Biology subjects

Paul, T.

Publications and source records attributed to Paul, T..

18 recordsLinked to original sources

bioRxiv2026

Zyxin and LPP differ in their sensing of strained actin filaments at tricellular junctions

The actomyosin cytoskeleton plays important roles in cell-cell adhesion by generating and responding to forces. Actin-binding proteins support actomyosin networks by reinforcing actin filaments, promoting actin remodeling, and transmitting forces to transmembrane adhesion proteins. One family of actin-binding proteins, LIM domain-containing proteins, is recruited to strained actin filaments. Here, we investigate two members of the LIM domain family, Zyxin and Lipoma-Preferred Partner (LPP), using the embryonic epithelium of Xenopus laevis, where actin-associated cell-cell junctions connect cells to promote tissue integrity and barrier function. Specifically, we compare Zyxin and LPP's response to increased tension at tricellular junctions (TCJs), sites of heightened mechanical strain within the tissue. Upon increased tension, Zyxin and LPP mechanoaccumulate to different extents relative to F-actin, suggesting distinct mechanisms. Our results demonstrate that Zyxin's and LPP's LIM domain-containing regions (LCRs) are sufficient for mechanoaccumulation as well as responsible for the difference in mechanoaccumulation, while their N-termini play a regulatory role in their mechanosensitive responses. Docking simulations show that a hydrophobic interaction between the LCR and the "crack site" that forms in F-actin filaments under high force may underlie the LCR's sensing of strained F-actin. Additionally, the docking simulations reveal that previously-identified conserved residues are present at the binding interface. Mutations of conserved residues in Zyxin or LPP reduce the extent of mechanoaccumulation at TCJs, supporting the docking prediction. Together, this study advances our understanding of Zyxin and LPP's sensing of strained actin at TCJs under mechanical challenge.

cell biology↗

bioRxiv2026

Integrated in silico identification of fungal-derived dual-target inhibitors for anti-schistosomal drug discovery

Praziquantel, which has limited efficacy against young parasites and reduces susceptibility, is the principal therapy for schistosomiasis, a neglected tropical illness. This work identified fungal-derived compounds with potential dual inhibitory action against Schistosoma mansoni DHODH and cathepsin B1 using an integrated computational method. From 1,831 fungal metabolites, 120 were selected for molecular docking after structure standardisation, drug-likeness evaluation, ADMET, and toxicity screening. Ganoderlactone B (CID_122184973) and Spiroapplanatumine F (CID_132962217) strongly bound to DHODH and CB1, with docking affinities of -10.6 and -10.0 kcal/mol and -9.0 and -8.9, respectively. Docking validation showed good discrimination between active compounds and decoys with area-under-the-curve values of 0.98 for DHODH and 0.96 for CB1. The protein-ligand interaction study showed hydrogen bonding, hydrophobic interactions, and van der Waals contacts at the binding sites. In 100 ns molecular dynamics simulations, protein complexes exhibited modest backbone deviations and maintained compactness, although CID_132962217 showed sustained binding and a constrained conformation. MM-PBSA analysis identified CID_122184973 as the best common ligand for both targets. At the B3LYP/6-31G level, density functional theory calculations showed that CID_139584993 had the lowest HOMO-LUMO energy gap and hardness values of 3.552 and 1.776 eV, respectively, and the highest softness value of 0.282 eV-1, indicating greater electronic reactivity. Electrostatic potential mapping and QSAR predictions supported their interaction and antiparasitic potential. Overall, CID_122184973 and CID_132962217 are promising fungal scaffolds for dual-target anti-schistosomal drug development. Experimental enzyme inhibition, parasite viability, toxicity, and in vivo research are needed to confirm computational findings.

bioinformatics↗

bioRxiv2026

Disrupting a Convergent Acetylation Circuit Collapses Leukemic Identity Across AML Subtypes

Transcriptional condensates anchored by chromatin readers are increasingly recognized as organizing hubs for gene expression, but how their assembly and stability are regulated remains poorly understood. Here, we identify an acetylation-dependent feed-forward circuit that controls the integrity of the Super Elongation Complex (SEC), a key driver of transcriptional elongation. We show that the SAGA histone acetyltransferase catalytic subunits KAT2A/KAT2B license acetylation of both histone H3 lysine 9 (H3K9ac) and SEC components themselves, including ENL, AFF1, and AFF3. Loss of this dual acetylation activity, achieved via a cereblon-recruiting PROTAC (GSK983/GSK699), displaces the chromatin reader ENL from target loci, dissolves ENL-anchored transcriptional condensates, and disrupts SEC-dependent transcriptional output - linking histone and non-histone acetylation to the physical integrity of a core transcriptional machine. Using genome-scale dependency data, we show that the SAGA complex is a selective chromatin dependency in acute myeloid leukemia (AML) AML and hematological malignancies and disrupting this feed-forward transcriptional circuit in AML demonstrates subtype independent antileukemia effects. KAT2A/B degradation drives potent, broad-spectrum antileukemic activity across genetically diverse AML cell lines, primary patient samples, and an isogenic KMT2A-rearranged model bearing cooperating oncogenic mutations, with H3K9ac loss concentrated asymmetrically at core AML oncogene loci such as MYC, MYB, and the HOXA cluster. Together, these findings define an acetylation-dependent circuit governing SEC integrity and establish KAT2A/B degradation as a mechanism-based, pan-AML therapeutic strategy, with implications for transcriptional condensate regulation beyond leukemia. HIGHLIGHTSO_LIThe SAGA complex is a selectively essential chromatin dependency across hematological malignancies and particularly in AML C_LIO_LIKAT2A/B degradation drives broad anti-leukemic activity across genetically diverse AML subtypes including chemo-refractory disease C_LIO_LIKAT2A/B degradation depletes H3K9ac at AML oncogene loci and dismantles ENL-anchored condensates C_LIO_LIKAT2A/B licenses regulation of super elongation complex acetylation and ENL interaction with SEC complex components C_LI

cancer biology↗

bioRxiv2025

Linking Genomic Landscape to Disease Mechanism: Core Genetic Factors Underlying Pathogenesis and Antimicrobial Resistance in Diarrheal Pathogens

BackgroundDiarrheal diseases remain a major global health burden, as they severely affect children, particularly in Bangladesh. After decades of research, the molecular mechanisms of diarrheal pathogens for disease pathogenesis and antibiotic resistance are still unknown, notably in Gram-negative bacteria. This pilot study fills the gap by employing whole genome sequencing and pan-genome analysis to analyze Bangladeshi diarrheal pathogens to identify genetic variables that cause disease pathogenesis and antibiotic resistance. ResultsHence, we investigated the genetic diversity of bacterial isolates from 31 clinical stool samples by a combination of whole-genome sequencing (WGS) and pan-genomic analysis. A core group of 50 genes, conserved across a significant number of strains, was identified via pan-genomic analysis, with considerable variation in accessory genes. This signifies a significant degree of genetic flexibility. Gene ontology analysis yielded substantial insights into prospective therapeutic targets by emphasizing the critical function of these core genes in bacterial survival and pathogenicity. Furthermore, the findings of the antimicrobial susceptibility test (AST) revealed concerning resistance trends, particularly to fluoroquinolones and beta-lactams, underscoring the necessity for enhanced surveillance and alternative therapeutic approaches. ConclusionThis study provides a comprehensive genetic framework to improve understanding of the complexity of diarrheal infections and the mechanisms underlying their resistance, fostering opportunities for potential therapeutic advancements.

microbiology↗

bioRxiv2025

Spinning disk confocal microscopy with a 25 Megapixel Camera

Spinning disk confocal microscopy enables fast optical sectioning with low phototoxicity but is often inaccessible due to high hardware costs. We present a low-cost solution using a 25 megapixel machine vision CMOS camera (Sony IMX540, FLIR Blackfly S) and a custom-built spinning disk. The system uses a back-illuminated sensor with high quantum efficiency (69% at 525 nm) and low read noise (2.31 electrons). High-resolution images of Thy1-GFP mouse brain slices and H&E-stained rat testis verified performance across 3D tissue volumes. The custom disk, made with 18 {micro}m pinholes (180 {micro}m pitch) on a chrome photomask and mounted to an optical chopper motor, enables stable, near-telecentric imaging. Micro-Manager software integration allows synchronized control of all hardware, which demonstrates that affordable CMOS sensors can potentially replace sCMOS in spinning disk microscopy, offering an open-source, scalable solution for advanced imaging.

bioengineering↗

bioRxiv2025

Myo1e/f at the podosome base regulate podosome dynamics and promote macrophage migration

Cells of the monocyte lineage form specialized membrane-associated, actin-rich structures, called podosomes. Podosomes play important roles in cell adhesion and migration as well as the proteolytic degradation of the extracellular matrix. While podosomes are always closely associated with the plasma membrane, the structural components linking the podosome core, composed of branched actin, to the membrane are not fully understood. In this study we show that class I myosins, Myo1e and Myo1f, localize to a specific region of podosomes, underneath the podosome core and near the ventral plasma membrane, and that this localization is mainly mediated by the Myo1e/f TH2 domains. Respective knockdowns or knockouts of Myo1e/f lead to increased podosome size, altered turnover and lateral mobility, which is likely due to Myo1e/f regulating the attachment of core actin filaments to the plasma membrane. In addition, Myo1e/f double knockout macrophages were characterized by a reduction in 3D and 2D migration, even though these cells exhibited increased ability to degrade the extracellular matrix. Along with the other membrane-associated podosome components, such as the transmembrane proteins MT-MMP and CD44, and the GPI-anchored DNase X, Myo1e and Myo1f mark the membrane-proximal region of podosomes. We propose to label this region as the podosome "base", an additional substructure joining the current trifecta of the podosome cap, core, and ring.

cell biology↗

bioRxiv2025

Mechanistic insights into direct DNA and RNA strand transfer and dynamic protein exchange of SSB and RPA

Single-stranded DNA-binding proteins (SSBs) are essential for genome stability, facilitating replication, repair, and recombination by binding ssDNA, recruiting other proteins, and dynamically relocating in response to cellular demands. Using single-molecule fluorescence resonance energy transfer (smFRET) assays, we elucidated the mechanisms underlying direct strand transfer from one locale to another, protein exchange, and RNA interactions at high resolution. Both bacterial SSB and eukaryotic replication protein A (RPA) exhibited direct strand transfer to competing ssDNA, with rates strongly influenced by ssDNA length. Strand transfer proceeded through multiple failed attempts before a successful transfer, forming a ternary intermediate complex with transient interactions, supporting a direct transfer mechanism. Both proteins efficiently exchanged DNA-bound counterparts with freely diffusing molecules, while hetero-protein exchange revealed that SSB and RPA could replace each other on ssDNA in a length-dependent manner, indicating that protein exchange does not require specific protein-protein interactions. Additionally, both proteins bound RNA and underwent strand transfer to competing RNA, with RPA demonstrating faster RNA transfer kinetics. Competitive binding assays confirmed a strong preference for DNA over RNA. These findings provide critical insights into the dynamic behavior of SSB and RPA in nucleic acid interactions, advancing our understanding of their essential roles in genome stability, regulating RNA metabolism, and orchestrating nucleic acid processes.

molecular biology↗

bioRxiv2025

No Disconnection Syndrome after Near-Complete Callosotomy

Sensorimotor processing in the human brain is largely lateralized, with the corpus callosum integrating these processes into a unified experience. Following complete callosotomy, this integration breaks down, resulting in disconnection syndromes. We asked how much of the corpus callosum is sufficient to support functional unity--the absence of disconnection syndrome--by comparing three complete callosotomy patients with one retaining only the splenium. Using lateralized tasks across visual, tactile, visuospatial, and language domains, we predicted domain-specific deficits in the splenium-only patient based on established anatomical models of callosal topography. Strikingly, while complete callosotomy patients exhibited disconnection syndromes, the splenium patient demonstrated functional unity across all domains--as if his entire corpus callosum were intact. Our findings highlight the brains remarkable capacity to maintain behavioral integration through minimal preserved pathways, highlighting how the structure-dependent reorganizational capacity of the human brain allows to preserve functional unity.

neuroscience↗

bioRxiv2025

Full inter-hemispheric integration sustained by a fraction of posterior callosal fibers

The dynamic integration of the lateralized and specialized capacities of the cerebral hemispheres constitutes a hallmark feature of human brain function. This inter-hemispheric exchange of information critically depends upon the corpus callosum. Classical descriptions of callosal organization outline a topographic gradient, such that specific fibers integrate distinct aspects of brain function. Here we present a challenge to this conventional model. Using neuroimaging data obtained from a new cohort of adult corpus callosotomy patients, we leverage modern network neuroscience techniques to show--for the first time--that full inter-hemispheric integration can be achieved via a small proportion ([~]1 cm) of intact posterior callosal fibers. Only complete callosotomy patients demonstrated the expected dissolution of typical inter-hemispheric network architectures, aligning with disconnection syndromes long-thought to reflect diminished information propagation and communication across the brain. These findings motivate a novel mechanistic understanding of synchronized inter-hemispheric neural activity for large-scale human brain function and behavior.

neuroscience↗

bioRxiv2024

Controlled by disorder: phosphorylation modulates SRSF1 domain availability for spliceosome maturation

Serine/arginine-rich splicing factor 1 (SRSF1) is key in the mRNA lifecycle including transcription, splicing, nonsense-mediated decay, and nuclear export. Consequently, its dysfunction is linked to cancers, viral evasion, and developmental disorders. The functionality of SRSF1 relies on its interactions with other proteins and RNA molecules. These processes are regulated by phosphorylation of its unstructured arginine/serine-rich tail (RS). Here, we characterize how phosphorylation affects SRSF1s protein and RNA interaction and phase separation. Using NMR paramagnetic relaxation enhancement and chemical shift perturbation, we find that when unphosphorylated, SRSF1s RS interacts with its first RNA-recognition motif (RRM1). Phosphorylation of RS decreases its interactions with RRM1 and increases its interactions with the RNA-binding site. This change in SRSF1s intramolecular interactions increases the availability of protein-interacting sites on RRM1 and weakens RNA binding of SRSF1. Phosphorylation alters the phase separation of SRSF1 by diminishing the role of arginine in intermolecular interactions. These findings provide an unprecedented view of how SRSF1 influences the early-stage spliceosome assembly. SUMMARYPhosphorylation of SRSF1 is pivotal in pre-mRNA processing and is dysregulated in various pathologies. Modeling of SRSF1 based on NMR restraints reveals phosphorylation alters the accessibility of protein-protein and protein-RNA interaction sites on SRSF1s RRM1 domain, altering its binding preferences

biochemistry↗

bioRxiv2024

GDNF family receptor alpha-like (GFRAL) expression is restricted to the caudal brainstem

The TGF-{beta} cytokine, growth differentiation factor 15 (GDF15) is a critical mediator of the physiologic response to a range of cellular stresses. While circulating levels of GDF15 are normally very low, these levels increase substantially under a number of acute and chronic pathogenic states including mycotoxin exposure, infection and cancer. GDF15 controls a range of physiologic outputs including reduced appetite, gastric motility, hyperalgesia, emesis, energy expenditure and immune cell function via the GDNF family receptor alpha-like (GFRAL). While the area postrema and nucleus of the solitary tract (AP/NTS) within the caudal brainstem are the only known sites of Gfral-expressing cells, Gfral may also be expressed in other cell types. We therefore utilized single molecule in-situ hybridizations and genetic mouse models to label Gfral-expressing cells from development to adult mouse. With both approaches, we found Gfral-labelled cells in the brainstem and extremely rare Gfral-labelled cells in peripheral tissues in the mouse under normal physiological conditions. Confirming these findings, single nucleus RNA-sequencing of human tissues demonstrated nearly undetectable levels of Gfral mRNA in sites outside the AP/NTS. Our findings confirm AP/NTS neurons are the major site of Gfral expression.

molecular biology↗

bioRxiv2024

H2O2 mediated MAPK-mTOR crosstalk determines the XIAP and FLIP degradation pathways and development of resistance to Imatinib

Abnormal or aggregated proteins degradation is very crucial to protect the cell against proteotoxic stress. Cellular proteins are usually degraded in a ubiquitin-dependent manner by proteasomes and macro-autophagy/autophagy. Both processes use ubiquitin, binding of which target them to proteasomes via ubiquitin-like domains or to phagophores (the precursors to autophagosomes) via Atg8/LC3 binding motifs. Since both pathways use ubiquitin, the question that arises is how degradative pathway choice is achieved. Here in this paper, we have shown that mTOR pathway acts as major player in deciding which degradation pathway to choose. Here, we used Imatinib resistant (K562R) and Imatinib-sensitive (K562S) K562 cell as our previous study showed that Ubiquitin-proteasome pathway is selected for degradation of two proteins XIAP and FLIP in Imatinib-resistant K562 cells. H2O2 treatment in K562R cells degrades XIAP and FLIP via proteasomal pathway whereas H2O2 degrades them via lysosomal pathway in K562S cells. We found H2O2 mediated mTOR activation suppressed autophagy pathway in K562R cells and protein takes proteasomal degradation rout. However, proteins get degraded via autophagy when mTOR remains suppressed in K562S cells. We also found that H2O2-mediated activation of activation of ERK in turn activated mTOR in K562R cells because ROS inhibited ERK phosphorylation and thus mTOR remained inhibited in K562S cells. Moreover, we found that endogenous H2O2 levels are way higher in K562R cells than in K562S cells. Finally, and most interestingly, our data clearly suggested that activation of mTOR is responsible for developing resistance to Imatinib in K562R cells. Thus, this paper delineates a very crucial role of H2O2 and mTOR in both the selection of protein degradation pathway and development of drug resistant.

cancer biology↗

bioRxiv2023

A stochastic population model for the impact of cancer cell dormancy on therapy success

AO_SCPLOWBSTRACTC_SCPLOWTherapy evasion - and subsequent disease progression - is a major challenge in current oncology. An important role in this context seems to be played by various forms of cancer cell dormancy. For example, therapy-induced dormancy, over short timescales, can create serious obstacles to aggressive treatment approaches such as chemotherapy, and long-term dormancy may lead to relapses and metastases even many years after an initially successful treatment. The underlying dormancy-related mechanisms are complex and highly diverse, so that the analysis even of basic patterns of the population-level consequences of dormancy requires abstraction and idealization, as well as the identification of the relevant specific scenarios. In this paper, we focus on a situation in which individual cancer cells may switch into and out of a dormant state both spontaneously as well as in response to treatment, and over relatively short time-spans. We introduce a mathematical toy model, based on stochastic agent-based interactions, for the dynamics of cancer cell populations involving individual short-term dormancy, and allow for a range of (multi-drug) therapy protocols. Our analysis shows that in our idealized model, even a small initial population of dormant cells can lead to therapy failure under classical (and in the absence of dormancy successful) single-drug treatments. We further investigate the effectiveness of several multidrug regimes (manipulating dormant cancer cells in specific ways) and provide some basic rules for the design of (multi-)drug treatment protocols depending on the types and parameters of dormancy mechanisms present in the population.

cancer biology↗

bioRxiv2023

Unearthing SRSF1's Novel Function in Binding and Unfolding of RNA G-Quadruplexes

SRSF1 governs splicing of over 1,500 mRNA transcripts. SRSF1 contains two RNA-recognition motifs (RRMs) and a C-terminal Arg/Ser-rich region (RS). It has been thought that SRSF1 RRMs exclusively recognize single-stranded exonic splicing enhancers, while RS lacks RNA-binding specificity. With our success in solving the insolubility problem of SRSF1, we can explore the unknown RNA-binding landscape of SRSF1. We find that SRSF1 RS prefers purine over pyrimidine. Moreover, SRSF1 binds to the G-quadruplex (GQ) from the ARPC2 mRNA, with both RRMs and RS being crucial. Our binding assays show that the traditional RNA-binding sites on the RRM tandem and the Arg in RS are responsible for GQ binding. Interestingly, our FRET and circular dichroism data reveal that SRSF1 unfolds the ARPC2 GQ, with RS leading unfolding and RRMs aiding. Our saturation transfer difference NMR results discover that Arg residues in SRSF1 RS interact with the guanine base but other nucleobases, underscoring the uniqueness of the Arg/guanine interaction. Our luciferase assays confirm that SRSF1 can alleviate the inhibitory effect of GQ on gene expression in the cell. Given the prevalence of RNA GQ and SR proteins, our findings unveil unexplored SR protein functions with broad implications in RNA splicing and translation.

biophysics↗

bioRxiv2023

Defining RNA oligonucleotides that reverse deleterious phase transitions of RNA-binding proteins with prion-like domains

RNA-binding proteins with prion-like domains, such as FUS and TDP-43, condense into functional liquids, which can transform into pathological fibrils that underpin fatal neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS)/frontotemporal dementia (FTD). Here, we define short RNAs (24-48 nucleotides) that prevent FUS fibrillization by promoting liquid phases, and distinct short RNAs that prevent and, remarkably, reverse FUS condensation and fibrillization. These activities require interactions with multiple RNA-binding domains of FUS and are encoded by RNA sequence, length, and structure. Importantly, we define a short RNA that dissolves aberrant cytoplasmic FUS condensates, restores nuclear FUS, and mitigates FUS proteotoxicity in optogenetic models and human motor neurons. Another short RNA dissolves aberrant cytoplasmic TDP-43 condensates, restores nuclear TDP-43, and mitigates TDP-43 proteotoxicity. Since short RNAs can be effectively delivered to the human brain, these oligonucleotides could have therapeutic utility for ALS/FTD and related disorders.

biochemistry↗

bioRxiv2023

Switch-like Compaction of Poly(ADP-ribose) Upon Cation Binding

Poly(ADP-ribose) (PAR) is a homopolymer of adenosine diphosphate ribose that is added to proteins as a post-translational modification to regulate numerous cellular processes. PAR also serves as a scaffold for protein binding in macromolecular complexes, including biomolecular condensates. It remains unclear how PAR achieves specific molecular recognition. Here, we use single-molecule fluorescence resonance energy transfer (smFRET) to evaluate PAR flexibility under different cation conditions. We demonstrate that, compared to RNA and DNA, PAR has a longer persistence length and undergoes a sharper transition from extended to compact states in physiologically relevant concentrations of various cations (Na+, Mg2+, Ca2+, and spermine). We show that the degree of PAR compaction depends on the concentration and valency of cations. Furthermore, the intrinsically disordered protein FUS also served as a macromolecular cation to compact PAR. Taken together, our study reveals the inherent stiffness of PAR molecules, which undergo switch-like compaction in response to cation binding. This study indicates that a cationic environment may drive recognition specificity of PAR. SignificancePoly(ADP-ribose) (PAR) is an RNA-like homopolymer that regulates DNA repair, RNA metabolism, and biomolecular condensate formation. Dysregulation of PAR results in cancer and neurodegeneration. Although discovered in 1963, fundamental properties of this therapeutically important polymer remain largely unknown. Biophysical and structural analyses of PAR have been exceptionally challenging due to the dynamic and repetitive nature. Here, we present the first single-molecule biophysical characterization of PAR. We show that PAR is stiffer than DNA and RNA per unit length. Unlike DNA and RNA which undergoes gradual compaction, PAR exhibits an abrupt switch-like bending as a function of salt concentration and by protein binding. Our findings points to unique physical properties of PAR that may drive recognition specificity for its function.

biophysics↗

bioRxiv2022

Single-molecule fluorescence microscopy demonstrates fast dynamics of the variant surface glycoprotein coat on living trypanosomes

The fluidity of Trypanosoma bruceis dense coat of GPI-anchored variant surface glycoproteins (VSGs) is fundamental for the survival of the parasite. In order to maintain the integrity of the coat, it is recycled on the time scale of a few minutes. This is surprisingly fast as endo- and exocytosis take place in the same small membrane invagination called the flagellar pocket. Here, we present measurements of VSG dynamics on the single-molecule level in living trypanosomes. A large number of short protein trajectories sampling the parasites surface were analysed in two distinct scenarios: diffusion and directed motion. To this end, we employed a previously published algorithm and implemented two extensions to consider rim effects as well as localisations errors inherent to single-mole tracking. Neglect of the latter can have a significant distortive effect on the measured diffusion coefficient; in our case resulting in an underestimation by 20 %. We found large heterogeneity in the local diffusion coefficients and velocities with a surprisingly high average value of [Formula] and [Formula], respectively. To decide on the locally dominant motion mode, we present a guideline based on random walk simulations. We find that VSG dynamics is indeed dominated by diffusion. Complementary simulations on long time scales not accessible in the experiment showed that passive VSG randomisation is fast enough to prevent re-endocytosis newly exocytosed VSGs and to accomplish turnover of the full VSG coat within a few minutes. Author summarySingle-molecule tracking in biological systems often suffers from trajectories being too short to obtain statistically robust decisions on the present motion mode. We faced this issue when investigating the dynamics of the protein surface coat of African trypanosomes. To address the question whether diffusion or directed motion governs coat dynamics, we have adopted an algorithm based on temporal decomposition and spatial binning of an ensemble of single-molecule trajectories. We introduced several extensions to the original approach, including the consideration of localisation errors inherent to single-molecule tracking. This improvement alone already prevented the diffusion coefficient from being underestimated by 20 %. We analysed the coat dynamics in two scenarios, diffusion and directed motion, and offer a decision guideline to identify the locally dominating motion mode. Our extended algorithm is available to the scientific community via GitHub. For the trypanosome surface coat we found that the motion is indeed mainly characterised by diffusion with a surprisingly high diffusion coefficient. This finding solves a long-standing question how the parasite maintains its protein coat.

biophysics↗

bioRxiv2020

White matter brain aging In Relationship to Schizophrenia and Its Cognitive Deficit

We hypothesized that cerebral white matter deficits in schizophrenia (SZ) are driven in part by accelerated white matter aging and are associated with cognitive deficits. We used machine learning model to predict individual age from diffusion tensor imaging features and calculated the delta age ({Delta}age) as the difference between predicted and chronological age. Through this approach, we translated multivariate white matter imaging features into an age-scaled metric and used it to test the temporal trends of accelerated aging-related white matter deficit in SZ and its association with the cognition. Followed feature selection, a machine learning model was trained with fractional anisotropy values in 34 of 43 tracts on a training set consisted of 107 healthy controls (HC). The brain age of 166 SZs and 107 HCs in the testing set were calculated using this model. Then, we examined the SZ-HC group effect on {Delta}age and whether this effect was moderated by chronological age using the regression spline model. The results showed that {Delta}age was significantly elevated in the age >30 group in patients (p < 0.001) but not in age [<=] 30 group (p = 0.364). {Delta}age in patients was significantly and negatively associated with both working memory ({beta} = -0.176, p = 0.007) and processing speed ({beta} = -0.519, p = 0.035) while adjusting sex and chronological age. Overall, these findings indicate that the {Delta}age is elevated in SZs and become significantly from middle life stage; the increase of {Delta}age in SZs is associated with the decline neurocognitive performance.

neuroscience↗