediction with emphasis on physically informed features that capture the biological environment of the cleavage site, hence terming our approach piCRISPR. Features were gained from the large, diverse crisprSQL off-target cleavage dataset. We find that our best-performing models highlight the importance of sequence context and chromatin accessibility for cleavage prediction and compare favourably with literature standard prediction performance. We further show that our novel, environmentally sensitive features are crucial to accurate prediction on sequence-identical locus pairs, making them highly relevant for clinical guide design. The source code and trained models can be found ready to use at github.com/florianst/picrispr.

bioinformatics↗

bioRxiv2021

Full assembly of HIV-1 particles requires assistance of the membrane curvature factor IRSp53.

During HIV-1 particle formation, the requisite plasma membrane curvature is thought to be solely driven by the retroviral Gag protein. Here, we reveal that the cellular I-BAR protein IRSp53 is required for the progression of HIV-1 membrane curvature to complete particle assembly. Partial gene editing of IRSp53 induces a decrease in viral particle production and a viral bud arrest at half completion. Single molecule localization microscopy at the cell plasma membrane shows a preferential localization of IRSp53 around HIV-1 Gag assembly sites. In addition, we observe the presence of IRSp53 in purified HIV-1 particles. Finally, HIV-1 Gag protein localizes preferentially to IRSp53 I-BAR domain induced curved membranes on giant unilamellar vesicles. Overall, our data reveal a strong interplay between IRSp53 I-BAR and Gag at membranes during virus assembly. This highlights IRSp53 as a crucial host factor in HIV-1 membrane curvature and its requirement for full HIV-1 particle assembly.

biophysics↗

bioRxiv2020

Characterisation of interactions between the pluripotency transcription factors Nanog, Oct4 and Sox2

The pluripotency transcription factors (TFs) Nanog, Sox2, and Oct4 are at the centre of the gene regulatory network that controls cell identity in embryonic stem (ES) cells. However, the mechanisms by which these factors control cell fate, and their interactions with one another are not fully understood. Here we combine biophysical and novel biochemical assays to assess how these factors interact with each other quantitatively. A confocal microscopy method to detect binding of a target protein to a fluorescently labelled partner (coimmunoprecipitated bead imaging microscopy [CBIM]) is presented and used to demonstrate homotypic binding of Nanog and heterotypic binding between Nanog and Sox2 and between Nanog and Oct4. Using fluorescence correlation spectroscopy we show that in solution, Nanog but not Oct4 or Sox2 can form homomultimers. However, both Sox2 and Oct4 can form heterotypic multimers with Nanog in a manner that depends on the presence of tryptophan residues within the Nanog tryptophan repeat. Fluorescence Cross Correlation Spectroscopy shows the affinity of Nanog for dimer formation is in the order Sox2 > Nanog > Oct4. Importantly, live cell analysis demonstrates the existence of Nanog homomultimers in vivo. Together these findings extend understanding of the molecular interactions occurring between these central mediators of the pluripotency gene regulatory network at the single-molecule level.

biochemistry↗

bioRxiv2019

HIV-1 Gag specifically restricts PI(4,5)P2 and cholesterol mobility in living cells creating a nanodomain platform for virus assembly.

HIV-1 Gag protein self-assembles at the plasma membrane of infected cells for viral particle formation. Gag targets lipids, mainly the phosphatidylinositol (4, 5) bisphosphate, at the inner leaflet of this membrane. Here, we address the question whether Gag is able to trap specifically PI(4,5)P2 or other lipids during HIV-1 assembly in the host CD4+ T lymphocytes. Lipid dynamics within and away from HIV-1 assembly sites was determined using super-resolution STED microscopy coupled with scanning Fluorescence Correlation Spectroscopy in living T cells. Analysis of HIV-1 infected cells revealed that, upon assembly, HIV-1 is able to specifically trap PI(4,5)P2, and cholesterol, but not phosphatidylethanolamine or sphingomyelin. Furthermore, our data show that Gag is the main driving force to restrict PI(4,5)P2 and cholesterol mobility at the cell plasma membrane. This is first direct evidence showing that HIV-1 creates its own specific lipid environment by selectively recruiting PI(4,5)P2 and cholesterol, as a membrane nano-platform for virus assembly.

biophysics↗

bioRxiv2016

Self assembly of HIV-1 Gag protein on lipid membranes generates PI(4,5)P2/Cholesterolnanoclusters.

The self-assembly of HIV-1 Gag polyprotein at the inner leaflet of the cell host plasma membrane is the key orchestrator of virus assembly. The binding between Gag and the plasma membrane is mediated by specific interaction of the Gag matrix domain and the PI(4,5)P2 lipid (PIP2). It is unknown whether this interaction could lead to local reorganization of the plasma membrane lipids. In this study, using model membranes, we examined the ability of Gag to segregate specific lipids upon self-assembly. We show for the first time that Gag self-assembly is responsible for the formation of PIP2 lipid nanoclusters, enriched in cholesterol but not in sphingomyelin. We also show that Gag mainly partition into liquid-disordered domains of these lipid membranes. Our work strongly suggests that, instead of targeting pre-existing plasma membrane lipid domains, Gag is more prone to generate PIP2/Cholesterol lipid nanodomains at the inner leaflet of the plasma membrane during early events of virus assembly.

biophysics↗