bluuebunny/crossref_metadata_2025_split huggingface dataset:
Huntingtin polyglutamine expansions misdirect axonal transport by perturbing motor and adaptor recruitment
Authors: Prowse Emily N. P. , Turkalj Brooke A. , Sébastien Muriel , Beaudet Daniel , McBride Heidi M. , Brouhard Gary J. , Pouladi Mahmoud A. , Hendricks Adam G. 
Published: April 2024

SummaryHuntington’s disease (HD) is caused by polyglutamine (polyQ) expansions in huntingtin (HTT). Polyglutamine repeat lengths >35Q lead to neurodegeneration and longer repeats correspond to earlier symptom onset. HTT scaffolds kinesin-1 and dynein to a variety of vesicles and organelles directly and through adaptors. To characterize the effects of HTT polyQ expansions on axonal transport, we tracked BDNF vesicles, mitochondria, and lysosomes in neurons induced from an isogenic set of human stem cell lines with repeat lengths of 30, 45, 65, and 81Q. Mild and intermediate pathogenic polyQ expansions caused increased BDNF motility, while HTT-81Q misdirected BDNF towards the distal tip. In comparison, mitochondria and lysosome transport showed mild defects with polyQHTT. We next examined the effect of polyQHTT in combination with neuroinflammatory stress. Under stress, BDNF cargoes in HTT-30Q neurons were more processive. Stress in HTT-81Q resulted in a stark decrease in the number of BDNF cargoes. However, the few remaining BDNF cargoes displayed more frequent long-range motility in both directions. Under neuroinflammatory stress, lysosomes were more abundant in HTT-81Q neurons, and motile lysosomes moved less processively and had an anterograde bias while lysosomes in HTT-30Q where not strongly affected. To examine how HTT-polyQ expansions altered the motors and adaptors on vesicular cargoes, we isolated BDNF cargoes from neurons and quantified the proteins associated with them. BDNF-endosomes isolated from HTT-81Q neurons associated with 2.5 kinesin-1 and 3.9 HAP1 molecules on average, compared to 1.0 kinesin-1 and 1.0 HAP1 molecule for HTT-30Q neurons. Together, these results show that polyQ expansions in HTT cause aberrant motor and adaptor recruitment to cargoes, resulting in dysregulated transport and responses to neuroinflammatory stress.
Structure ofEscherichia coliDNA gyrase with chirally wrapped DNA supports ratchet-and-pawl mechanism for an ATP-powered supercoiling motor
Authors: Michalczyk Elizabeth , Pabiś Marta , Heddle Jonathan , Ghilarov Dmitry 
Published: April 2024

AbstractGyrase is essential for replication and transcription in bacteria, and as such is an important target for antibiotics including fluoroquinolones. Gyrase is a molecular machine that channels the energy of ATP hydrolysis into negative supercoiling of DNA. The mechanism proposed more than 40 years ago involves stabilising and inverting a chiral DNA loop; however, the molecular basis for this is poorly understood, as the loop was never directly observed. We present high-resolution cryoEM structures of theEscherichia coligyrase - 217 bp DNA holocomplex, and of the moxifloxacin-bound gyrase complex with cleaved 217 bp DNA. Each structure constrains an intact figure-of-eight positively supercoiled DNA loop, poised for strand passage. The loop is stabilised by a GyrA β-pinwheel domain which how we here show has a structure of a flat disc, and functions akin to a mini-nucleosome. Our data implies that during catalysis the ATPase domains of the enzyme undergo a large movement to push the transported DNA segment through the break in DNA. By comparing the catalytic site between native drug-free and moxifloxacin-bound gyrase structures that both contain a single metal ion we demonstrate that the enzyme is observed in a native pre-catalytic state. Finally, we propose a ‘ratchet and pawl’ mechanism for energy coupling in gyrase. These unexpected findings call for re-evaluation of existing data and offer a framework for further experiments designed to dissect the details of how gyrase molecular motor converts chemical energy into mechanical tension.
Soluble αβ-tubulins reversibly sequester TTC5 to regulate tubulin mRNA decay
Authors: Batiuk Alina , Höpfler Markus , Almeida Ana C. , En-Jie Deryn Teoh , Vadas Oscar , Vartholomaiou Evangelia , Hegde Ramanujan S. , Lin Zhewang , Gasic Ivana 
Published: April 2024

SummaryMicrotubules, built from heterodimers of α- and β-tubulins, control cell shape, mediate intracellular transport and power cell division. The concentration of αβ-tubulins is tightly controlled through a post-transcriptional mechanism involving selective and regulated degradation of tubulin-encoding mRNAs. Degradation is initiated by TTC5, which recognizes tubulin-synthesizing ribosomes and recruits downstream effectors to trigger mRNA deadenylation. Here, we have investigated how cells regulate TTC5 activity. Biochemical and structural proteomic approaches reveal that under normal conditions, soluble αβ-tubulins bind to and sequester TTC5, preventing it from engaging nascent tubulins at translating ribosomes. We identify the flexible C-terminal tail of TTC5 as a molecular switch, toggling between soluble αβ-tubulin-bound and nascent tubulin-bound states. Loss of sequestration by soluble αβ-tubulins constitutively activates TTC5, leading to diminished tubulin mRNA levels and compromised microtubule-dependent chromosome segregation during cell division. Our findings provide a paradigm for how cells regulate the activity of a specificity factor to adapt posttranscriptional regulation of gene expression to cellular needs.
Problem-Solving as a Language: A Computational Lens into Human and Monkey Intelligence
Authors: Yang Qianli , Zhu Zhihua , Si Ruoguang , Li Yunwei , Zhang Jiaxiang , Yang Tianming 
Published: April 2024

1AbstractHuman intelligence is characterized by our remarkable ability to solve complex problems. This involves planning a sequence of actions that leads us from an initial state to a desired goal state. Quantifying and comparing problem-solving capabilities across species and finding its evolutional roots is a fundamental challenge in cognitive science, and is critical for understanding how the brain carries out this intricate process. In this study, we introduce the Language of Problem-Solving (LoPS) model as a novel quantitative framework that investigates the structure of problem-solving behavior through a language model. We adapted the classic Pac-Man game as a cross-species behavioral paradigm to test both humans and macaque monkeys. Using the LoPS model, we extracted the latent structure — or grammar — embedded in the agents’ gameplay, revealing the non-Markovian temporal structure of their problem-solving behavior. The LoPS model captured fine-grained individual differences among the players and revealed the striking differences in the complexity and hierarchical organization of problem-solving behavior between humans and monkeys, reflecting the distinct cognitive capabilities of each species. Furthermore, both humans and monkeys evolved their LoPS grammars during learning, progressing from simpler to more complex ones, suggesting that the language of problem-solving is not fixed, but rather evolves to support more sophisticated and efficient problem-solving. Through the lens of a language model, our study provides insights into how humans and monkeys break down problem-solving into compositional units and navigate complex tasks. This framework deepens our understanding of human intelligence and its evolution, and establishes a foundation for future investigations of the neural mechanisms of problem-solving.
Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID pipeline
Authors: Lu Dan , Kalantar Katrina L. , Chu Victoria T. , Glascock Abigail L. , Guerrero Estella S. , Bernick Nina , Butcher Xochitl , Ewing Kirsty , Fahsbender Elizabeth , Holmes Olivia , Hoops Erin , Jones Ann E. , Lim Ryan , McCanny Suzette , Reynoso Lucia , Rosario Karyna , Tang Jennifer , Valenzuela Omar , Mourani Peter M. , Pickering Amy J. , Raphenya Amogelang R. , Alcock Brian P. , McArthur Andrew G. , Langelier Charles R. 
Published: April 2024

AbstractAntimicrobial resistant (AMR) pathogens represent urgent threats to human health, and their surveillance is of paramount importance. Metagenomic next generation sequencing (mNGS) has revolutionized such efforts, but remains challenging due to the lack of open-access bioinformatics tools capable of simultaneously analyzing both microbial and AMR gene sequences. To address this need, we developed the Chan Zuckerberg ID (CZ ID) AMR module, an open-access, cloud-based workflow designed to integrate detection of both microbes and AMR genes in mNGS and whole-genome sequencing (WGS) data. It leverages the Comprehensive Antibiotic Resistance Database and associated Resistance Gene Identifier software, and works synergistically with the CZ ID short-read mNGS module to enable broad detection of both microbes and AMR genes. We highlight diverse applications of the AMR module through analysis of both publicly available and newly generated mNGS and WGS data from four clinical cohort studies and an environmental surveillance project. Through genomic investigations of bacterial sepsis and pneumonia cases, hospital outbreaks, and wastewater surveillance data, we gain a deeper understanding of infectious agents and their resistomes, highlighting the value of integrating microbial identification and AMR profiling for both research and public health. We leverage additional functionalities of the CZ ID mNGS platform to couple resistome profiling with the assessment of phylogenetic relationships between nosocomial pathogens, and further demonstrate the potential to capture the longitudinal dynamics of pathogen and AMR genes in hospital acquired bacterial infections. In sum, the new AMR module advances the capabilities of the open-access CZ ID microbial bioinformatics platform by integrating pathogen detection and AMR profiling from mNGS and WGS data. Its development represents a critical step toward democratizing pathogen genomic analysis and supporting collaborative efforts to combat the growing threat of AMR.
Affective Symptoms in Pregnancy are Associated with the Vaginal Microbiome
Authors: Scheible Kristin , Beblavy Robert , Sohn Michael B. , Qui Xing , Gill Ann L. , Narvaez-Miranda Janiret , Brunner Jessica , Miller Richard K. , Barrett Emily S. , O’Connor Tom G. , Gill Steven R. 
Published: April 2024

ABSTRACTComposition of the vaginal microbiome in pregnancy is associated with adverse maternal, obstetric, and child health outcomes. Identifying the sources of individual differences in the vaginal microbiome is therefore of considerable clinical and public health interest. The current study tested the hypothesis that vaginal microbiome composition during pregnancy is associated with an individual’s experience of affective symptoms and stress exposure. Data were based on a prospective longitudinal study of a diverse and medically healthy community sample of 275 mother-infant pairs. Affective symptoms and stress exposure and select measures of associated biomarkers (diurnal salivary cortisol, serum measures of sex hormones) were collected at each trimester; self-report, clinical, and medical records were used to collect detailed data on socio-demographic factors and health behavior, including diet and sleep. Vaginal microbiome samples were collected in the third trimester (34-40 weeks) and characterized by 16S rRNA sequencing. Identified taxa were clustered into three community state types (CST1-3) based on dissimilarity of vaginal microbiota composition. Results indicate that depressive symptoms during pregnancy were reliably associated with individual taxa and CST3 in the third trimester. Prediction of functional potential from 16S taxonomy revealed a differential abundance of metabolic pathways in CST1-3 and individual taxa, including biosynthetic pathways for the neuroactive metabolites, serotonin and dopamine. With the exception of bioavailable testosterone, no significant associations were found between symptoms- and stress-related biomarkers and CSTs. Our results provide further evidence of how prenatal psychological distress during pregnancy alters the maternal-fetal microbiome ecosystem that may be important for understanding maternal and child health outcomes.ImportancePrenatal affective symptoms and stress are associated with maternal, obstetric, and child health outcomes, but the mechanisms underlying these links and their application to intervention remain unclear. The findings from this investigation extend prior microbiome-oriented research by demonstrating that the maternal vaginal microbiome composition has a biologically plausible mechanistic link with affective symptoms that also suggest additional clinical applications for assessment and intervention.
Chk2 homologue Mek1 limits Exo1-dependent DNA end resection during meiotic recombination inS. cerevisiae
Authors: Grubb Jennifer , Bishop Douglas K. 
Published: April 2024

AbstractThe conserved Rad2/XPG family 5’—3’ exonuclease, Exonuclease 1 (Exo1), plays many roles in DNA metabolism including during resolution of DNA double strand breaks (DSBs) via homologous recombination. Prior studies provided evidence that the end-resection activity of Exo1 is downregulated in yeast and mammals by Cdk1/2 family cyclin-dependent and checkpoint kinases, including budding yeast kinase Rad53 which functions in mitotic cells. Here we provide evidence that the master meiotic kinase Mek1, a paralogue of Rad53, limits 5’-3’ single strand resection at the sites of programmed meiotic DNA breaks. Mutational analysis suggests that the mechanism of Exo1 suppression by Mek1 differs from that of Rad53.Article SummaryMeiotic recombination involves formation of programmed DNA double strand breaks followed by 5’ to 3’ single strand specific resection by nucleases including Exo1. We find that the activity of budding yeast Exo1 is downregulated during meiotic recombination by the master meiotic kinase Mek1. The mechanism of downregulation of Exo1 by Mek1 in meiosis does not depend on the same phospho-sites as those used by the mitotic kinase Rad53, a relative of Mek1 that downregulates Exo1 in mitosis.
Engineering inducible signaling receptors to enable erythropoietin-free erythropoiesis
Authors: Shah Aadit P. , Majeti Kiran R. , Ekman Freja K. , Selvaraj Sridhar , Soupene Eric , Chati Prathamesh , Sinha Roshani , Luna Sofia E. , Charlesworth Carsten T. , McCreary Travis , Lesch Benjamin J. , Tran Tammy , Sharma Devesh , Chu Simon N. , Porteus Matthew H. , Cromer M. Kyle 
Published: April 2024

AbstractBlood transfusion plays a vital role in modern medicine. However, availability is contingent on donated blood, and frequent shortages pose a significant healthcare challenge.Ex vivomanufacturing of red blood cells (RBCs) derived from universal donor O-negative pluripotent stem cells emerges as a solution, yet the high cost of recombinant cytokines required forex vivoerythroid differentiation remains a major barrier. Erythropoietin (EPO) signaling through the EPO receptor is indispensable to RBC development, and EPO is one of the most expensive components in erythroid-promoting media. Here, we used design-build-test cycles to develop highly optimized small molecule-inducible EPO receptors (iEPORs) which were integrated at a variety of genomic loci using homology-directed repair genome editing. We found that integration of iEPOR at the endogenousEPORlocus in an induced pluripotent stem cell producer line enabled culture with small molecule to yield equivalent erythroid differentiation, transcriptomic changes, and hemoglobin production compared to cells cultured with EPO. Due to the dramatically lower cost of small molecules vs. recombinant cytokines, these efforts eliminate one of the most expensive elements ofex vivoculture media—EPO cytokine. Because dependence on cytokines is a common barrier toex vivocell production, these strategies could improve scalable manufacturing of a wide variety of clinically relevant cell types. More broadly, this work showcases how synthetic biology and genome editing may be combined to introduce precisely regulated and tunable behavior into cells, an advancement which will pave the way for increasingly sophisticated cell engineering strategies.
Neural correlates of flexible sound perception in the auditory midbrain and thalamus
Authors: Ying Rose , Stolzberg Daniel J. , Caras Melissa L. 
Published: April 2024

AbstractHearing is an active process in which listeners must detect and identify sounds, segregate and discriminate stimulus features, and extract their behavioral relevance. Adaptive changes in sound detection can emerge rapidly, during sudden shifts in acoustic or environmental context, or more slowly as a result of practice. Although we know that context- and learning-dependent changes in the spectral and temporal sensitivity of auditory cortical neurons support many aspects of flexible listening, the contribution of subcortical auditory regions to this process is less understood. Here, we recorded single- and multi-unit activity from the central nucleus of the inferior colliculus (ICC) and the ventral subdivision of the medial geniculate nucleus (MGV) of Mongolian gerbils under two different behavioral contexts: as animals performed an amplitude modulation (AM) detection task and as they were passively exposed to AM sounds. Using a signal detection framework to estimate neurometric sensitivity, we found that neural thresholds in both regions improved during task performance, and this improvement was driven by changes in firing rate rather than phase locking. We also found that ICC and MGV neurometric thresholds improved and correlated with behavioral performance as animals learn to detect small AM depths during a multi-day perceptual training paradigm. Finally, we reveal that in the MGV, but not the ICC, context-dependent enhancements in AM sensitivity grow stronger during perceptual training, mirroring prior observations in the auditory cortex. Together, our results suggest that the auditory midbrain and thalamus contribute to flexible sound processing and perception over rapid and slow timescales.Significance statementWhat a listener hears depends on several factors, such as whether the listener is attentive or distracted, and whether the sound is meaningful or irrelevant. Practice can also shape hearing by improving the detection of particular sound features, as occurs during language or musical learning. Understanding how changes in sound perception are implemented in the brain is important for developing strategies to optimize healthy hearing, and for treating disorders in which these processes go awry. We report that neurons in auditory midbrain and thalamus exhibit rapid shifts in sound sensitivity that depend on the sound’s behavioral relevance, and slower improvements that emerge over several days of training. Our results suggest that subcortical areas make an important contribution to flexible hearing.
UK BioCoin: Swift Trait-Specific Summary Statistics Regression for UK Biobank
Authors: He Jing-Cheng , Qi Guo-An , Ying Jiacheng , Qian Yu , Han Lide , Mao Yingying , Zheng Hou-Feng , Jiang Hangjin , Chen Guo-Bo 
Published: April 2024

AbstractSummary statistics derived from large-scale biobanks facilitate the sharing of genetic discoveries while minimizing the risk of compromising individual-level data privacy. However, these summary statistics, such as those from the UK Biobank (UKB) provided by Neale’s lab, are often adjusted by a fixed set of covariates to all traits (12 covariates including 10 PCs, sex and age), preventing the exploration of trait-specific summary statistics. In this study, we present a novel computational device UK BioCoin (UKC), which is designed to provide an efficient framework for trait-specific adjustment for covariates. Without requiring access to individual-level data from UKB, UKC leverages summary statistics regression technique and resources from UKB (289 GB of 199 phenotypes and 10 million SNPs), to enable the generation of GWAS summary statistics adjusted by user-specified covariates. Through a comprehensive analysis of height under trait-specific adjustments, we demonstrate that the GWAS summary statistics generated by UKC closely mirror those generated from individual-level UKB GWAS (ρ ≥0.99 for effect sizes andρ ≥0.99 forp-values). Furthermore, we demonstrate the results for GWAS, SNP-heritability estimation, polygenic score, and Mendelian randomization, after various trait-specific covariate adjustments as allowed by UKC, indicating UKC a platform that harnesses in-depth exploration for researchers lacking access to UKB. The whole framework of UKC is portable for other biobank, as demonstrated in Westlake Biobank, which can equivalently be converted to a ‘UKC-like” platform and promote data sharing. UKC has its computational engine fully optimized, and the computational efficiency of UKC is about 70 times faster than that of UKB. We package UKC as a Docker image of 20 GB (https://github.com/Ttttt47/UKBioCoin), which can be easily deployed on an average computer (e.g. laptop).One sentence summaryWe develop UK BioCoin (UKC), which allows fine-tuning of covariates for each UK Biobank trait but does not relay on UK Biobank individual-level data. It will change the current landscape of GWAS and reshape its downstream analyses.
Metabolically intact nuclei are fluidized by the activity of the chromatin remodeling motor BRG1
Authors: Byfield Fitzroy J. , Eftekhari Behnaz , Kaymak-Loveless Kaeli , Mandal Kalpana , Li David , Wells Rebecca G. , Chen Wenjun , Brujic Jasna , Bergamaschi Guilia , Wuite Gijs J.L. , Patteson Alison E. , Janmey Paul A. 
Published: April 2024

AbstractThe structure and dynamics of the cell nucleus regulate nearly every facet of the cell. Changes in nuclear shape limit cell motility and gene expression. Although the nucleus is generally seen as the stiffest organelle in the cell, cells can nevertheless deform the nucleus to large strains by small mechanical stresses. Here, we show that the mechanical response of the cell nucleus exhibits active fluidization that is driven by the BRG 1 motor of the SWI/SNF/BAF chromatin-remodeling complex. Atomic force microscopy measurements show that the nucleus alters stiffness in response to the cell substrate stiffness, which is retained after the nucleus is isolated and that the work of nuclear compression is mostly dissipated rather than elastically stored. Inhibiting BRG 1 stiffens the nucleus and eliminates dissipation and nuclear remodeling both in isolated nuclei and in intact cells. These findings demonstrate a novel link between nuclear motor activity and global nuclear mechanics.