Biology subjects

Murakami, K.

Publications and source records attributed to Murakami, K..

At least 19 recordsLinked to original sources

bioRxiv2026

A monoallelic immunopeptidome atlas of 10 prevalent canine DLA-88 alleles

Characterization of naturally processed MHC class I (MHC-I)-bound peptides is essential for defining allele-specific peptide-binding features and understanding the functional consequences of MHC-I polymorphism. However, immunopeptidome analyses of dog leukocyte antigen (DLA) class I (DLA-I) molecules remain limited and comprehensive monoallelic ligand datasets for prevalent DLA-88 alleles are still lacking. Here, we established canine melanoma-derived cell populations expressing individual functional DLA-88 alleles and generated a monoallelic immunopeptidome atlas of prevalent DLA-88 alleles. Using liquid chromatography-tandem mass spectrometry, we identified 32,702 naturally processed peptides of 7 to15 amino acids across 10 DLA-88 alleles, substantially expanding the available DLA-88 immunopeptidome landscape. These 10 alleles exhibited canonical peptide length distributions and allele-specific binding motifs that reflected variation in binding-groove pseudo-sequences defined from human MHC-I peptide-contact residues. Ligand sharing between DLA-88 alleles was associated with binding site distance. Incorporation of the comprehensively characterized DLA-88 ligand datasets in this study increased by more than fourfold the number of published canine DLA-I alleles with ligand-characterized reference alleles predicted to have similar peptide-binding features. We also found that antigen-processing signatures were highly conserved with those reported in humans. As a proof-of-concept application, we selected 54 DLA-88-bound peptides identified in our immunopeptidome analysis as candidate peptides for canine cancer immunotherapy by evaluating the normal tissue expression profiles of their source proteins. This DLA-88 immunopeptidome atlas provides insights into allele-dependent differences in antigen presentation and represents a valuable resource for developing accurate DLA-88-binding peptide prediction tools and supporting peptide-based immunological studies in dogs.

immunology↗

bioRxiv2026

Conformational plasticity of the human norovirus GII.3 capsid reveals alternative P domain interaction networks

Human noroviruses (HuNoVs) are a leading cause of acute gastroenteritis worldwide, yet no effective antiviral therapeutics are currently available. Although environmentally induced capsid conformational changes associated with infectivity have been reported in murine noroviruses (MNVs), comparable conformational switching has not been demonstrated in HuNoVs. In this study, we generated HuNoV GII.3 virus-like particles (VLPs) using a baculovirus expression system and identified two distinct T = 3 particle populations coexisting within VLP preparations derived from a single strain through cryo-electron microscopy single-particle analysis. Comparative structural analysis revealed that these two T = 3 capsid conformations correspond to the resting and rising states of the protruding (P) domain. Rearrangement of the P domain alters intermolecular interactions between adjacent capsid subunits, resulting in distinct capsid surface architectures. In the resting state, intermolecular contacts were mediated predominantly by the P2 subdomain, with limited contribution from the P1 subdomain. In contrast, the rising state exhibited a shift toward an alternative interaction interface primarily involving the P1 subdomain. These findings demonstrate previously unrecognized structural polymorphism in the HuNoV capsid and provide evidence that conformational switching may occur in HuNoVs. Our results offer new insights into norovirus capsid dynamics and may inform future structure-based vaccine and antiviral drug development.

microbiology↗

bioRxiv2026

Somatosensory information drives modification of a motor memory

The role of somatosensory information in motor memory modification remains controversial. One view holds that somatosensory information plays only a supportive role, such as feedback or sensory calibration, and is not directly involved in memory modification itself. An alternative view is that afferent somatosensory information, on its own, can modify motor memory. Here we resolve this controversy by isolating somatosensory information from voluntary motor execution using a hand-exoskeleton robot. Participants first learned a sequential finger movement task through voluntary practice. Their learned finger movements were recorded using a data glove. On subsequent days, they underwent a brief, 30-sec reinstatement session: either exoskeleton-based reinstatement, which reproduced their learned movements without voluntary execution, or voluntary reinstatement, in which they executed the trained task. Exoskeleton-based reinstatement led to subsequent performance gains comparable to those induced by voluntary reinstatement. This gain was not explained by replay of visual information, mental rehearsal, enhanced arousal, or warm-up effects induced by exoskeleton-driven movements. Rather, the results indicate that brief reinstatement of somatosensory information alone is sufficient to drive performance gain. We further found that exoskeleton-based exposure to a sequence that only partially matched the trained sequence yielded performance gains, whereas voluntary execution of the same partially matched sequence did not. This dissociation suggests that somatosensory information broadly activates a relevant motor skill memory, whereas voluntary execution activates memory in a sequence-specific manner. Together, these findings resolve a long-standing controversy in motor learning research by showing that afferent somatosensory information alone enables sequential motor memory modification through a route distinct from voluntary execution.

neuroscience↗

bioRxiv2026

Central versus peripheral neural control of a coordinated walking pattern in Drosophila.

Walking involves coordinate rhythmic movements at every joint of every leg. Central pattern generator (CPG) circuits in the spinal or ventral nerve cord provide such a rhythmic drive to all the legs1-3. In turn, each leg provides rhythmic sensory feedback through peripheral proprioceptive neurons2,4-6. Disentangling contributions from these two rhythmic drives, has been a long-standing hurdle in uncovering both the structure and function of neural-circuits governing the generation of a coordinated walking output2,3,7. Here, using the highly tractable Drosophila model and a novel sensory-deprivation paradigm, we uncovered central and peripheral neural pathways underlying walking pattern generation. We provide evidence that each leg is governed by its own CPG module with an inherent cycle period that is unmasked when proprioceptive feedback is reduced. We find that contact driven load inputs and descending brain inputs are critical for coordinating the intra-leg movements and shaping the microstructure of a single legs step-cycle. We show that central coupling pathways underlie inter-leg coordination and that proprioceptive inputs and descending brain commands can flexibly modulate this coupling in a task-specific manner. We identify co-stimulation of specific descending neurons as a mechanism for speeding-up this walking rhythm. Finally, by constraining connectome search8 based on the empirical results, we identify putative neural-circuit motifs underlying generation of a coordinated six-legged walking pattern.

neuroscience↗

bioRxiv2026

Genetic variation in early-season leaf photosynthesis in sugar beet and its relationship with Cercospora leaf spot resistance

Improving photosynthesis is a promising approach to enhance sugar beet productivity. However, genetic variation in leaf photosynthesis and its relationship with disease resistance remain underexplored. We evaluated 98 sugar beet genotypes representing different breeding categories, including commercial F1 hybrids, seed-parent lines, and pollinator lines, in Hokkaido, northern Japan. Leaf gas exchange was measured during early growth under field conditions around the infection period of Cercospora leaf spot (CLS). To account for fluctuating irradiance during large-scale phenotyping, we applied a multilevel mixed-effects light-response model to estimate genotype-specific photosynthetic characteristics. Substantial genotypic variations in photosynthetic characteristics were detected. F1 hybrids exhibited higher photosynthetic capacity than breeding lines, whereas differences among breeding categories were unclear due to large within-category variation. Some breeding lines exhibited photosynthetic rates higher than those of hybrids, indicating exploitable genetic resources within the present genetic panel. We did not detect statistically significant trade-off between leaf photosynthesis and CLS resistance among 98 genotypes; in a subset of 19 genotypes analysed in detail, the relationship was even synergistic. Our results highlight the genetic diversity of leaf photosynthesis and its category-dependent structure, and suggest that selection for enhanced photosynthesis can proceed without substantial trade-off with CLS resistance. HighlightLeaf photosynthesis of 98 sugar beet genotypes showed significant genetic variation and dependence on breeding category. Active photosynthesis incurred minimal trade-off with Cercospora leaf spot resistance.

plant biology↗

bioRxiv2025

Canonical transcription termination mechanisms explain a minority of operons in cyanobacteria

Cyanobacteria are the most abundant phototrophs and hold potential as a carbon-negative platform for bioengineering applications. However, these efforts have been hampered by limited mechanistic understanding of their gene expression, including transcription termination. Unlike most bacteria, cyanobacteria lack the transcription termination factor Rho, raising the speculation that all transcription ends with intrinsic terminators. Here we show that most transcription units (TUs) in Synechococcus elongatus PCC 7942 are not terminated by known termination pathways. Although many TUs (52%) have unique, well-defined 3' ends, only a small fraction have features that resemble canonical intrinsic terminators (22%). The noncanonical 3' ends broadly lacked strong secondary structure, making it unclear how these ends are protected against 3'-5' exonucleolytic decay. Furthermore, many TUs (46%) have diverse positions of mRNA 3' ends, suggesting a potentially diffuse termination signal. Finally, we observed a moderate increase in RNA levels downstream of most defined 3' ends in the absence of the transcription-repair coupling factor Mfd. This finding indicates that Mfd plays a limited, but widespread, role in RNA end formation, potentially through termination of stalled RNAPs. Together, our work reveals unique end architectures of the cyanobacterial transcriptome and suggests that undescribed transcription termination mechanisms are active in the phylum. ImportanceOur understanding of bacterial transcription regulation is largely based on model organisms like Escherichia coli and Bacillus subtilis, yet many of these mechanisms appear absent or divergent in cyanobacteria. These differences limit our fundamental understanding of gene regulation and the applied potential of cyanobacteria in sustainable biomanufacturing. To address this gap, we characterized transcription termination in the model cyanobacterium Synechococcus elongatus PCC 7942. We resolve a longstanding question by showing that intrinsic termination alone cannot account for most termination events in this organism. Pervasive transcript ends lacking intrinsic terminator features and the absence of Rho suggest the existence of novel termination mechanism(s) and highlight a largely unexplored regulatory landscape. Simultaneously, our work expands the repertoire of functionally characterized cyanobacterial intrinsic terminators, offering a new toolkit to fine-tune gene expression using terminators of defined strengths. These findings pave the way for more predictable and powerful applications of cyanobacteria in green biotechnology.

microbiology↗

bioRxiv2025

Development of an RNA Aptamer as a Therapeutic Agent for Synucleinopathies

The aggregation of -synuclein (Syn), a 140-mer protein, has been implicated in the pathogenesis of Parkinsons disease, multiple system atrophy, and dementia with Lewy bodies. KTKEGV repeats (KR) of Syn are key mediators of prion-like propagation and neurodegeneration. Despite the availability of symptomatic treatments, no current therapy effectively delays disease progression. Here we report a 77-nucleotide (nt) RNA aptamer (1R6) with potent affinity and selectivity for Syn1-95 (KD = 18 nM) through in vitro selection. 1R6 significantly inhibited Syn oligomerization and {beta}-sheet-rich fibril assembly and promoted disaggregation of preformed fibrils. Additionally, 1R6 suppressed Syn seeding, as determined by FRET-based cellular biosensor cell assay. Cellular studies revealed that 1R6 cotransfection completely prevented Syn-induced cytotoxicity. To assess the protective effects of 1R6 in vivo, we used a Drosophila melanogaster model expressing human Syn in neurons. Flies fed with 1R6 showed improved locomotor defects, reduced photoreceptor degeneration, and decreased Syn levels in the head. Structural characterization through 1H-15N heteronuclear multiple quantum correlation nuclear magnetic resonance experiments demonstrated that 1R6 targets KR motifs, a finding further supported by in silico simulations. Our findings indicate that RNA aptamers, such as 1R6, may represent promising therapeutic candidates for synucleinopathies, thus opening new avenues in the treatment of these diseases.

neuroscience↗

bioRxiv2025

Proteomic and in silico dissection of MetaAggregates in amyotrophic lateral sclerosis brains

RNA-binding proteins (RBPs), key translation regulators, are thought to be involved in the pathogenesis of amyotrophic lateral sclerosis (ALS). The pathological entities associated with ALS are known as "MetaAggregates": heterogeneous coaggregates composed of amyloids, RBPs, and RNA G-quadruplexes (rG4s). In this study, to explore the molecular constituents of ALS-associated MetaAggregates, we developed a proteomic approach using a psoralen-conjugated RBP and crosslinked it with a biotinylated rG4 to enable the isolation of MetaAggregates from ALS brain extracts. Single-cell RNA-seq using in vitro ALS models identified ELAVL4 as a cytoplasmic RBP and revealed the enrichment of an IGFBP2-derived rG4 structure in ALS-specific neurons. Mass spectrometry and amyloidogenicity-based principal component analysis revealed 79 candidate proteins with roles in RNA processing, metabolism, trafficking, and stress responses. Docking simulations highlighted a subset of proteins with potential pro-aggregation characteristics, diverse cytosolic associations and functional links to RNA processing relevant to ALS. Through proteomic and in silico dissection of ALS-associated MetaAggregates, the findings of this study establish a conceptual framework for the exploration of unrecognized amyloidogenic drivers of neurodegeneration.

neuroscience↗

bioRxiv2025

Avoidance engages dopaminergic punishment in Drosophila

It was classically suggested that behaviour can cause emotions (Darwin 1872). For example, smiling can make us feel happier, and in rodents the induced patterns of cardiac activity and breathing that are indicative of fear can in turn evoke it (Coles et al. 2022, Hsueh et al. 2023, Jhang et al. 2024). However, the adaptive significance of such feedback is unclear. We show that inducing backward movement, an element of avoidance behaviour in Drosophila, engages negative valence signals in these animals, and reveal the neuronal mechanisms and adaptive significance of this effect. We develop a paradigm with odours as conditioned stimuli paired with optogenetically induced backward movement instead of a punishing unconditioned stimulus, and combined these experiments with pharmacology, high-resolution video tracking, functional imaging, connectome analyses, and modelling. Our results show that backward movement engages dopaminergic punishment neurons and supports aversive memories. Such avoidance-to-punishment feedback counterbalances extinction learning and maintains learned avoidance, reducing the risk of further punishment. This can explain the long-standing "avoidance paradox", the observation that avoidance adaptively persists even when it is successful and no punishment is received (Bolles 1972). Our results provide a neurobiologically grounded argument for an integrated view of behaviour organization and valence processing.

neuroscience↗

bioRxiv2025

Structural Insights into Allosteric Regulation of GdpP: A Conformationally Dynamic Phosphodiesterase

The phosphodiesterase GdpP is a central regulator of the bacterial second messenger c-di-AMP and a key driver of antibiotic resistance in pathogenic Firmicutes. GdpP integrates environmental signals through its sensory PAS domain to control its C-terminal catalytic domain activity, but the molecular basis for this allosteric communication has remained unknown due to the lack of structural data for the complete cytosolic region. Here, we present the first Cryo-EM structures of the cytosolic region of Streptococcus mutans GdpP (SmGdpP74) in multiple conformational states, revealing a sophisticated tetrameric architecture that enables asymmetric catalytic regulation. Our structural and functional analyses demonstrate that SmGdpP74 operates through substrate-induced conformational transition, with the DHHA1 domain interface serving as the primary determinant of asymmetric catalysis. The non-canonical GGDEF domain functions as a tetrameric scaffolding hub that positions the DHH-DHHA1 catalytic domains, representing the first detailed example of a GGDEF domain repurposed to stabilize heterologous catalytic domains. We identify a flexible GGDEF-DHH linker as a critical coupling element that transmits conformational signals between domains, with the conserved KRSR motif acting as a molecular switch for heme-mediated inhibition. Additionally, the flexibility of this linker is essential for the enzymes catalytic activity. Based on these findings, we propose a comprehensive mechanistic model where SmGdpP74 integrates substrate availability with conformational changes for efficient hydrolysis and allosteric control of its enzymatic activity through the PAS domain. These structural insights provide a foundation for rational drug design targeting allosteric regulatory mechanisms in GdpP, potentially offering new approaches to combat antibiotic resistance in pathogenic Firmicutes.

molecular biology↗

bioRxiv2025

Optimization of Crop Rotation Calendar to Maximize System-Level Productivity under Climate Change

Crop rotation offers multifaceted benefits for climate adaptation and mitigation. As rising temperatures accelerate crop development, it is necessary to adjust the rotation order and sowing dates of crops in a rotation system. Such an adjustment can enhance agricultural productivity at the whole rotation system level even under warmer conditions. Here, we present a computational approach to identify the crop rotation calendar (the order and sowing dates of rotation crops) that maximizes total crop output with available climatic resources. In this study, the rotation order indicates the cyclical sequence of crop species without intercropping, cover crop and fallow. This approach involves two steps: (1) generating crop windows (the timing and length of crop duration from sowing to harvest) and corresponding outputs (production per unit land area per harvest) for the rotation crops using a crop growth model with daily weather inputs; and (2) applying an optimization algorithm to identify a single subset of crop windows of rotation crops that maximizes the total crop output while satisfying agronomic constraints. We applied this method to a four-year, four-crop rotation system in northern Japan, with historical and projected climates from 2000 to 2100. The results revealed that adjusting crop windows would reduce the time to complete all rotation crops in the system (shortened rotation cycle) and enhance the system-level annual productivity [kgDW ha-1 year-1] with time. The increase in this productivity is approximately 0.5 % per year under high warming of the Shared Socioeconomic Pathway 5-8.5. Optimizing the rotation order in addition to the rotation crops sowing dates showed the changes in the most productive rotation orders, demonstrating the dynamic nature of rotation planning under climate change. Our methodology offers a flexible, scalable means of designing cropping system to harness the positive effect of climate change on long-term food security.

plant biology↗

bioRxiv2025

Evaluation of anti-noroviral compounds on human norovirus replication using 2D monolayers of human intestinal organoids

We evaluated the anti-noroviral effects of compounds including molnupiravir, on human norovirus (HuNoV) replication using 2D monolayers of human intestinal organoids (HIOs), which have been widely used in HuNoV infection studies. We found that these compounds exhibited lower antiviral activity in 2D HIO monolayers compared with that in apical-out 3D HIOs, a recently developed culture system for HuNoV. This suggests that the anti-noroviral efficacy of these compounds may vary depending on the assay system used.

microbiology↗

bioRxiv2025

Muc6-expressing gastric isthmus progenitors contribute to regeneration and metaplasia supported by myeloid-mesenchymal interactions

Gastric mucosal homeostasis is maintained by tissue-resident stem and progenitor cells residing in the isthmus region. Following mucosal injury, surviving cells contribute to regeneration, coinciding with characteristic pathological changes such as atrophic gastritis and metaplasia. To comprehensively understand the cellular dynamics involved in this process, we performed single-cell and spatial transcriptomics using newly generated transgenic mice. In human samples and mouse models, loss of gastric chief cells precedes, and even induces, loss of parietal cells during the progression of atrophy and metaplasia, validating the causal relationship underlying the decrease of these two lineages. Single-cell analysis confirmed robust stemness and metaplastic changes in the Muc6-expressing neck lineage following either chief or parietal cell ablation, and lineage-tracing experiments revealed that Muc6-expressing isthmus progenitors serve as a source of metaplasia and regeneration. Mechanistically, mucosal injury recruits IL-1-expressing myeloid cells, which stimulates NRG1 production in stromal fibroblasts, leading to mucosal proliferation and regeneration mediated by Myc activation in isthmus progenitors. These findings highlight the injury-responsible stem cell-like function of Muc6-expressing isthmal progenitors, which play a critical role in mucosal homeostasis and disease progression. Visual abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/648856v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@10fc2eaorg.highwire.dtl.DTLVardef@1c5b82corg.highwire.dtl.DTLVardef@1be747dorg.highwire.dtl.DTLVardef@d1d722_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Structural Characterization of Native RNA Polymerase II Transcription Complexes and Nucleosomes in Drosophila melanogaster

Structural studies of eukaryotic RNA polymerase II (Pol II) transcription complexes often depend on in vitro assembly by mixing purified Pol II with synthetic DNA/RNA scaffolds, recombinant transcription factors, and/or histones, followed by stalling transcription at defined positions by adding selected nucleotide triphosphate substrates. These studies have yielded remarkable results for understanding nucleosome transcription by Pol II with elongation factors but may fail to represent transcription in native conditions. To investigate Pol II transcription within metazoan cells, we developed an approach to isolate the native transcription complexes from Drosophila melanogaster embryos. Utilizing one-step FLAG-tag affinity purification and mild chromatin treatment with Micrococcal Nuclease (MNase), we preserved the native transcription complex for cryo-EM and proteomics studies. In silico purification through the cryo-EM classifications determined structures of multiple forms of native transcription complex, nucleosome and other macromolecules. Remarkably, we determined the structures of metazoan Rpb4/Rpb7 stalk-less elongation complex as well as hexameric nucleosome lacking an H2A/H2B dimer, revealing that diverse elongation complexes and nucleosomes are involved in active transcription in vivo. Nucleosome is positioned only downstream of Pol II in the nucleosome elongation complex, underscoring it as a major energy barrier and a time-consuming step during Pol II progression through nucleosomal DNA. Proteomics identified co-purified factors responsible for initiation and elongation stages of transcription, as well as RNA modification factors. This study lays the groundwork for structural study of native transcription in eukaryotes, with future work focused on studies of transient and minor populations of transcription complexes.

molecular biology↗

bioRxiv2024

Exploring Organ-Specific Extracellular Vesicles in Metabolic Improvements Following Bariatric Surgery in Adolescents with Obesity

Aims/hypothesisVertical sleeve gastrectomy (VSG) leads to significant metabolic improvements, though the underlying molecular mechanisms are not yet fully understood. Emerging evidence suggests that small extracellular vesicles (sEVs) contribute to metabolic improvements post-VSG; however, it is still unclear which organ-specific sEV correlate with various metabolic parameters and how they exert these effects. The study aimed to establish the role of organ-specific sEVs in the metabolic improvements associated with VSG. MethodsDemographic, anthropometric, and blood samples were collected pre-VSG and 3- and 6-month post-VSG in adolescents with obesity. Blood samples were utilized to measure metabolic parameters and to isolate sEVs. sEV RNAs were analyzed via small RNA sequencing then bioinformatics analyses. ResultsA significant reduction in mRNA cargo from liver-specific genes was observed post- VSG, whereas adipose tissue- or skeletal muscle-specific genes showed no such reduction. Liver-derived RNA correlated with BMI, leptin, and resistin, while adipose-derived RNA correlated with leptin. Analysis of delta values (post-minus pre-surgery) revealed that adipose-derived RNA cargo correlated with markers of liver damage and HOMA-IR, whereas liver-derived RNA cargo correlated with BCAAs. ConclusionsVSG modulates the EV system in the liver and adipose tissue. Liver-derived sEVs appear to regulate adipose metabolism, while adipose-derived sEVs are associated with liver function, suggesting a dynamic crosstalk between these tissues through sEVs that shapes systemic metabolic outcomes. Research in ContextO_ST_ABSWhat is already known about this subject?C_ST_ABS- Vertical sleeve gastrectomy (VSG) is the most performed bariatric surgery, leading to significant metabolic improvements. - Small extracellular vesicles (sEVs) and their RNA cargo play a crucial role in metabolic regulation. - Levels of branched-chain amino acids (BCAAs), which are known metabolic regulators, decrease following bariatric surgery. What is the key question?- How do sEVs, BCAA and other metabolic molecules interact to drive the significant metabolic improvements observed after VSG? What are the new findings?- The levels of liver-specific RNA cargo in sEVs decrease after VSG and are correlated with BMI and leptin levels at 6 months post-surgery, suggesting a potential role for liver-specific RNA cargo in the metabolic benefits associated with VSG. - Changes in BCAA levels from baseline to 6 months post-surgery correlate with changes in liver-specific RNA cargo in sEVs, indicating liver-specific RNA cargo in sEVs may influence metabolic parameters through BCAA modulation. - Changes in the level of adipose-specific RNA cargo in sEVs from baseline to 6 month post-surgery correlate with changes HOMA-IR and ALT levels. How might this impact on clinical practice in the foreseeable future?The study identifies liver- and adipose-derived sEV RNA cargo as potential targets for non-invasive therapies that could replicate the metabolic benefits of VSG. While further investigation is needed, these findings suggest a tentative alternative for adolescents facing obesity who may be ineligible or reluctant to undergo bariatric surgery.

cell biology↗

bioRxiv2024

An attention-based deep neural network model to detect cis-regulatory elements at the single-cell level from multi-omics data

Cis-regulatory elements (cREs) play a crucial role in regulating gene expression and determining cell differentiation and state transitions. To capture the heterogeneous transitions of cell states associated with these processes, detecting cRE activity at the single-cell level is essential. However, current analytical methods can only capture the average behavior of cREs in cell populations, thereby obscuring cell-specific variations. To address this limitation, we proposed an attention-based deep neural network framework that integrates DNA sequences, genomic distances, and single-cell multi-omics data to detect cREs and their activities in individual cells. Our model shows higher accuracy in identifying cREs within single-cell multi- omics data from healthy human peripheral blood mononuclear cells than other existing methods. Furthermore, it clusters cells more precisely based on predicted cRE activities, enabling a finer differentiation of cell states. When applied to publicly available single-cell data from patients with glioma, the model successfully identified tumor-specific SOX2 activity. Additionally, it revealed the heterogeneous activation of the ZEB1 transcription factor, a regulator of epithelial-to-mesenchymal transition-related genes, which conventional methods struggle to detect. Overall, our model is a powerful tool for detecting cRE regulation at the single-cell level, which may contribute to revealing drug resistance mechanims in cell sub- populations.

bioinformatics↗

bioRxiv2024

Structural Insights into the Role of the Proline Rich Region in Tau Function

Tau is a microtubule-associated protein that plays an important role in modulating axonal microtubules in neurons. Intracellular tau aggregates are found in a broad class of disorders, including Alzheimers disease, termed tauopathies. Tau is an intrinsically disordered protein, and its structural disorder appears to be critical to its microtubule-related functions. Tubulin binding sites are found in taus proline-rich region (PRR), microtubule binding repeats (MTBR: R1-R4), and pseudo-repeat, R'. While many post-translational modifications have been identified on tau, phosphorylation sites, which both regulate tubulin dimer and microtubule interactions and are correlated with disease, cluster with high frequency within the PRR. Here, we use fluorescence correlation spectroscopy and structural mass spectrometry techniques to characterize the impact of phosphomimic mutations in the PRR on tubulin dimer binding and probe the structure of the PRR-tubulin dimer complex. We find that phosphomimics cumulatively diminish tubulin dimer binding and slow microtubule polymerization. Additionally, we map two [~]15 residue regions of the PRR as primary tubulin dimer binding sites and propose a model in which PRR enhances lateral interactions between tubulin dimers, complementing the longitudinal interactions observed for MTBR. Together these measurements provide insight into the previously overlooked relevance of taus PRR in functional interactions with tubulin. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=181 SRC="FIGDIR/small/614010v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@360dd3org.highwire.dtl.DTLVardef@c5d75aorg.highwire.dtl.DTLVardef@bd76eeorg.highwire.dtl.DTLVardef@cb433c_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2024

Differentiation of Acute Disseminated Encephalomyelitis from Multiple Sclerosis Using a Novel Brain Lesion Segmentation and Classification Pipeline

Multiple Sclerosis (MS) is a chronic autoimmune disease affecting the central nervous system, while Acute Disseminated Encephalomyelitis (ADEM) is a sudden, often monophasic inflammatory condition of the brain and spinal cord. Only 17% of ADEM cases are correctly diagnosed on the first visit due to overlapping clinical and radiological presentations with Multiple Sclerosis (MS) [1]. Both ADEM and MS are demyelinating diseases, meaning they cause brain lesions by damaging the myelin sheath, leading to scar tissue that disrupts nerve signals [2]. Previous machine learning pipelines have differentiated Neuromyelitis Optica Spectrum Disorder (NMOSD) (a different demyelinating disease) from MS and ADEM from NMOSD based on MRI imagery with varying accuracies [3, 4]. Our novel Classifier for Demyelinating Disease (CDD) pipeline is the first to differentiate ADEM from MS using MRI imagery. It does this in two stages: a segmentation stage which creates segmentation masks of the lesions and a classification stage to classify them as either ADEM or MS. Additionally, we introduce a novel ADEM dataset from open-access medical case reports. The CDD pipeline achieves an accuracy of 90.0% on our validation dataset, making it a potentially viable diagnostic tool in the future. All data and code is available here. 2

neuroscience↗