bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polygenic score informed by genome-wide association studies of multiple ancestries and related traits improves risk prediction for coronary artery disease
Authors: Patel Aniruddh P. , Wang Minxian , Ruan Yunfeng , Koyama Satoshi , Clarke Shoa L. , Yang Xiong , Tcheandjieu Catherine , Agrawal Saaket , Fahed Akl C. , Ellinor Patrick T. ,   Genes & Health Research Team,   the Million Veteran Program, Tsao Phillip S. , Sun Yan V. , Cho Kelly , Wilson Peter W. F. , Assimes Themistocles L. , van Heel David A. , Butterworth Adam S. , Aragam Krishna G. , Natarajan Pradeep , Khera Amit V. 
Published: March 2023

AbstractAccurate stratification of coronary artery disease (CAD) risk remains a critical need. A new polygenic score (GPSMult) incorporates CAD genome-wide association data across five ancestries (>269,000 cases, >1,178,000 controls) with genetic association data for ten CAD risk factors. GPSMultassociates with an OR/SD 2.14, (95%CI:2.10-2.19,P<0.001) for prevalent CAD and HR/SD 1.73 (95%CI 1.70-1.76,P<0.001) for incident CAD. When compared with the previously published GPS2018in external datasets, GPSMultdemonstrated 73%, 46%, and 113% increase in effect size for individuals of African, European, and South Asian ancestry, respectively, and significantly outperformed recently published CAD polygenic scores. GPSMultidentifies individuals with CAD risk extremes, including the top 3% of the population at equivalent risk for a new CAD event as those with prior CAD having a second event. Integrating GPSMultwith the Pooled Cohort Equations results in 7.0% [95%CI:5.9%-8.2%,P<0.001] net reclassification improvement at the 7.5% threshold. Large-scale integration genetic association data for CAD and related traits from diverse populations meaningfully improves polygenic risk prediction.
RNA Polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation
Authors: Martell Danya J. , Merens Hope E. , Fiorini Claudia , Caulier Alexis , Ulirsch Jacob C. , Ietswaart Robert , Choquet Karine , Graziadei Giovanna , Brancaleoni Valentina , Domenica Cappellini Maria , Scott Caroline , Roberts Nigel , Proven Melanie , Roy Noémi BA , Babbs Christian , Higgs Douglas R. , Sankaran Vijay G. , Churchman L. Stirling 
Published: March 2023

SummaryThe controlled release of promoter-proximal paused RNA polymerase II (Pol II) into productive elongation is a major step in gene regulation. However, functional analysis of Pol II pausing is difficult because factors that regulate pause release are almost all essential. In this study, we identified heterozygous loss-of-function mutations inSUPT5H, which encodes SPT5, in individuals with β-thalassemia unlinked toHBBmutations. During erythropoiesis in healthy human cells, cell cycle genes were highly paused at the transition from progenitors to precursors. When the pathogenic mutations were recapitulated bySUPT5Hediting, Pol II pause release was globally disrupted, and the transition from progenitors to precursors was delayed, marked by a transient lag in erythroid-specific gene expression and cell cycle kinetics. Despite this delay, cells terminally differentiate, and cell cycle phase distributions normalize. Therefore, hindering pause release perturbs proliferation and differentiation dynamics at a key transition during erythropoiesis, revealing a role for Pol II pausing in the temporal coordination between the cell cycle and differentiation.
Electron microscopic analysis of the influence of iPSC-derived motor neurons on bioengineered human skeletal muscle tissues
Authors: Nguyen Christine T. , Chávez-Madero Carolina , Jacques Erik , Musgrave Brennen , Yin Ting , Saraci Kejzi , Gilbert Penney M. , Stewart Bryan A. 
Published: March 2023

Abstract3D bioengineered skeletal muscle macrotissues are increasingly important for studies of cell biology and development of therapeutics. Tissues derived from immortalized cells obtained from patient samples or from stem cells can be co-cultured with motor-neurons to create models of human neuromuscular junctions in culture. In this study, we present foundational work on 3D cultured muscle ultrastructure, with and without motor neurons, which is enabled by the development of a new co-culture platform. Our results show that tissues from Duchenne muscular dystrophy patients are poorly organized compared to tissues grown from healthy donor and that the presence of motor neurons invariably improves sarcomere organization. Electron micrographs show that in the presence of motor neurons, filament directionality, banding patterns, z-disc continuity and appearance of presumptive SSR and T-tubule profiles all improve in healthy, DMD and iPSC derived muscle tissue. Further work to identify the underlying defects of DMD tissue disorganization and the trophic mechanisms by which motor neurons support muscle are likely to yield potential new therapeutic approaches for treating patients suffering from Duchenne muscular dystrophy.
The geometry of appetitive-aversive value representations in medial prefrontal networks
Authors: Winke Nanci , Herry Cyril , Jercog Daniel 
Published: March 2023

AbstractThe value of rewards and punishments – namely, how good or bad they are perceived – guides approach or avoidance behaviors. Valence refers to the negative or positive “sign” of the state elicited by an event, whereas salience refers to the amount of attention an event attracts, disregarding its valence. While identifying these signals conveys critical information for understanding circuits involved in emotional processing, they are often confounded due to their underlying correlation. Moreover, whereas the study of the neural basis of value coding has been intensively investigated in the appetitive domain, the neural substrates for how aversive values are established for different threat intensities and guide defensive behavior have yet to be discovered. The dorsomedial prefrontal cortex (dmPFC) is a key region in the control of defensive actions, although how different aversive values are encoded at the neuronal level within this region and drive defensive behaviors remains unknown.Here, we developed an instrumental approach/avoidance task in mice that, by matching motivational salience levels elicited by cues predicting rewards or punishments, allows univocally disentangling the presence of either salience, valence, or value coding from brain signals. We performed freely moving large neuronal population calcium imaging in the dmPFC of mice performing our task, conducting appetitive/aversive outcome devaluation/revaluation behavioral tests. We found that, while a similar fraction of single neurons decoded valence and value information, and only a minor fraction decoded salience, value coding was observed at the neuronal population level. Moreover, different value representations of the same valence lay within similar subspaces of the neural state space while values of opposed valence were encoded in orthogonal subspaces, unveiling how the brain stores associative appetitive and aversive information in medial prefrontal networks.
Efficiency Estimates for Electromicrobial Production of Branched-chain Hydrocarbons
Authors: Sheppard Timothy J. , Specht David A. , Barstow Buz 
Published: March 2023

AbstractElectromicrobial production is a process where microorganisms use electricity as a charge and energy source for the production of complex molecules, often from starting compounds as simple as CO2. The aviation industry is in need for sustainable fuel alternatives that can meet their requirements of high-altitude performance while also meeting 21stcentury carbon emissions standards. The electromicrobial production of jet fuel components with CO2-derived carbon provides a unique opportunity to generate jet fuel blends that are compatible with modern engines with net-neutral carbon emissions. In this study, we analyze the pathways necessary to generate single- and multi-branched-chain hydrocarbonsin vivoutilizing both extracellular electron uptake (EEU) and H2-oxidation as methods for electron delivery, the Calvin cycle for CO2-fixation and the ADO decarboxylation pathway. We find the maximum electrical-to-fuel energy conversion efficiencies for single- and multi-branched chain hydrocarbons areand. Utilizing this information, as well as previously collected predictions on straight-chain alkane and terpenoid biosynthesis, we calculate the efficiency of electromicrobial production of jet fuel blends containing straight-chain, branched-chain, and terpenoid components. Increasing the fraction of branched-chain alkanes in the blend from zero to 47% only lowers the electrical energy conversion efficiency fromto.
A nucleosome switch primes Hepatitis B Virus infection
Authors: Prescott Nicholas A. , Mansisidor Andrés , Bram Yaron , Biaco Tracy , Rendleman Justin , Faulkner Sarah C. , Lemmon Abigail A. , Lim Christine , Hamard Pierre-Jacques , Koche Richard P. , Risca Viviana I. , Schwartz Robert E. , David Yael 
Published: March 2023

SummaryChronic hepatitis B virus (HBV) infection is an incurable global health threat responsible for causing liver disease and hepatocellular carcinoma. During the genesis of infection, HBV establishes an independent minichromosome consisting of the viral covalently closed circular DNA (cccDNA) genome and host histones. The viral X gene must be expressed immediately upon infection to induce degradation of the host silencing factor, Smc5/6. However, the relationship between cccDNA chromatinization and X gene transcription remains poorly understood. Establishing a reconstituted viral minichromosome platform, we found that nucleosome occupancy in cccDNA drives X transcription. We corroborated these findings in cells and further showed that the chromatin destabilizing molecule CBL137 inhibits X transcription and HBV infection in hepatocytes. Our results shed light on a long-standing paradox and represent a potential new therapeutic avenue for the treatment of chronic HBV infection.
A proximity-dependent biotinylation map of cytosol-facing organelle outer membrane proteome in living Arabidopsis cells
Authors: Bao Xinyue , Jia Huifang , Zhang Xiaoyan , Zhao Yanming , Li Xiangyun , Lin Ping , Ma Chongyang , Wang Pengcheng , Song Chun-Peng , Zhu Xiaohong 
Published: March 2023

AbstractThe cytosol-facing outer membrane (OM) of organelles communicates with other cellular compartments to exchange proteins, metabolites and signaling molecules. Cellular surveillance systems also target OM-resident proteins to control organellar homeostasis and ensure cell survival under stress. Using traditional approaches to discover OM proteins and identify their dynamically interacting partners remains challenging. In this study, we developed an OM proximity labeling (OMPL) system using biotin ligase-mediated proximity biotinylation to map the proximity proteome of the OMs of mitochondria, chloroplasts, and peroxisomes in living Arabidopsis (Arabidopsis thaliana) cells. We demonstrate the power of this system with the discovery of cytosolic factors and OM receptor candidates involved in local protein translation and translocation, membrane contact sites, and organelle quality control. This system also performed admirably for the rapid isolation of intact mitochondria and peroxisomes. Our data support the notion that TOM20-3 is a candidate for both a mitochondrial and a chloroplast receptor, and that PEX11D is a candidate for a peroxisome receptor for the coupling of protein translation and import. OMPL-generated OM proximity proteomes are valuable sources of candidates for functional validation and suggest directions for further investigation of important questions in cell biology.
Long-read sequence analysis of MMEJ-mediated CRISPR genome editing reveals complex on-target vector insertions that may escape standard PCR-based quality control
Authors: Higashitani Yuki , Horie Kyoji 
Published: March 2023

ABSTRACTCRISPR genome editing is a powerful tool for elucidating biological functions. To modify the genome as intended, it is essential to understand the various modes of recombination that can occur. In this study, we report unexpected complex vector insertions that were identified during the generation of conditional alleles by CRISPR editing using microhomology-mediated end joining (MMEJ). The targeting vector contained two loxP sequences and flanking 40-bp microhomologies. The genomic regions corresponding to the loxP sequences were cleaved with Cas9 in mouse embryonic stem cells. PCR screening for targeted recombination revealed a high frequency of bands of a larger size than expected. Nanopore sequencing of these bands revealed complex vector insertions mediated not only by MMEJ but also by non-homologous end joining and homologous recombination in at least 17% of the clones. A new band appeared upon improving the PCR conditions, suggesting the presence of unexpectedly modified alleles that escape standard PCR screening. This prompted us to characterize the recombination of each allele of the genome-edited clones using heterozygous single nucleotide polymorphisms, leading to confirmation of the presence of homozygous alleles. Our study indicates that careful quality control of genome-edited clones is needed to exclude complex, unexpected, on-target vector insertion.
PPP1R3B is a metabolic switch that shifts hepatic energy storage from lipid to glycogen
Authors: Creasy Kate Townsend , Mehta Minal B. , Park Joseph , Schneider Carolin V. , Shewale Swapnil V. , Millar John S. , Hand Nicholas J. , Baur Joseph A. , Rader Daniel J. 
Published: March 2023

SummaryObesity is a growing worldwide epidemic that carries numerous metabolic complications including increased risk of type 2 diabetes (T2D), cardiovascular disease (CVD), and non-alcoholic fatty liver disease (NAFLD). Multiple genome-wide association studies (GWAS) have associated thePPP1R3Blocus with cardiometabolic traits including fasting glucose and insulin levels (T2D traits), plasma lipids (CVD traits), and indications of hepatic steatosis and liver damage (NAFLD traits)1–5. ThePPP1R3Bgene encodes the glycogen regulatory protein PPP1R3B (also known as GL) which has an established role in liver glycogen metabolism and plasma glucose homeostasis6,7. The metabolic and NAFLD GWAS single nucleotide polymorphisms (SNPs) in this region, which are all in high linkage disequilibrium, result in increased liverPPP1R3Bexpression and hepatic glycogen accumulation, but have provided conflicting results on the impacts on hepatic steatosis and liver damage. Here we investigate the consequences of bothPpp1r3boverexpression and deletion in mouse and cell models and find that dysregulatedPpp1r3bexpression in either direction promotes metabolic dysfunction and liver injury. Hepatocyte overexpression ofPpp1r3bincreases hepatic glycogen storage, prolongs fasting blood glucose levels, and confers protection from hepatic steatosis, but increases plasma ALT in aged animals. Conversely, deletion of hepatocytePpp1r3beliminates hepatic glycogen, causes impaired glucose disposal, and results in hepatic steatosis with age or high sucrose diet. We investigated the metabolic pathways contributing to steatosis and found thatPpp1r3bdeletion and diminished glycogenesis diverts the storage of exogenous glucose to hepatic triglycerides (TG), and stored liver lipids are preferentially used for energy during fasting through lipid oxidation and ketogenesis. Further, we interrogated two large human biobank cohorts and found carriers of SNPs associated with increasedPPP1R3Bexpression have increased plasma glucose, decreased hepatic fat, and lower plasma lipids, while putative loss-of-function (pLoF) variant carriers have increased hepatic fat and elevated plasma ketones and lipids, consistent with the results seen in our mouse models. These findings suggest hepatic PPP1R3B serves as a metabolic switch favoring hepatic energy storage as glycogen instead of TG.
Mutant huntingtin expression in the hypothalamus promotes ventral striatal neuropathology
Authors: Soylu-Kucharz Rana , Adlesic Natalie , Davidsson Marcus , Björklund Tomas , Björkqvist Maria , Petersén Åsa 
Published: March 2023

AbstractHuntington’s disease is a fatal neurodegenerative disorder caused by an expanded CAG triplet repeat in the huntingtin (HTT) gene. Previous research focused on neuropathology in the striatum and its association with a typical movement disorder. Direct effects of mutant HTT (mHTT) in the striatum may cause neuropathology, although non-cell autonomous effects have also been suggested. Important non-motor features of HD include psychiatric symptoms and metabolic dysfunction, which may be linked to hypothalamic neuropathology. As hypothalamic neurons project to the ventral striatum, we hypothesized that expression of mHTT in the hypothalamus leads to disrupted neurotransmission in the ventral striatum and causes pathology. The overall aim of this study was to investigate the impact of mHTT expression in the hypothalamus on ventral striatal neuropathology and its contribution to non-HD motor symptoms. We demonstrate that selective expression of mHTT in the hypothalamus leads to the loss of dopamine and cAMP-regulated phosphoprotein (DARPP-32) immunopositive neurons in the ventral striatum in mice. Contrary to the effects of direct expression of mHTT in the hypothalamus, selective overexpression of mHTT in the ventral striatum does not affect body weight. Selective expression of mHTT in the ventral striatum leads to mHTT inclusion formation and loss of DARPP-32 neurons without affecting motor activity or anxiety-like behavior. We show that DARPP-32 neuron loss in the ventral striatum is recapitulated in the R6/2 mouse model of HD. Chemogenetic activation of hypothalamic neurons projecting to the ventral striatum had a blunted response in the R6/2 mice compared to wild-type mice, indicating a disrupted hypothalamus-ventral striatal circuitry. In summary, the expression of mHTT in the hypothalamus may impact the development of ventral striatal pathology in mice. This opens the possibility that non-cell-autonomous effects in the reward circuitry play a role in HD.
The Golgi checkpoint: Golgi unlinking during G2 is required for correct spindle formation and cytokinesis
Authors: Mascanzoni Fabiola , Ayala Inmaculada , Iannitti Roberta , Luini Alberto , Colanzi Antonino 
Published: March 2023

AbstractThe decision to enter mitosis requires not only the control of DNA replication but also additional and crucial preparatory steps such as, for example, partial disassembly of the Golgi complex during G2. The Golgi complex is fundamental for the processing and sorting of proteins and lipids in the secretory pathway. It is organized as stacks of cisternae laterally connected by tubules to form a continuous Golgi ribbon. During G2, the Golgi ribbon is unlinked into isolated stacks in preparation for cell division. This structural reorganization is necessary for entry into mitosis, indicating that a “Golgi mitotic checkpoint” controls the correct segregation of this organelle. To understand the physiological significance of the pre-mitotic Golgi unlinking, we devised a strategy to accumulate cells in G2 with an intact Golgi ribbon and then induce entry into mitosis. Here, we show that forcing the entry of cells into mitosis with an intact Golgi ribbon causes remarkable cell division defects, including spindle multipolarity and binucleation, favoring cell transformation. We also find that the cells entering mitosis with an intact Golgi ribbon show reduced levels at the centrosome of the kinase Aurora-A, a pivotal regulator of spindle formation. Overexpression of Aurora-A rescues spindle formation, indicating that the Golgi-dependent Aurora-A recruitment has a crucial role in spindle formation. Thus, our results show that alterations of the pre-mitotic Golgi segregation have profound consequences on the fidelity of the mitotic process, representing potential risk factors for cell transformation and cancer development.
Prediction of SARS-CoV-2 transmission dynamics based on population-level cycle threshold values: A Machine Learning and mechanistic modeling study
Authors: Khan Afraz A. , Sbihi Hind , Irvine Michael A. , Jassem Agatha N. , Joffres Yayuk , Klaver Braeden , Janjua Naveed , Bharmal Aamir , Ng Carmen H. , Wilmer Amanda , Galbraith John , Romney Marc G. , Henry Bonnie , Hoang Linda M. N. , Krajden Mel , Hogan Catherine A. 
Published: March 2023

AbstractBackgroundPolymerase chain reaction (PCR) cycle threshold (Ct) values can be used to estimate the viral burden of Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV-2) and predict population-level epidemic trends. We investigated the use of machine learning (ML) and epidemic transmission modeling based on Ct value distribution for SARS-CoV-2 incidence prediction during an Omicron-predominant period.MethodsUsing simulated data, we developed a ML model to predict the reproductive number based on Ct value distribution, and validated it on out-of-sample province-level data. We also developed an epidemiological model and fitted it to province-level data to accurately predict incidence.ResultsBased on simulated data, the ML model predicted the reproductive number with highest performance on out-of-sample province-level data. The epidemiological model was validated on outbreak data, and fitted to province-level data, and accurately predicted incidence.ConclusionsThese modeling approaches can complement traditional surveillance, especially when diagnostic testing practices change over time. The models can be tailored to different epidemiological settings and used in real time to guide public health interventions.FundingThis work was supported by funding from Genome BC, Michael Smith Foundation for Health Research and British Columbia Centre for Disease Control Foundation to C.A.H. This work was also funded by the Public Health Agency of Canada COVID-19 Immunity Task Force COVID-19 Hot Spots Competition Grant (2021-HQ-000120) to M.G.R.
The commensal protistTritrichomonas musculusexhibits a dynamic life cycle that induces extensive remodeling of the gut microbiota
Authors: Popovic Ana , Cao Eric Yixiao , Han Joanna , Nursimulu Nirvana , Alves-Ferreira Eliza V.C. , Burrows Kyle , Kennard Andrea , Alsmadi Noor , Grigg Michael E. , Mortha Arthur , Parkinson John 
Published: March 2023

AbstractCommensal protists and gut bacterial communities exhibit complex relationships, mediated at least in part through host immunity. To improve our understanding of this tripartite interplay, we investigated community and functional dynamics between the murine protistTritrichomonas musculus(T. mu) and intestinal bacteria in healthy and B cell-deficient mice. We identified dramatic, protist-driven remodeling of resident microbiome growth and activities, in parallel withT. mufunctional changes, accelerated in the absence of B cells. Metatranscriptomic data revealed nutrient-based competition between bacteria and the protist. Single cell transcriptomics identified distinctT. mulife stages, providing new evidence for trichomonad sexual replication and the formation of pseudocysts. Unique cell states were validatedin situthrough microscopy and flow cytometry. Our results reveal complex microbial dynamics during the establishment of a commensal protist in the gut, and provide valuable datasets to drive future mechanistic studies.