bioRxiv Science⌕ Search

Biology subjects

Smith, J.

Publications and source records attributed to Smith, J..

At least 19 recordsLinked to original sources

Conformational Reorganization of a Processive Cellulase on Crystalline Cellulose

Enzymes that degrade insoluble polymers must couple catalytic chemistry to productive engagement with heterogeneous substrate interfaces, yet direct structural information on these interfacial states remains limited. We investigated the conformational organization of the processive cellulase Trichoderma reesei Cel7A both free in solution and bound to an insoluble cellulose substrate using small-angle neutron scattering (SANS). Use of biosynthetically deuterated bacterial cellulose allowed the scattering contribution of the cellulose-associated Cel7A holoenzyme to be selectively highlighted using SANS with contrast matching. SANS measurements performed under conditions supporting high or low catalytic activity revealed distinct differences between the free and cellulose-bound enzyme. Under poorly active conditions, the conformational distributions of free and bound Cel7A were similar. In contrast, catalytically favorable conditions produced an additional interdomain correlation in the bound enzyme, consistent with redistribution toward a substrate-selected conformational ensemble. Molecular dynamics simulations showed that free Cel7A samples can assume compact, intermediate, and extended conformations, but these solution-state ensembles did not reproduce the structural features of cellulose-bound Cel7A. These results identify productive cellulose engagement as a structurally distinct state of the Cel7A holoenzyme and support a dynamic model in which the linker and carbohydrate-binding module modulate interfacial positioning of the catalytic domain rather than functioning as a rigid mechanical unit during processive hydrolysis. More broadly, the findings suggest that heterogeneous biocatalysis depends not only on substrate binding and active-site chemistry, but also on interface-selected conformational states that determine whether binding becomes productive. The study further demonstrates how deuteration and neutron contrast variation can reveal functional macromolecular conformations directly within complex interfacial environments.

biochemistry↗

Widely Used Calculations of Intracranial Volume Provide Inaccurate Estimates in Developmental Cohorts: Evidence and Solutions for the Neuroimaging Community

Intracranial volume (ICV) is often estimated as part of automated neuroimaging processing pipelines and commonly used to account for and characterize cranial size. FreeSurfer's estimated intracranial volume (eTIV) produces implausible longitudinal estimates in developmental samples when using versions prior to FreeSurfer 8. Across two different adolescent datasets, we document eTIV changes of up to 39% between 1.5 - 2 year sessions for FreeSurfer 7, with errors more pronounced on Siemens scanners and in female participants. These errors are markedly reduced in FreeSurfer 8 and AssemblyNet. However, the widespread use of FreeSurfer 7 raises concern about developmental neuroimaging studies that utilize eTIV without quality control.

neuroscience↗

iPSC-Derived Myotubes from ME/CFS Patients Reveal Signature Genes, Isoforms and Pathways with Drug Repurposing Potential

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a complex multisystem disorder. Its hallmark feature, post-exertional malaise (PEM), is a delayed and prolonged worsening of symptoms following even minor exertion. As PEM commonly includes muscle pain, weakness, exercise intolerance and impaired recovery, skeletal muscle dysfunction may contribute to its pathophysiology, but the underlying molecular processes remain poorly understood. We generated induced pluripotent stem cell-derived skeletal muscle myotubes from individuals with ME/CFS (n = 6) and healthy controls (n = 7) to investigate disease-associated transcriptomic alterations and identify potential therapeutic candidates. Myogenic progenitor cells from both groups differentiated into elongated, multinucleated myotubes expressing titin and myosin heavy chain, while qPCR profiling of myogenic differentiation markers further supported successful differentiation. Gene-level analysis identified three differentially expressed genes at an FDR-adjusted p < 0.05: ERVH48-1, CDX4 and SLC2A14. Isoform-switching analysis identified 16 genes with significant differential isoform usage, including CACNA1H, MIEF2, SMAD2 and CHD4. Gene set enrichment analysis identified broader pathway-level alterations involving RNA processing, protein synthesis, proteostasis, mitochondrial quality control, metabolism and muscle-related processes. Library of Integrated Network-based Cellular Signatures Phase 2 (LINCS2) analysis further prioritised 14 compounds associated with mitochondrial metabolism, glucose and lipid regulation, PPAR signalling, calcium and excitatory signalling, neuroimmune activity and cellular stress responses. Overall, ME/CFS iPSC-derived myotubes showed modest gene-level differences alongside broader isoform- and pathway-level alterations, supporting their use for investigating skeletal muscle biology and prioritising candidates for functional validation.

cell biology↗

Developmental pleiotropy revealed by mosaic heterozygous Snrpb deletion underlies CCMS-like axial skeletal defects

Cerebro-Costo-Mandibular Syndrome (CCMS) is a rare congenital disorder due to pathogenic variants in the core spliceosomal gene SNRPB. Affected individuals present with axial skeletal abnormalities, including cleft palate, micrognathia, posterior rib gaps, and a bell-shaped thorax. The molecular basis of these axial defects remains poorly understood, limiting the development of targeted interventions. To study the temporal and molecular requirements of SNRPB during axial development, we generated a mouse model of CCMS using an inducible Cre-lox system to conditionally delete Snrpb. Mosaic deletion of exons 2-3 of Snrpb after gastrulation resulted in the full spectrum of CCMS-like abnormalities, including micrognathia, posterior rib gaps and a reduced thoracic cavity. Despite normal somite morphology and patterning, transcriptomic analysis of E9.5 mutant somites revealed upregulation of p53 pathway genes and mis-expression of retinoic acid (RA) signaling components, consistent with reduced RA signaling. Alternatively spliced genes in Snrpb mutant somites were associated with post-transcriptional regulation, including chromatin modifiers. To test if RA pathway supplementation can rescue axial defects, we performed dietary RA supplementation; however, this failed to rescue mutant phenotypes, suggesting that p53 activation and chromatin dysregulation additionally contribute to disease pathogenesis. Together, these findings establish the first in vivo model of CCMS-associated axial skeletal abnormalities and indicate that Snrpb dysfunction disrupts the early specification of axial skeletal identity without overtly altering somite patterning.

developmental biology↗

Preclinical Evaluation of Chemoradiation Resistance Using 18F-FDG PET/CT in Head and Neck Squamous Cell Carcinoma

PurposeThere is an urgent need for improved prognostic tools and biological understanding of chemoradiation resistance in head and neck squamous cell carcinoma (HNSCC). This study established a preclinical imaging dataset aimed at identifying prognostic imaging features from 18F-FDG micro-PET/CT scans in HNSCC mouse models. MethodsThree orthotopic murine models were utilized: two human papillomavirus (HPV)-negative (MOC1, MOC2) and one HPV-positive (MLM1). When tumor volume exceeded 50 mm3, chemoradiation was initiated using cisplatin (5 mg/kg) and image-guided radiation therapy (8 Gy) on days 0 and 7. 18F-FDG micro-PET/CT imaging was performed on day 14. Tumors were manually segmented on PET/CT, and quantitative image features including tumor volume, SUVmean, and SUVmax were extracted. Treatment response was evaluated by relative tumor size on day 11 compared to day 0. Tumor growth and survival were compared across models using multiple-effects model and log-rank. Imaging feature associations were evaluated by Mann-Whitney U tests. Associations between survival, SUVmax, and tumor volume were assessed using Cox proportional hazards modeling and Kaplan-Meier analysis with log-rank testing. ResultsA total of 121 mice were treated and imaged. Significant differences in tumor growth and survival were observed among the three models (p < 0.01 for pairwise growth comparisons; p < 0.0001 for survival). Day 11 treatment response groups demonstrated significantly different growth trajectories following chemoradiation (p < 0.0001). SUVmax was significantly associated with survival (p = 0.0009), whereas SUVmean was not significant (p = 0.13). PET tumor volume demonstrated the strongest association with survival (p < 0.0001). A multivariate Cox proportional hazards model incorporating SUVmax and tumor volume significantly stratified survival risk (p < 0.0001). ConclusionOverall, these findings demonstrate that 18F-FDG PET/CT-derived metrics, particularly SUVmax and tumor volume, are robust predictors of chemoradiation response in orthotopic murine models of HNSCC.

cancer biology↗

Bio-CM{superscript 2}: Distributed computational optics for cortex-widecellular imaging

Understanding distributed biological systems, particularly neural circuits, requires simultaneous cellular-resolution imaging across millimeter-scale fields of view (FOV). Existing miniature microscopes remain fundamentally constrained by trade-offs among FOV, spatial resolution, and optical complexity, limiting their ability to bridge cellular microscopy with cortex-scale imaging. Here we introduce distributed computational optics, a framework that distributes image formation across coordinated optical modules and computationally integrates their measurements into a unified image. We realize this framework in Bio-CM2, a computational miniature mesoscope that partitions the imaging field across four optical modules while converging their measurements onto a common image sensor. This architecture overcomes the aberration-scaling limitations of conventional miniature optics while avoiding the hardware complexity of multi-camera systems and the contrast degradation associated with optical multiplexing. Bio-CM2 achieves a 7.5 x 10 mm2 FOV while enabling cellular-resolution in vivo imaging at video rates. We demonstrate its utility through two complementary imaging modalities in head-fixed mice: cortex-wide functional vascular imaging, enabling simultaneous quantification of pial arteriole vasomotion and mesoscale hemodynamic functional connectivity, and cellular-resolution calcium imaging, resolving the activity of over 3,000 neurons together with mesoscale neuronal functional connectivity. We further demonstrate the versatility of the platform through cellular-resolution imaging of entire coronal mouse brain sections, population-scale imaging of freely behaving Caenorhabditis elegans, and odor-evoked calcium imaging of the main olfactory bulb in head-fixed mice, highlighting its broad applicability across diverse biological systems and imaging modalities. By overcoming the conventional trade-off between FOV and spatial resolution in a compact miniature platform, Bio-CM2 establishes distributed computational optics as a scalable framework for multiscale biological imaging.

bioengineering↗

Cessation of diel vertical migration by an inshore dinoflagellate bloom under prey deprivation

Many dinoflagellates are mixotrophic and regulate their vertical position to navigate dynamic gradients in light, nutrients, and prey. Here, it is shown that the obligate kleptoplastidic mixotroph, Dinophysis acuminata, transitions from diel vertical migration to formation of a stationary, sub-surface thin layer in response to prolonged prey deprivation. An inshore bloom within a salt marsh kettle pond was recorded through continuous in-situ imaging, automated oxygen and fluorescence depth profiling, and targeted water chemistry measurements. During the blooms initial development, D. acuminata cells were photosynthetically active and divided vegetatively while vertically migrating. As photosynthesis and growth slowed, vertical migration ceased and cells formed a stable thin layer that promoted conditions for local acidification and nitrogen remineralization. Surface avoidance by the thin layer drove selective retention of cells within the relatively deep kettle hole. Together, these findings illustrate linkage of metabolic state and swimming behavior in D. acuminata and show how swimming behavior can drive development of toxic blooms within inshore systems. They also illustrate how D. acuminata and other eurytolerant bloom-forming species can exploit and shape physicochemical gradients associated with coastal eutrophication.

ecology↗

“Mapping of Gonadal Development in Cryptorchidism: UTF-1 and Germ Cell Dysgenesis”

Study questionHow does cryptorchidism affect germ cell development and UTF-1-mediated pluripotency potential at the time of orchiopexy? Summary answerCryptorchidism was associated with the following germ cell abnormalities: germ cell clustering with many cords/tubules lacking germ cells and reduced UTF-1 expression, suggesting limited germ cell differentiation into spermatogonia What is known alreadyCryptorchidism, affecting 1.6-9% of male newborns, is known to increase the risk of infertility and testicular cancer due to abnormal germ cell development. Germ cells and pluripotent stem cell gene, UTF-1, play critical roles in spermatogonia differentiation, self-renewal, and spermatogenesis. No prior study has evaluated the testicular development by immunohistochemically mapping of these cell populations, Study design, size, durationA cross-sectional study of 31 postnatal cryptorchid testis and 5 age-matched scrotal testicular biopsies obtained from UCSFs pathology department performed between 1993-2023. Participants/materials, setting, methodsSpecimens were grouped by age at surgery (6-18 months, 19 months-7 years, 8-12 years, and [&ge;]13 years) and testis location (palpable vs. non-palpable). Scrotal prepubertal testis biopsies were sourced through the Pedi-LIFE program, a fertility preservation research biobank, with at least one control per age group. Immunohistochemistry was performed to stain specimens for germ cell (DDX4, OCT4, TSPY), pluripotent cell marker (UTF-1), as well as other key testis cell markers (A-actin, AR, P450, Sox-9), with staining graded based on control expression levels. The number of germ cells per seminiferous tubule was quantified and compared across anatomical locations using appropriate statistical analyses. Main results and the role of chanceThis study included 36 specimens, comprising 31 cryptorchid testes (86%) and 5 scrotal control testes (16%). The cryptorchid group exhibited testicular dysgenesis and reduced germ cell expression, correlated with increased age and testis location. Qualitative assessment revealed reduced germ cell expression across all ages in cryptorchid testes. The number of germ cells per tubule was markedly reduced in cryptorchid compared with scrotal testes after 19 months of age for DDX4, TSPY, and UTF-1. Germ cell clusters were identified in 15 out of 31 cryptorchid specimens (48%) stained for DDX4 and TSPY. UTF-1 expression was lower in cryptorchid testes across all age groups. No significant differences were noted in other testicular cell markers. Large scale dataNA Limitations, reasons for cautionFirst, the power and generalizability of the study are limited by the availability of specimens within each age group, particularly for scrotal testes, as biopsies of these tissues are not routinely performed. Second, a cross-sectional study design limits a longitudinal comparison to evaluate changes in marker expression, delayed maturation, or irreversible germ cell loss. Third, immunohistochemistry data is semi-quantitative, and protein detection is affected by antibody sensitivity and tissue preservation and influenced by antibody sensitivity. Lastly, scrotal testis used as controls were obtained from cryopreserved tissue from patients with other unrelated pathology, which may influence histological profiles. Wider implications of the findingsCollectively, our findings support a model in which cryptorchidism involves both germ cell depletion and disrupted SSC lineage formation, with UTF-1 downregulation and germ cell clustering as early signatures of testicular dysgenesis. These features may help identify high-risk patients for worsening gonadal dysgenesis and infertility and can provide a rationale for earlier orchiopexy or SSC-preserving strategies. Study funding/competing interest(s)The authors declare no conflicts of interest and received no funding for this study. Data Availability StatementThe data underlying this article cannot be shared publicly due to ethical and legal restrictions related to the use of human tissue specimens, which may compromise donor privacy and confidentiality. Data are available from the corresponding author upon reasonable request and subject to institutional and ethical approvals.

Developmental Biology↗

Extracellular matrix defects destabilise apical cytoarchitecture and mechanical properties during early Down syndrome neurodevelopment

Down syndrome (DS) is associated with altered brain development, especially in the cerebellum. However, how trisomy 21 (TS21) is linked to cerebellar defects remains poorly understood. Cerebellar organoids reveal that TS21 leads to extracellular matrix (ECM) alterations, perturbing downstream pathways linked to reduction of apical RAB11+ endosomes. These changes lead to impaired apical maintenance and altered progenitor composition. Significantly, ECM-enriched culture rescues apical defects in TS21 organoids, supporting a functional role for ECM in preserving apical organisation and progenitor niche integrity. In the developing human DS cerebellum and 2D neural cultures, where exogenous ECM is present, severe epithelial disorganisation is attenuated. Nevertheless, ECM organisation and mechanical properties remain altered in 2D cultures. Our findings identify TS21-driven ECM abnormalities as a mechanism impairing apical integrity, progenitor composition and mechanical proprieties in neural stem cell models of DS. Altogether, we established apical maintenance instability as an early developmental defect contributing for DS neuropathology.

Developmental Biology↗

Characterizing the Effects of Chronic Cannabis Vapour Exposure and Withdrawal on Cannabinoid Triad, Somatic Signs and Behavioural Network Reorganization Adult Male Rats

RationaleCannabis withdrawal contributes to relapse in individuals with cannabis use disorder, yet preclinical studies have largely focused on withdrawal induced by injected cannabinoids rather than inhaled cannabis, which remains the most common route in humans. The behavioural effects of chronic exposure to vapourized cannabis flower and resulting withdrawal after cessation of exposure remain poorly characterized. ObjectivesTo determine the behavioural effects of chronic vapourized high-THC cannabis flower exposure on cannabinoid tetrad, somatic withdrawal and behavioural transition networks in rats following both chronic vapour exposure and administration of the cannabinoid receptor 1 (CB1) receptor antagonist SR141716A (rimonabant). MethodsTwo studies were conducted using adult male Sprague Dawley rats. The first study (N = 16) exposed rats to either air or vapourized high-THC cannabis flower three times a day for seven days using a Volcano vapourizer, followed by intraperitoneal administration of the CB1 antagonist SR141716A (3 mg/kg). The second study (N = 24) included two air controls and two cannabis groups, with one of each receiving either saline or SR141716A. Behavioural assessments included triad measurements to confirm the cannabis effect, along with withdrawal assessment via a sucrose preference test and somatic signs 30 minutes following rimonabant administration. ResultsRepeated cannabis vapour exposure produced reduced locomotor activity, hypothermia, and increased tail-flick latency. Rimonabant administration precipitated withdrawal characterized by increased total withdrawal scores and somatic signs, including blinking, body shakes/tremors, and grooming-related behaviours. Behavioural network analyses revealed substantial reorganization of behavioural transition structure during both chronic cannabis exposure and withdrawal. Chronic cannabis exposure was associated with reduced network modularity, a condensed behavioural repertoire, and altered behavioural centrality measures. At the same time, precipitated withdrawal further increased the influence of exploratory behaviours, particularly sniffing, and reduced the network prominence of locomotor-associated behaviours, such as walking, beyond that detected using conventional behavioural measures alone. ConclusionChronic exposure to vapourized cannabis flower followed by CB1 receptor antagonism produces reliable withdrawal symptoms in rats. Behavioural network analyses further reveal that cannabis exposure and withdrawal are both associated with widespread reorganization of behavioural dynamics, suggesting that withdrawal alters not only individual behaviours but also the structure of behavioural transitions. These findings establish a translational model of cannabis withdrawal using inhaled cannabis flower vapour and identify behavioural network analysis as a sensitive approach for characterizing withdrawal-related behavioural states.

neuroscience↗

Enhancer-gene regulatory interactions in colorectal cancer revealed through genome-wide CRISPRi perturbations

BackgroundEstablishing functional relationships between distal enhancers and their target genes is a central challenge in genome biology and cancer genetics. CRISPR/dCas9-mediated perturbations followed by single-cell RNA sequencing (Perturb-seq) has emerged as an efficient means of establishing enhancer-target gene relationships. ResultsWe used genome-wide CRISPRi Perturb-seq with 35,139 guide RNAs targeting 12,117 enhancers to create a functional enhancer-gene map of colorectal cancer (CRC), identifying 238 significant regulatory associations (FDR < 0.1). Integration of chromatin accessibility (ATAC-seq), histone modification profiling (ChIP-seq), and ultra-high resolution chromatin conformation capture (Micro-C) data revealed that enhancer regulation in CRC is constrained by topological domains and often targets the nearest gene, findings corroborated by Activity-by-Contact modelling. ConclusionsWe present here a comprehensive, genome-scale functional atlas of enhancer-gene associations in CRC. This resource should provide a foundation for studying gene regulation in colorectal tumorigenesis and for prioritising candidate non-coding drivers in cancer sequencing studies. PLAIN LANGUAGE SUMMARYO_ST_ABSMapping the hidden DNA switches that control colon cancer genesC_ST_ABSThe total amount of DNA in humans is vast, but only a tiny proportion of it is directly related to genes. While people may know that genes act as blueprints for the body, there are also short stretches of DNA called "enhancers", that fine-tune how strongly genes are activated. When these enhancers get damaged or mutated, it can trigger disease, suggesting that changes to these "control switches" themselves, and not just the genes, can be a driver of cancer. Thus, understanding how these enhancers function is key to uncovering the mechanisms that drive colorectal cancer. In this study, we aimed to map the role of enhancers in colorectal (bowel) cancer development. We used Perturb-seq, a cutting-edge genetic tool that allowed us to systematically turn off more than 12,000 individual enhancers, to identify which ones control which genes. We successfully linked 238 enhancers to the genes they regulate. Combining these results with other biological information, such as the 3D-shape of the DNA, allowed us to build a detailed picture of how enhancers physically interact with their target genes inside cancer cells. This work provides a comprehensive "wiring diagram" of enhancer-gene connections in colorectal cancer, and a resource for researchers seeking to develop new treatment approaches.

genomics↗

Oral exposure to Perfluorooctanoic acid disrupts the microbiota-gut-liver axis and enhances the severity of chemically induced colitis in mice.

Inflammatory bowel diseases (IBD) affect millions of patients worldwide and impair quality of life. Although genetic and environmental factors are known to disrupt the gastrointestinal (GI) epithelial barrier and increase susceptibility to IBD, the precise contribution of specific environmental exposures remains unclear. Per- and polyfluoroalkyl substances (PFAS), or "forever chemicals," are widely used in consumer products and contaminate food and water sources, resulting in chronic oral exposure worldwide. Perfluorooctanoic acid (PFOA), a common PFAS, has been epidemiologically associated with the development of IBD, particularly in older adults. Here, we assessed the effects of oral PFOA exposure on the GI tract, liver, and susceptibility to colitis. C57BL/6 mice were exposed to PFOA (0.1 mg/kg or 1.0 mg/kg) beginning at weaning (post-natal day [P]21) for a time course of 4 or 8 weeks. GI physiology/pathology (Ussing chambers; histology), expression of pro-inflammatory cytokines (qPCR), microbiota composition (16S sequencing), bile acids production (qPCR; LC/MS), and liver pathology (histology) were assessed. Colitis susceptibility was evaluated in genetically predisposed (IL10 knockout) mice, and in induced (dextran sodium sulfate [DSS]) mouse models following PFOA exposure (8 weeks at 1.0 mg/kg). Oral PFOA exposure increased intestinal permeability, mildly increased cytokine expression, altered gut microbiota composition, disrupted liver and serum bile acids, and caused hepatic hypertrophy at higher doses and longer exposure. Although PFOA did not increase disease susceptibility in genetically predisposed Il10 KO mice, it significantly worsened DSS-induced colitis, but only in male mice. Together, these findings demonstrate that early-life PFOA exposure disrupts the gut-liver axis and may contribute to colitis development in a sex dependent manner.

pharmacology and toxicology↗

Efficient and Robust Genomic DNA Isolation and Next-Generation Sequencing Library Preparation from Recalcitrant Wild Grape Species

This protocol details the extraction of high-molecular-weight genomic DNA from grapevine tissues (wild and cultivated Vitis spp., including pathogen-infected samples) and the subsequent preparation of Illumina(R) whole-genome sequencing libraries using bead-bound Tn5 transposase. It is designed to overcome challenges from polyphenolic compounds and secondary metabolites in wild plants, providing a cost-effective workflow for large-scale population genomics. It includes recipes for buffers, incubation times, critical notes, and troubleshooting tips to maximize yield and library quality. Although designed for the grapevine DNA, this protocol is potentially applicable to other similar wild plant species HighlightsO_LIOptimized CTAB-PTB DNA extraction protocol for field-collected wild plant tissues. C_LIO_LIEffective removal of polyphenols and secondary metabolites associated with DNA using PTB. C_LIO_LICost-effective Illumina DNA Prep library preparation using bead-bound Tn5 transposase (Tagmentation). C_LIO_LIScalable workflow suitable for large-scale population genomics in Vitis species. C_LIO_LIValidated method for high-molecular-weight DNA and high-quality sequencing data. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=195 SRC="FIGDIR/small/713680v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@b637d4org.highwire.dtl.DTLVardef@10b563aorg.highwire.dtl.DTLVardef@14a32caorg.highwire.dtl.DTLVardef@4c9577_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

Systems-level analysis of RDK1 reveals compartment-specific kinase activity and a function in the maintenance of the mitochondrial proteome in Trypanosoma brucei

Repressor-of-differentiation kinase 1 (RDK1) is one of two kinases expressed in bloodstream form Trypanosoma brucei parasites that were found to repress premature and spontaneous differentiation into the insect procyclic form. However, the effect of RDK1 RNAi was previously limited to the expression of a single surface coat protein, EP1 procyclin. Thus, there remains a significant gap in knowledge on the impact of RDK1 expression in bloodstream form T. brucei parasites. Here, we employ a systems biology approach and performed several proteomics analyses to identify RDK1 protein interactions and to determine the impact of loss of RDK1 expression on the bloodstream form proteome and phosphoproteome to uncover clues about potential mechanisms for RDK1 function. We found that RDK1 is dual localized to the cell membrane and the mitochondrial inner membrane with the kinase domain oriented towards the cytoplasm and mitochondrial inner membrane. Unexpectedly, the most enriched RDK1-proximal proteins were mitochondrial proteins. Furthermore, RDK1 depletion causes bloodstream form parasites to significantly upregulate many mitochondrial proteins and glycosomal proteins, several of which are upregulated in procyclic form parasites. Surprisingly, the mitochondrial phosphoproteome is largely unaffected by RDK1 depletion, while RDK1-dependent phosphoregulation is restricted to the cell membrane localization of RDK1. Lastly, we determined that RDK1 does not possess adenyl cyclase activity or alter intracellular cAMP levels; however, the dysregulated phosphoproteins correlate with functions in cyclic nucleotide signaling. In conclusion, RDK1 exhibits localization-specific kinase activity to regulate cyclic nucleotide signaling and mitochondrial proteomic maintenance in bloodstream form parasites. IMPORTANCETrypanosoma brucei is the unicellular parasite that causes African sleeping sickness and nagana disease in livestock across 36 sub-Saharan African countries. The parasite encounters different environmental niches as it is transmitted from an infected human to the tsetse fly vector as the fly takes a blood meal. T. brucei must sense environmental cues to initiate intracellular signaling pathways to promote effective differentiation and cellular remodeling from the mammalian bloodstream forms to the insect procyclic form. RDK1 is one of two kinases shown to repress premature differentiation to procyclic form, which would be detrimental for parasite survival in the human host. Therefore, it is essential to uncover mechanisms of RDK1 function to better understand how T. brucei maintains homeostasis in the human host and signals for effective cellular remodeling during parasite transmission.

microbiology↗

Structural Basis of Mitochondrial Transcription Regulation via Interactions of PolRMT and TFAM with Upstream Promoter DNA

Mitochondrial DNA (mtDNA) transcription is essential for cellular energy production and is carried out by a streamlined transcription system in which transcription factor A (TFAM), transcription factor B2 (TFB2M), and the mitochondrial RNA polymerase (PolRMT) assemble at defined promoters to initiate transcription. Previous structural studies elucidated the core initiation mechanism but relied on truncated promoter templates that excluded upstream regulatory DNA interactions. Here, we present two conformations of mitochondrial transcription initiation complexes assembled on the heavy-strand promoter (HSP): a TFAM-bound complex with extended upstream DNA and a TFAM-free complex containing short linear DNA. The TFAM-bound structure reveals a transcription-stimulatory interface between PolRMT and the upstream promoter region (UPR) enabled by TFAM-induced promoter bending. Consistent with this structural observation, UPR truncation reduces transcription from all mtDNA promoters, an effect abolished by mutation of the PolRMT interface. In contrast, the TFAM-free structure reveals a transcription-inhibitory interaction of linear upstream DNA with the PolRMT tether helix, which would sterically clash with TFAM binding. Deletion of the tether helix increases off-target transcription, supporting an autoinhibitory role that enhances promoter specificity. Together, these findings reveal how interactions of TFAM and PolRMT with upstream promoter DNA influence activity and specificity of mitochondrial transcription initiation.

biochemistry↗

Input-and cell-type-specific developmental alterations to thalamic synapses in a Dravet syndrome mouse model

Dravet syndrome is an epileptic encephalopathy most often caused by loss-of-function mutations in the SCN1A gene, leading to haploinsufficiency of the voltage-gated sodium channel NaV1.1. Seizures begin during infancy and generally wane throughout childhood, but behavioral symptoms, such as intellectual disability, motor impairments, and autistic features, remain through adulthood. Seizures primarily stem from inhibitory neuron hypo-excitability in the cortex, hippocampus, and thalamus, but circuit abnormalities underlying persistent behavioral symptoms are poorly understood. Prior work showed synapse dysfunction in thalamocortical neurons in four-week-old DS mice. To understand when synaptic deficits develop and whether they could contribute to persistent thalamic dysfunction, we investigated synapse function in the ventral posterolateral (VPL) and ventral posteromedial (VPM) thalamus prior to seizure onset (P13-P17), after the period of highest seizure burden (P28-P32), and in adulthood (P58-P63). Recordings of VPL and VPM synaptic activity showed excitatory input to the VPL was significantly reduced after seizure onset and this reduction persisted through adulthood, while VPM excitatory input was unaffected. We further showed a selective reduction in the function and number of excitatory sensory synapses in the VPL, with no change to cortical synapses. VPL and VPM neurons both showed inhibitory synapse dysfunction at four weeks, which persisted into adult DS mice only in VPL neurons. These results revealed persistent input- and cell-type-specific alterations to thalamic synapses that develop after seizure onset and are maintained into adulthood, suggesting that synaptic deficits could contribute to ongoing circuit dysfunction in DS.

neuroscience↗

A Machine Learning- 3D Microvessel Platform Identifies Kinase Targets Restoring Blood-Brain-Barrier Endothelial Integrity.

Disruption of the brain endothelial barrier is a hallmark of traumatic brain injury (TBI), and contributes to cerebral edema, coagulopathy, and delayed neurological deficits, yet there are no mechanism-guided therapies that directly stabilize human brain vessels. Here we used a three-dimensional (3D) human brain endothelial vessel platform with quantifiable macromolecular barrier function to assess responses to thrombin and plasma from patients with TBI. This endothelial-focused 3D system isolates the central cellular regulator of blood-brain barrier function and enables mechanistic analysis of endothelial signaling and drug responses as a foundation for personalized vascular therapeutics. By integrating this platform with machine learning-guided kinase analysis, we identified kinase pathways associated with barrier stabilization versus disruption and nominated inhibitors that reversed thrombin- and TBI plasma-induced leakage as well as compounds that exacerbated endothelial loss. This work establishes an important first step toward precision vascular therapeutics in TBI, by linking patient-derived plasma phenotypes to specific endothelial barrier responses and pharmacologically tractable kinase signaling, and it provides a generalizable framework for mechanistic drug discovery across neurovascular disorders. SIGNIFICANCE STATEMENTBlood-brain barrier (BBB) disruption drives cerebral edema, coagulopathy, ischemia, and neurological deficits after TBI. Targeting kinases as therapeutics is promising but challenged by complex inhibitor profiles and patient variability. We present a machine learning-guided platform built on 3D perfusable human brain endothelial-centric microvessels to systematically screen and select kinase inhibitors that reverse TBI-induced endothelial barrier breakdown. By pinpointing key kinase and gene regulators and demonstrating restoration of endothelial barrier integrity in patient-derived plasma models, our approach provides a transformative strategy for stabilizing the endothelial barrier after TBI and offers a versatile framework for therapeutic discovery across neurovascular disorders.

bioengineering↗

Persistent Cognitive Impairment and Bone Health Following Helium (4He) Ion Exposure: Implications for Space Travel

The current study investigated the long-term neurobehavioral and physiological effects of low-dose helium (4He; 250 MeV/n) ion exposure, a significant component of galactic cosmic radiation (GCR), on male Long Evans rats. Groups of rats were trained on the rodent psychomotor vigilance test (rPVT) and irradiated at the NASA Space Radiation Laboratory at Brookhaven National Laboratory. Following exposure, they were tested in the rPVT from 30 - 180 days, and assessed for social recognition memory at 30, 90, and 180 days. At each time point, blood and bone samples were collected for subsequent analysis. We found that acute exposure to 4He ions (25 cGy) significantly impaired sustained attention, resulting in increased lapses in attention, increased reaction time measures, and decreased correct responses. However, exposure to 5 cGy 4He ions only increased some reaction time measures in the rPVT. Both groups displayed impaired social recognition memory. When deficits were found, they persisted for 180 days post-exposure, showing no signs of recovery. Notably, impairments in sustained attention appeared to worsen over time. While these low exposure doses of 4He did not significantly alter overall bone mechanical properties, specific individual parameters of bone strength were affected, and age-related changes likely played a role in observed skeletal integrity changes. Furthermore, we identified significant correlations between circulating cytokines (TNF-, IL-1{beta}), undercarboxylated osteocalcin (ucOC) levels, and bone biomechanical properties with behavioral performances. These findings suggest the potential for these blood- and bone-based targets to serve as diagnostic biomarkers for radiation-induced neurobehavioral effects, opening avenues for future countermeasure development. The sustained and progressive nature of the neurobehavioral deficits observed underscores the critical need for effective countermeasures to protect astronaut health and performance during exploration-class missions.

animal behavior and cognition↗