bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coupling Between Functionality and Trafficking to the Axon Initial Segment in KCNQ2/3 K+Channels
Authors: Yoshioka Daisuke , Okamura Yasushi 
Published: October 2024

SummaryKCNQ2/3 are the predominant voltage-gated K+channels localized at the axon initial segment (AIS), the critical site for the initiation of action potentials and the plasticity of excitability. Both the functionality and spatial distribution of KCNQ2/3 provide the basis for the regulation of neuronal excitability and the pathogenesis of various neurological disorders, including epilepsy. However, less is known about how functionality is coupled with trafficking regulation in KCNQ2/3. Here, we study the AIS localization of KCNQ2/3 by performing both multiple- and single-molecule imaging analyses. We found that low-activity mutations in the KCNQ3 subunit affect all of the 3D dynamics composed of lateral diffusion and exo/endocytosis processes through disruption of interaction with ankyrin-G, consequently suppressing the AIS targeting of KCNQ2/3. Thus, the functionality of KCNQ2/3 is coupled with its trafficking regulation, enhancing our understanding of the mechanisms underlying physiological and pathophysiological changes in neuronal excitability.
A global effort to benchmark predictive models and reveal mechanistic diversity in long-term stroke outcomes
Authors: Matsulevits Anna , Alvez Pedro , Atzori Manfredo , Beyh Ahmad , Corbetta Maurizio , Pup Federico Del , Dulyan Lilit , Foulon Chris , Hope Thomas , Ioannucci Stefano , Jobard Gael , Lemaitre Hervé , Neville Douglas , Nozais Victor , Rorden Christopher , Saprikis Orionas-Vasilis , Sibon Igor , Sperber Christoph , Teghipco Alex , Thirion Bertrand , Tshimanga Louis Fabrice , Umarova Roza , Vaidelyte Ema Birute , den Hoven Emiel van , Rodriguez Esteban Villar , Zanola Andrea , Tourdias Thomas , de Schotten Michel Thiebaut 
Published: October 2024

AbstractStroke remains a leading cause of mortality and long-term disability worldwide, with variable recovery trajectories posing substantial challenges in anticipating post-event care and rehabilitation planning. To address these challenges, we established the NeuralCup consortium to benchmark predictive models of stroke outcome through a collaborative, data-driven approach. This study presents findings from 15 international teams who used a comprehensive dataset including clinical and imaging data, to identify and compare predictors of motor, cognitive, and emotional outcomes one year post-stroke. Our analyses integrated traditional statistical approaches and novel machine learning algorithms to uncover ’optimal recipes’ for predicting each domain. The differences in these ‘optimal recipes’ reflect distinct brain mechanisms in response to different tasks. Key predictors across all domains included infarct characteristics, T1-weighted MRI sequences, and demographic factors. Additionally, integrating FLAIR imaging and white matter tract analysis significantly improved the prediction of cognitive and motor outcomes, respectively. These findings support a multifaceted approach to stroke outcome prediction, underscoring the potential of collaborative data science to develop personalized care strategies that enhance recovery and quality of life for stroke survivors. To encourage further model development and validation, we provide access to the training dataset athttp://neuralcup.bcblab.com
Molecular mechanism of thyroxine transport by monocarboxylate transporters
Authors: Tassinari Matteo , Tanzi Giorgia , Maggiore Francesco , Groeneweg Stefan , van Geest Ferdy S. , Freund Matthijs , Stavast Christiaan J. , Boniardi Irene , Pasqualato Sebastiano , Visser W. Edward , Coscia Francesca 
Published: October 2024

AbstractThyroid hormones (the common name for prohormone thyroxine and the bioactive form triiodothyronine) control major developmental and metabolic processes. Release of thyroid hormones from the thyroid gland into the bloodstream and their transport into target cells is facilitated by plasma membrane transporters, of which monocarboxylate transporter (MCT)8 and the highly homologous MCT10 are most important. Patients with MCT8 mutations suffer from a severe neurodevelopmental and metabolic disorder, however, the molecular mechanism underlying thyroid hormone transport is unknown. Using cryogenic-sample electron microscopy (cryo-EM), we determined the ligand-free and thyroxine-bound human MCT8 structures in the outward-open state and the thyroxine-bound human MCT10 in the inward-facing state. Our structural analysis revealed a network of conserved gate residues involved in conformational changes upon thyroxine binding, triggering ligand release on the opposite compartment. We then determined the structure of a folded, but inactive patient-derived MCT8 mutant, indicating a subtle conformational change which explains its reduced transport activity. In addition, we determined the structure of MCT8 bound to its inhibitor silychristin, revealing an interaction with residues essential to drive transition to the inward-facing state, thereby locking the protein in the outward-facing state. This study provides molecular and structural insights into normal and disordered thyroid hormone transport.
B cell expression of the enzyme PexRAP, an intermediary in ether lipid biosynthesis, promotes antibody responses and germinal center size
Authors: Cho Sung Hoon , Jones Marissa A. , Meyer Kaylor , Anderson David M. , Chetyrkin Sergei , Calcutt M. Wade , Caprioli Richard M. , Semenkovich Clay F. , Boothby Mark R. 
Published: October 2024

ABSTRACTThe qualities of antibody (Ab) responses provided by B lymphocytes and their plasma cell (PC) descendants are crucial facets of responses to vaccines and microbes. Metabolic processes and products regulate aspects of B cell proliferation and differentiation into germinal center (GC) and PC states as well as Ab diversification. However, there is little information about lymphoid cell-intrinsic functions of enzymes that mediate ether lipid biosynthesis, including a major class of membrane phospholipids. Imaging mass spectrometry (IMS) results had indicated that concentrations of a number of these phospholipids were substantially enhanced in GC compared to the background average in spleens. However, it was not clear if biosynthesis in B cells was a basis for this finding, or whether such cell-intrinsic biosynthesis contributes to B cell physiology or Ab responses. Ether lipid biosynthesis can involve the enzyme PexRAP, the product of theDhrs7bgene. Using combinations of IMS and immunization experiments in mouse models with inducibleDhrs7bloss-of-function, we now show that B lineage-intrinsic expression of PexRAP promotes the magnitude and affinity maturation of a serological response. Moreover, the data revealed aDhrs7b-dependent increase in ether phospholipids in primary follicles with a more prominent increase in GC. Mechanistically, PexRAP impacted B cell proliferation via enhanced survival associated with controlling levels of ROS and membrane peroxidation. These findings reveal a vital role of this peroxisomal enzyme in B cell homeostasis and the physiology of humoral immunity.
Microbially Produced Bile Acids are Associated with High Levels of IgG Autoantibodies and Worse Mental Well-being in Fibromyalgia Subjects
Authors: Jakobsson Jenny E. , Carlsson Henrik , Erngren Ida , Menezes Joana , Krock Emerson , Hunt Matthew A. , Sohlin Jeanette Tour , Al-Grety Asma , Sandor Katalin , Kosek Eva , Svensson Camilla I. , Kultima Kim 
Published: October 2024

AbstractFibromyalgia (FM) is a disease primarily associated with chronic widespread pain, but other common symptoms are anxiety and depression. We previously proposed that autoimmunity contributes to FM based on findings of increased immunoglobulin G binding to satellite glial cells (anti-SGC IgG) in FM subjects compared to healthy controls (HC). Emerging research suggests that an altered gut microbiota composition is connected to psychological symptoms in FM rather than pain. Gut microbiota can produce or alter bile acids (BAs) and short-chain fatty acids (SCFAs), which have immune and inflammatory functions. Here, we investigate alterations in BA and SCFA concentrations in FM subjects compared to healthy controls (HC) and potential associations with FM symptoms and anti-SGC IgG levels.Bile acids and SCFAs were quantified using liquid chromatography coupled with high-resolution mass spectrometry and anti-SGC IgG levels were assessed with immunocytochemistry. The correlations between FM symptoms, anti-SGC IgG levels, and serum concentrations of 24 BAs and 11 SCFAs in 35 FM subjects and 32 matched HC were examined.Fibromyalgia subjects had significantly higher levels of microbially produced BAs than HC. Strikingly, 11 out of 24 BAs were significantly elevated in FM subjects with high, compared to those with low, anti-SGC IgG levels. Concentrations of specific BAs were associated with increased disease severity and worse mental well-being.These results revealed increased levels of secondary BAs in FM subjects compared to HC. The strong association between BAs, anti-SGC IgG levels, and mental well-being may help elucidate the importance of BAs in the psychological symptoms of FM.Significance statementFibromyalgia (FM) is a chronic pain syndrome that significantly impacts an individual’s quality of life. In addition to persistent pain, people with FM often experience depression, anxiety, and irritable bowel syndrome. Previously, we identified autoantibodies that bind to satellite glial cells in the dorsal root ganglia associated with more severe FM symptoms. Our current results demonstrate a novel association between these autoantibodies in FM and bile acids (BAs). Bile acids are essential for lipid metabolism but also act as signaling molecules. We show that patients with elevated levels of autoantibodies also exhibit increased levels of BAs. Furthermore, the BAs strongly correlate with worse FM symptom severity, particularly affecting mental well-being. Our study suggests that lowering BA levels could alleviate the psychological symptoms associated with FM.
An ensemble method for predicting and designing of druggable proteins
Authors: Jain Shipra , Gupta Srijanee , Raghava Gajendra P. S. 
Published: October 2024

AbstractIn the past, numerous proteins/peptides have been discovered, which have a wide range of therapeutic properties like anticancer, antimicrobial, antihypertensive. Only few hundreds of proteins are druggable (approved by US FDA), most of the proteins fails in clinical trials. In this study, an attempt had been made to understand properties of FDA approved proteins to develop models for predicting druggable proteins. Our main dataset 356 FDA approved proteins as positive dataset and equal number of randomly selected proteins as negative dataset. We used 80% data for training and 20% for independent validation, no protein in validation dataset have more than 40% similarity with any protein in training dataset. We deployed machine learning based models using a five-fold cross-validation and test on validation dataset. Our random forest-based model developed using SVC-L1 selected features obtained maximum performance AUC of 0.80 with MCC 0.61 on validation data. In addition to this, we performed MERCI-based motif analysis to find motifs in druggable proteins. Finally, we developed an ensemble-based method combining best performing machine learning model with motifs and achieved AUC 0.92 with MCC 0.83 on independent validation dataset. We developed a web server and standalone package ThPPred to facilitate scientific community in predicting and designing druggable proteins (https://webs.iiitd.edu.in/raghava/thppred/).HighlightsAnalysis of FDA approved or druggable proteinsDiscrimination of druggable and non-druggable proteinsMachine learning based models for predicting druggable moleculesIdentification of motifs in druggable proteinsA web server for providing service to community
MLL/WDR5 complex recruits KIF2C to midbody to ensure MT depolymerization and furrow compaction during cytokinesis
Authors: Kataria Avishek , Hemalatha Neeraja , Chinchole Akash , Tyagi Shweta 
Published: October 2024

AbstractMixed-lineage leukemia (MLL) protein is a well characterized epigenetic regulator whose non-canonical activities remain under appreciated. Here we show that MLL and its associated protein WDR5, localize to the midbody. Loss of MLL/WDR5 results in defective midbody formation, which displays a wide midzone-like microtubule structure, along with chromosome bridges, resulting in binucleated cells. We show that MLL and WDR5 interact with kinesin 13 motor—KIF2C, and targets it to the midbody. The depolymerase activity of KIF2C promotes correct localization of centralspindlin complex, compaction of midzone MTs and finally furrow completion. By characterizing the previously undiscovered role of MLL and KIF2C in the regulation of cytokinesis, our work underscores the importance of these proteins at the interface of actin and microtubule cytoskeleton regulation, pathways that are frequently altered in oncogenesis.
Exposure to complex mixtures of urban sediments containing Tyre and Road Wear Particles (TRWPs) increases the germ-line mutation rate inChironomus riparius
Authors: Rigano Lorenzo , Schmitz Markus , Linnemann Volker , Krauss Martin , Hollert Henner , Pfenninger Markus 
Published: October 2024

AbstractTyre and road wear particles (TRWPs) are a significant yet often underestimated source of environmental pollution, contributing to the accumulation of microplastics and a complex mixture of contaminants in both terrestrial and aquatic ecosystems. Despite their prevalence, the long-term evolutionary effects of TRWPs, beyond their immediate toxicity, remain largely unknown. In this study, we assessed mutagenicity in the non-biting midgeChironomus riparius, upon exposure to urban sediment collected from a runoff sedimentation basin. To assess the extent of mutagenic effects over multiple generations, we combined the urban sediment exposure model with short-term mutation accumulation lines (MALs) and subsequent whole genome sequencing (WGS). Our results reveal that the exposure to urban sediment significantly increases mutation rates compared to control groups by 50%, independent of concentration (0.5% and 10%). To infer potential causal processes, we conducted a comparative analysis with known mutational spectra from experiments with other studies. This comparison showed that the mutation profiles induced by urban sediment clearly clustered with those caused by Benzo[a]Pyrene (BaP), a known polycyclic aromatic hydrocarbon (PAH). A comprehensive chemical characterization of the sediment confirmed a considerable impact of road runoff and traffic-related contamination, including PAHs of primarily petrogenic origin. This suggests that PAH-like compounds present in urban sediments may play a significant role in the observed mutagenic effects. Our study shows that urban sediments influence mutation rates and alter mutational spectra in exposed organisms, potentially compromising genomic stability and shaping evolutionary trajectories. Additionally, we show that comparatively analysing mutational spectra may provide valuable insights into mutational processes. These genetic changes may have profound long-term effects on population dynamics and ecosystem health, underscoring the importance of understanding the evolutionary consequences of environmental pollution.
Differential expression of GABARAPs in GBM renders temozolomide sensitivity in a p53-dependent manner
Authors: Chaudhary Megha , Soni Naveen , Dongre Shweta , Tiwari Ashwani , Malik Nargis , Chosdol Kunzang , Bissa Bhawana 
Published: October 2024

AbstractGlioblastoma (GBM) is one of the most debilitating and extremely aggressive tumors, with a median survival of less than a year. GBMs have high metastatic potential and frequently acquire chemoresistance. The current multimodal treatment approaches for GBM include surgical tumor resurrection, radiotherapy, and chemotherapy but these approaches leave the patient with long-term disabilities such as depletion of cognitive abilities, leukoencephalopathy, and recurrence in 6-8 months. Glioma cells are highly dependent on autophagy to survive and proliferate. Autophagy inhibition has proven to be a beneficial strategy for restricting glioma growth. However, the autophagy pathway cannot be efficiently targeted due to the lack of specific autophagy inhibitors. Understanding the vulnerabilities in autophagy gene expression can help to design better autophagy inhibitors. This study demonstrates the differential expression of GABARAP family members in low-grade glioma and GBM. Our study highlights the differential expression of GABARAP family members in response to autophagy inhibition and induction. Moreover, the knockdown of specific GABARAP family members enhanced proliferation and reduced temozolomide (TMZ) sensitivity of glial cells by decreasing the p53 expression. The selective expression pattern of GABARAP genes in Glioblastoma can be utilized to screen for patients who might respond better to temozolomide treatment. The differential expression of GABARAP family members highlights the subtle regulation of the autophagy pathway in response to environmental cues.
Octahedral small virus-like particles of dengue virus type 2
Authors: Johnson Adam , Traian Martín Dodes , Walsh Richard M. , Jenni Simon , Harrison Stephen C. 
Published: October 2024

ABSTRACTFlavivirus envelope (E) and precursor M (prM) proteins, when ectopically expressed, assemble into empty, virus-like particles (VLPs). Cleavage of prM to M and loss of the pr fragment converts the VLPs from immature to mature particles, mimicking a similar maturation of authentic virions. Most of the VLPs obtained by prM-E expression are smaller than virions; early, low-resolution cryo-EM studies suggested a simple, 60-subunit, icosahedral organization. We describe here the cryo-EM structure of immature, small VLPs from dengue virus type 2 and show that they have octahedral rather than icosahedral symmetry. The asymmetric unit of the octahedral particle is an asymmetric trimer of prM-E heterodimers, just as it is on icosahedral immature virions; the full, octahedrally symmetric particle thus has 24 such asymmetric trimers, or 72 prM-E heterodimers in all. Cleavage of prM and release of pr generates ovoid, somewhat irregular, mature particles. Previous work has shown that mature smVLPs have fusion properties identical to those of virions, consistent with local, virion-like clustering of 36 E dimers on their surface. The cryo-EM structure and the properties of these VLPs described here relate directly to on-going efforts to use them as vaccine immunogens.IMPORTANCEEctopic expression of flavivirus envelope (E) and precursor M (prM) proteins leads to formation and secretion of empty, virus-like particles (VLPs), which are candidate, non-infectious, virion-like components of flavivirus vaccines. We show that the immature particles of a major class of VLPs -- “small VLPs” (smVLPs), which have smaller diameter than those of virion size, -- are octahedrally (rather than icosahedrally) symmetric, with the same clustering of prM and E, as asymmetric trimers of prM-E heterodimers, found on immature virions. Cleavage of prM and formation of mature, smVLPs yields somewhat irregular, ovoid particles. Design and characterization of VLPs as vaccine components will need to take these properties into account.
Trim7 does not have a role in the restriction of murine norovirus infection in vivo
Authors: Annaswamy Srinivas Mridula , Pierce Linley R. , Olson Mikayla C. , Roberston Shelly J. , Sturdevant Gail L. , Best Sonja M. , Orchard Robert C. 
Published: October 2024

AbstractTrim7 is an E3 ubiquitin ligase that was recently identified as a central regulator of host- viral interactions with both pro-viral and anti-viral activity in cell culture. As an inhibitor, Trim7 overexpression ubiquitinates viral proteins by recognizing C-terminal glutamines that are hallmarks of 3C-like protease cleavage events. Here we sought to determine the physiological impact of Trim7 in resolving murine norovirus (MNV) infection of mice as MNV is potently inhibited by Trim7 in vitro. Utilizing two independently derived Trim7 deficient mouse lines we found no changes in the viral burden or tissue distribution of MNV in both an acute and persistent model of infection. Additionally, no changes in cytokine responses were observed after acute MNV infection of Trim7-deficient mice. Furthermore, removal of potentially confounding innate immune responses such as STING and STAT1 did not reveal any role for Trim7 in regulating MNV replication. Taken together, our data fails to find a physiological role for Trim7 in regulating MNV infection outcomes in mice and serves as a caution for defining Trim7 as a broad acting antiviral.ImportanceIntrinsic antiviral molecules that restrict viral replication are important drivers of viral evolution and viral tropism. Recently, Trim7 was shown to provide cell intrinsic protection against RNA viruses, including murine norovirus. Biochemically, Trim7 recognizes the cleavage product of viral proteases, suggesting a novel and broad mechanism to restrict viral replication. Here, we tested whether Trim7 had a physiological role in restricting murine norovirus replication in mice. Unexpectedly, we found no impact of viral replication or innate immune responses during murine norovirus infection. Our findings urge caution in defining Trim7 as a broad antiviral factor in the absence of in vivo evidence.
Early-life antibiotic exposure leads to gut microbial dysbiosis associated with neurodevelopment and neuroregeneration
Authors: Zhao Qing , Fan Pianpian , Gu Qie , Mo Xiaoyu , Tan Xuemei , Zhou Xinying , Yang Fan , Zhou Xiang , Li Qingchu 
Published: October 2024

AbstractEarly-life is a critical period for neurodevelopment and establishment of gut microbiota, which are highly susceptible to antibiotic exposure. Here, we aimed to investigate association between gut microbiota and metabolites with neurodevelopment and neuroregeneration in early-life after antibiotic exposure. To induce microbial dysbiosis in offspring, a broad-spectrum antibiotic cocktail was administered to mice dams. The prefrontal lobe, spinal cord tissues and gut sample of offspring were collected at different time with or without spinal cord crush injury. 16S rRNA sequencing and metabolomics were performed to analyze the gut microbiota and metabolites. NG2 glia were cultured and treated by mitochondrial fusion and fission compounds and metabolites. Maternal antibiotic exposure significantly affected neuronal maturation, NG2 glia proliferation, prefrontal cortex myelination and injured spinal cord neuroregeneration of offspring. Mice in antibiotic exposure group exhibited disruption of gut microbiota and metabolites, along with lower Ace, Chao and Shannon indexes, higher relative abundance ofEnterobacterandEscherichia_Shigella,lowerlactobacillusandStreptococcusgenus, and downregulated Cyclo(Arg-Gly-Asp-D-Phe-Val), Ampicilloyl, DG(8:0/i-19:0/0:0), Petasinine and 6-Hydroxymelatonin glucuronide. These metabolites were enriched in alpha-Linolenic acid metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, linoleic acid metabolism. 6-Hydroxymelatonin glucuronide, PC(20:3/0:0), PC(20:2/0:0), Ameltolide, DG(8:0/i-19:0/0:0), Inproquone, and Chorismate were the cores of networks between gut microbiota and metabolites and negatively associated with neurodevelopment and neuroregeneration. Additionally, gut microbiota metabolites promoted NG2 glia differentiation, partly through reversing the effects of mitochondrial fusion/fission compounds. Totally, antibiotic exposure in early-life changed the composition, abundance, and metabolites of gut microbiota in offspring, which was associated with neurodevelopment and neuroregeneration.