bluuebunny/crossref_metadata_2025_split huggingface dataset:
Grapevine bacterial communities across the Central Valley of California
Authors: Swift Joel F. , Migicovsky Zoë , Trello Grace E. , Miller Allison J. 
Published: July 2023

AbstractPlant organs (compartments) host distinct microbiota which shift in response to variation in both development and climate. Grapevines are woody perennial crops that are clonally propagated and cultivated across vast geographic areas, and as such, their microbial communities may also reflect site-specific influences. These site-specific influences, and the microbial differences across site compose ‘terroir’, the environmental influence on wine produced in a given region. Commercial grapevines are typically composed of a genetically distinct root (rootstock) grafted to a shoot system (scion) which adds an additional layer of complexity. In order to understand spatial and temporal patterns of bacterial diversity in grafted grapevines, we used 16S rRNA metabarcoding to quantify soil and compartment microbiota (berries, leaves, and roots) for grafted grapevines in commercial vineyards across three counties in the Central Valley of California over two successive growing seasons. Community composition revealed compartment-specific dynamics. Roots assembled site-specific bacterial communities that reflect rootstock genotype and environment influences, whereas bacterial communities of leaves and berries displayed associations with time. These results provide further evidence of a microbial terroir within the grapevine root systems but also reveal that the microbiota of above-ground compartments are only weakly associated with the local microbiome in the Central Valley of California.
A familial missense variant in the Alzheimer’s Disease geneSORL1impairs its maturation and endosomal sorting
Authors: Fazeli Elnaz , Child Daniel D. , Bucks Stephanie A. , Stovarsky Miki , Edwards Gabrielle , Rose Shannon E. , Yu Chang-En , Latimer Caitlin , Kitago Yu , Bird Thomas , Jayadev Suman , Andersen Olav M. , Young Jessica E. 
Published: July 2023

AbstractTheSORL1gene has recently emerged as a strong Alzheimer’s Disease (AD) risk gene. Over 500 different variants have been identified in the gene and the contribution of individual variants to AD development and progression is still largely unknown. Here, we describe a family consisting of 2 parents and 5 offspring. Both parents were affected with dementia and one had confirmed AD pathology with an age of onset >75 years. All offspring were affected with AD with ages at onset ranging from 53yrs-74yrs. DNA was available from the parent with confirmed AD and 5 offspring. We identified a coding variant, p.(Arg953Cys), inSORL1in 5 of 6 individuals affected by AD. Notably, variant carriers had severe AD pathology, and theSORL1variant segregated with TDP-43 pathology (LATE-NC). We further characterized this variant and show that this Arginine substitution occurs at a critical position in the YWTD-domain of theSORL1translation product, SORL1. Functional studies further show that the p.R953C variant leads to retention of the SORL1 protein in the endoplasmic reticulum which leads to decreased maturation and shedding of the receptor and prevents its normal endosomal trafficking. Together, our analysis suggests that p.R953C is a pathogenic variant ofSORL1and sheds light on mechanisms of how missenseSORL1variants may lead to AD.
Blood prognostic biomarker signatures for hemorrhagic cerebral cavernous malformations (CCMs)
Authors: Croft Jacob , Grajeda Brian , Abou-Fadel Johnathan S , Ellis Cameron C , Igor Estevao , Almeida Igor C. , Zhang Jun 
Published: July 2023

AbstractBackgroundCerebral cavernous malformations (CCMs) is a neurological disorder that causes enlarged intracranial capillaries in the brain, leading to an increased risk of hemorrhagic strokes, which is a leading cause of death and disability worldwide.ObjectivesThe current treatment options for CCMs are limited, highlighting the need for prognostic biomarkers to predict the risk of hemorrhagic events to better inform treatment decisions and identify future pharmacological targets.Eligibility CriteriaThe study is centered on a comparative proteomic analysis between hemorrhagic CCMs (HCs) and healthy controls, while excluding patients with non-hemorrhagic CCMs (NHCs) from the analysis due to the experimental design.Sources of EvidenceRecent research has identified several serum biomarkers and blood circulating biomarkers in a selected cohort of homogeneous CCM patients and animal models.MethodProteomic profiles from both human and mouse CCM models were examined, and pathway enrichment analyses were performed using three approaches (GO, KEGG, and DOSE). To account for multiple comparisons, t-tests were employed to evaluate differences. A p-value below 0.05 was deemed statistically significant.ResultsThe authors have developed the first panel of candidate biomarker signatures, featuring both etiological and prognostic markers in two distinct pathways. This panel of biomarker signatures demonstrates a robust correlation with the likelihood of hemorrhagic CCMs.ConclusionsThis groundbreaking biomarker panel paves the way for further investigation of potential blood biomarkers to determine the risk of hemorrhagic CCMs.
Strain-release alkylation of Asp12 enables mutant selective GTP-state targeting of K-Ras(G12D)
Authors: Zheng Qinheng , Zhang Ziyang , Guiley Keelan G. , Shokat Kevan M. 
Published: July 2023

AbstractK-Ras is the most commonly mutated oncogene in human cancer, yet direct small-molecule targeting of K-Ras mutants has been mostly unsuccessful until recently. The discovery of an allosteric pocket under Switch-II with covalent cysteine-crosslinking molecules has allowed for the development of targeted therapies that selectively engage the highly reactive acquired cysteine in the K-Ras(G12C) mutation without affecting the wild-type protein. Sotorasib and adagrasib, two advanced Switch-II Pocket inhibitors, have received FDA approval to treat K-Ras(G12C)-driven non-small cell lung cancer. However, the most frequent K-Ras mutation G12D particularly prevalent in pancreatic ductal adenocarcinoma has remained untargetable with covalent drugs due to the poor nucleophilicity of the somatic aspartate residue. Here we present a set of malolactone-based electrophiles which exploit ring strain to crosslink K-Ras(G12D) at the mutant aspartate to form stable covalent complexes. Structural insights from x-ray crystallography and exploitation of the stereoelectronic requirements for attack of the electrophile allowed development of a substituted malolactone which resisted attack by aqueous buffer but rapidly crosslink with the aspartate-12 of K-Ras in both GDP- and GTP-state. The signaling-competent GTP-state targeting allowed effective suppression of downstream signaling and proliferation of cancer cells harboring K-Ras(G12D) mutation, and tumor growth of cell line-derive xenograft in mice. Our results demonstrate the rational design of covalent inhibitors to target a non-catalytic carboxylic acid side chain in K-Ras(G12D) which has resisted traditional drug discovery efforts.
Patterns of Rising HIV Positivity in Northern Madagascar: Evidence of an Urgent Public Health Concern
Authors: Robinson Kyle E. , Long Jackson K. , Fardine Mamantsara , Stephano Adriantiana M. , Grewal Eric P. 
Published: July 2023

ABSTRACTDespite over two decades of progress against HIV/AIDS in adjacent sub-Saharan Africa, HIV rates and deaths due to AIDS are exponentially rising in Madagascar. Furthermore, a growing body of evidence suggests that, due to a scarcity of general-population screening data, even the startling increase demonstrated by official models vastly underestimates the true population prevalence of HIV. Thus, we aimed to implement a real-world HIV screening and treatment protocol to serve a general population stemming from across Northern Madagascar. In collaboration with the Malagasy Ministry of Health, we provided point-of-care HIV screening and confirmatory testing for over 1,000 participants from 73 towns, villages, and cities recording an overall HIV prevalence of2.94%. Notably, we observed a13.1%HIV prevalence rate among urban populations and showed that proximity to a major route of travel was significantly associated with HIV risk. We also observed a link between HIV risk and various occupations, including those associated with increased mobility (such as mining). Importantly, all HIV-positive individuals were initiated on antiretroviral therapy in concordance with local health authorities. To our knowledge, this study marks the largest primary test data-based HIV study to date among Madagascar’s general population, showing a greatly higher HIV prevalence (3.0%) than previously reported modeling based figures (0.3%). Our rates aligned with the pattern of higher prevalence demonstrated in smaller general-population screening studies occuring more commonly prior to political strife in the mid-2000s. These findings demonstrate evidence of a growing HIV epidemic in Northern Madagascar and underscore the need for future investment into more comprehensive HIV screening and control initiatives in Madagascar.
Oculomotor analysis to assess brain health: preliminary findings from a longitudinal study of multiple sclerosis using novel tablet-based eye-tracking software
Authors: de Villers-Sidani Étienne , Voss Patrice , Bastien Natacha , Cisneros-Franco J. Miguel , Hussein Shamiza , Mayo Nancy E. , Koch Nils A. , Blanchette François , Guitton Daniel , Giacomini Paul S. 
Published: July 2023

AbstractA growing body of evidence supports the link between eye movement anomalies and brain health. Indeed, the oculomotor system is composed of a diverse network of cortical and subcortical structures and circuits that are susceptible to a variety of degenerative processes. Here we show preliminary findings from the baseline measurements of an ongoing longitudinal cohort study in MS participants, designed to determine if disease and cognitive status can be estimated and tracked with high accuracy based on eye movement parameters alone. Using a novel gaze-tracking technology that can reliably and accurately track eye movements with good precision without the need for infrared cameras, using only an iPad Pro embedded camera, we show that several eye movement parameters significantly correlated with clinical outcome measures of interest. Eye movement parameters were extracted from fixation, pro-saccade anti-saccade, and smooth pursuit visual tasks, whereas the clinical outcome measures were the scores of several disease assessment tools and standard cognitive tests such as the Expanded Disability Status Scale (EDSS), Brief International Cognitive Assessment for MS (BICAMS), the Multiple Sclerosis Functional Composite (MSFC) and the Symbol Digit Modalities Test (SDMT). Furthermore, multiple regression analyses show that a small set of oculomotor parameters can explain up to 74% of the variance of the clinical outcome measures. Taken together, these findings not only replicate previously known associations between eye movement parameters and clinical scores, this time using a novel mobile-based technology, but also the notion that interrogating the oculomotor system with a novel eye-tracking technology can inform us of disease severity and evolution, as well as the cognitive status of MS participants.
Dysregulation of N-terminal acetylation causes cardiac arrhythmia and cardiomyopathy
Authors: Yoshinaga Daisuke , Feng Rui , Prondzynski Maksymilian , Shani Kevin , Tharani Yashasvi , Milosh Joseph , Walker David , Carreon Chrystalle Katte , Boss Bridget , Upton Sheila , Parker Kevin Kit , Pu William T. , Bezzerides Vassilios J. 
Published: July 2023

ABSTRACTBACKGROUNDN-terminal-acetyltransferases catalyze N-terminal acetylation (Nt-acetylation), an evolutionarily conserved co-translational modification. Nt-acetylation regulates diverse signaling pathways, yet little is known about its effects in the heart. To gain insights, we studied NAA10-related syndrome, in which mutations in NAA10, which catalyzes Nt-acetylation, causes severe QT prolongation, hypotonia, and neurodevelopmental delay.METHODSWe identified a missense variant in NAA10 (c.10C>A; p.R4S) that segregated with severe QT prolongation, arrhythmia, cardiomyopathy, and sudden death in a large kindred. We developed patient-derived and genome-edited human induced pluripotent stem cell (iPSC) models and deeply phenotyped iPSC-derived cardiomyocytes (iPSC-CMs) to dissect the mechanisms underlying NAA10-mediated cardiomyocyte dysfunction.RESULTSThe NAA10-R4S mutation reduced enzymatic activity, decreased expression levels of NAA10/NAA15 proteins, and destabilized the NatA complex. In iPSC-CM models of NAA10 dysfunction, dysregulation of the late sodium and slow rectifying potassium currents caused severe repolarization abnormalities, consistent with clinical QT prolongation and increased risk for arrhythmogenesis. Engineered heart tissues generated from mutant NAA10 cell lines had significantly decreased contractile force and sarcomeric disorganization, consistent with the cardiomyopathic phenotype in the identified family members. Diastolic calcium levels were increased with corresponding alterations in calcium handling pathways. We identified small molecule and genetic therapies that reversed the effects of NAA10 dysregulation of iPSC-CMs.CONCLUSIONSOur study defines novel roles of Nt-acetylation in cardiac ion channel regulation and delineates mechanisms underlying QT prolongation, arrhythmia, and cardiomyopathy caused by NAA10 dysfunction.
Anti-manic effect of deep brain stimulation of the ventral tegmental area in an animal model of mania induced by methamphetamine
Authors: Varela Roger B. , Boschen Suelen L. , Yates Nathanael , Houghton Tristan , Blaha Charles D. , Lee Kendall H. , Bennet Kevin E. , Kouzani Abbas Z. , Berk Michael , Quevedo João , Valvassori Samira S. , Tye Susannah J. 
Published: July 2023

AbstractBackgroundTreatment of refractory bipolar disorder (BD) is extremely challenging. Deep brain stimulation (DBS) holds promise as an effective treatment intervention. However, we still understand very little about the mechanisms of DBS and its application on BD.AimThe present study aimed to investigate the behavioural and neurochemical effects of ventral tegmental area (VTA) DBS in an animal model of mania induced by methamphetamine (m-amph).MethodsWistar rats were given 14 days of mamph injections, in the last day animals were submitted to 20 minutes of VTA DBS in two different patterns: intermittent low frequency stimulation (LFS) or continuous high frequency stimulation (HFS). Immediately after DBS, manic-like behaviour and nucleus accumbens (NAc) phasic dopamine (DA) release were evaluated in different groups of animals through open-field test and fast-scan cyclic voltammetry. Levels of NAc dopaminergic markers were evaluated by immunohistochemistry.ResultsM-amph induced hyperlocomotion in the animals and both DBS parameters reversed this alteration. Mamph increased DA reuptake time post-sham compared to baseline levels, and both LFS and HFS were able to block this alteration. LFS was also able to reduce phasic DA release when compared to baseline. LFS was able to increase dopamine transporter (DAT) expression in the NAc.ConclusionThese results demonstrate that both VTA LFS and HFS DBS exert anti-manic effects and modulation of DA dynamics in the NAc. More specifically the increase in DA reuptake driven by increased DAT expression may serve as a potential mechanism by which VTA DBS exerts its anti-manic effects.
The NAD+Precursor Nicotinamide Riboside Rescues Mitochondrial Defects and Neuronal Loss in iPSC derived Cortical Organoid of Alpers’ Disease
Authors: Hong Yu , Zhang Zhuoyuan , Yangzom Tsering , Chen Anbin , Lundberg Bjørn Christian , Fang Evandro Fei , Sullivan Gareth John , Tzoulis Charalampos , Bindoff Laurence A. , Liang Kristina Xiao 
Published: July 2023

AbstractAlpers’ syndrome is an early-onset neurodegenerative disorder usually caused by biallelic pathogenic variants in the gene encoding the catalytic subunit of polymerase-gamma (POLG), which is essential for mitochondrial DNA (mtDNA) replication. The disease is progressive, incurable, and inevitably it leads to death from drug-resistant status epilepticus. The neurological features of Alpers’ syndrome are intractable epilepsy and developmental regression, with no effective treatment; the underlying mechanisms are still elusive, partially due to lack of good experimental models. Here, we generated the patient-derived induced pluripotent stem cells from one Alpers’ patient carrying the compound heterozygous mutations of A467T (c.1399G>A) and P589L (c.1766C>T), and further differentiated them into cortical organoids and neural stem cells (NSCs) for mechanistic studies of neural dysfunction in Alpers’ syndrome. Patient cortical organoids exhibited a phenotype that faithfully replicated the molecular changes found in patient postmortem brain tissue, as evidenced by cortical neuronal loss and depletion of mtDNA and complex I (CI). Patient NSCs showed mitochondrial dysfunction leading to ROS overproduction and downregulation of the NADH pathway. More importantly, the NAD+precursor nicotinamide riboside (NR) significantly ameliorated mitochondrial defects in patient brain organoids. Our findings demonstrate that the iPSC model and brain organoids are goodin vitromodels of Alpers’ disease; this first-in-its-kind stem cell platform for Alpers’ syndrome enables therapeutic exploration and has identified NR as a viable drug candidate for Alpers’ disease and, potentially, other mitochondrial diseases with similar causes.
Automated escape system: identifying prey’s kinematic and behavioral features critical for predator evasion
Authors: Sunami Nozomi , Kimura Hibiki , Ito Hidechika , Hashimoto Koichi , Sato Yuta , Tachibana Soki , Hidaka Mikiya , Miyama Kouki , Watanabe Hirofumi , Kawabata Yuuki 
Published: July 2023

AbstractIdentifying the kinematic and behavioral variables of prey that influence the evasion from predator attacks is essential not only for comprehending the determinants of successful predator evasion but also for shedding light on the evolution of specific traits and the dynamics of predator-prey relationships on a larger scale. However, quantifying the relationship between these variables and the success or failure of predator evasion is challenging, particularly for variables with small variations within prey species. One promising approach to address this challenge is the use of a simulated prey system, which allows us to manipulate the kinematic and behavioral features of prey and expose them to real predators. Nevertheless, creating a system that moves comparably to real prey animals remains difficult, especially for invertebrate and lower vertebrate species that respond quickly to predators and escape rapidly.In this study, we have developed an automated escape system that is comparable to real prey species, responding to a predator within tens of milliseconds and escaping at over 1.0 m/s. The system automatically detects an approaching predator and pulls the prey away from the predator once the predator reaches a predetermined threshold distance. Reaction distance, response latency, as well as escaping speed, duration, and direction can be adjusted in the system.By repeatedly measuring the response latency and escaping speed of the system, we demonstrated the system’s ability to exhibit fast and rapid responses while maintaining consistency across successive trials. As a case study, we manipulated the escape speed and reaction distance of the prey to expose them to a predatory fish,Coreoperca kawamebari. The results show that both variables significantly affect the outcome of predator-prey interactions.These findings indicate that the developed escape system is useful for identifying kinematic and behavioral features of prey that are critical for predator evasion. Moreover, due to its relatively low cost and customizability, we propose that this system can be applied to investigate various aspects of animal behaviors (e.g., eliciting escape responses by artificial stimuli) in different animal species.
Fusion of histone variants to Cas9 enhances homology-directed repair
Authors: Kato-Inui Tomoko , Ono Terumi , Miyaoka Yuichiro 
Published: July 2023

AbstractAs a versatile genome editing tool, the CRISPR-Cas9 system induces DNA double-strand breaks at targeted sites to activate mainly two DNA repair pathways: HDR which allows precise editing via recombination with a homologous template DNA, and NHEJ which connects two ends of the broken DNA, which is often accompanied by random insertions and deletions. Therefore, how to enhance HDR while suppressing NHEJ is a key to successful applications that require precise genome editing. Histones are small proteins with a lot of basic amino acids that generate electrostatic affinity to DNA. Since H2A.X is involved in DNA repair processes, we fused H2A.X to Cas9 and found that this fusion protein could improve the HDR/NHEJ ratio. As various post-translational modifications of H2A.X play roles in the regulation of DNA repair, we also fused H2A.X mimicry variants to replicate these post-translational modifications including phosphorylation, methylation, and acetylation. However, none of them were effective to improve the HDR/NHEJ ratio. We further fused other histone variants to Cas9 and found that H2A.1 exhibited the improved HDR/NHEJ ratio better than H2A.X. Thus, the fusion of histone variants to Cas9 is a promising option to enhance precise genome editing.
BRD4 directs mitotic cell division by inhibiting DNA damage
Authors: Wu Tiyun , Hou Haitong , Dey Anup , Bachu Mahesh , Chen Xiongfong , Wisniewski Jan , Kudoh Fuki , Chen Chao , Chauhan Sakshi , Xiao Hua , Pan Richard , Ozato Keiko 
Published: July 2023

SUMMARYBRD4 binds to acetylated histones to regulate transcription and drive cancer cell proliferation. However, the role of BRD4 in normal cell growth remains to be elucidated. Here we investigated the question by using mouse embryonic fibroblasts with conditional Brd4 knockout (KO). We found that Brd4KO cells grow more slowly than wild type cells: they do not complete replication, fail to achieve mitosis, and exhibit extensive DNA damage throughout all cell cycle stages. BRD4 was required for expression of more than 450 cell cycle genes including genes encoding core histones and centromere/kinetochore proteins that are critical for genome replication and chromosomal segregation. Moreover, we show that many genes controlling R-loop formation and DNA damage response (DDR) require BRD4 for expression. Finally, BRD4 constitutively occupied genes controlling R-loop, DDR and cell cycle progression. We suggest that BRD4 epigenetically marks those genes and serves as a master regulator of normal cell growth.