bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome brings variations of gene expression, alternative splicing, and structural variations into gene-scale trait dissection in soybean
Authors: Li Delin , Wang Qi , Tian Yu , Lyv Xiangguang , Zhang Hao , Sun Yinglu , Hong Huilong , Gao Huawei , Li Yan-Fei , Zhao Chaosen , Wang Jiajun , Wang Ruizhen , Yang Jinliang , Liu Bin , Schnable Patrick S. , Schnable James C. , Li Ying-Hui , Qiu Li-Juan 
Published: July 2023

AbstractGenome-wide association study (GWAS) identifies trait-associated loci, but due in part to slow decay of linkage disequilibrium (LD), identifying the causal genes can be a bottleneck. Transcriptome-wide association study (TWAS) addresses this by identifying gene expression-phenotype associations or integrating gene expression quantitative trait loci (eQTLs) with GWAS results. Here, we used self-pollinated soybean as a model to evaluate the application of TWAS in the genetic dissection of traits in plant species that exhibit slow LD decay. The first RNA-Seq analysis of a soybean diversity panel was conducted, which identified the genetic regulation of 29,286 genes. Different TWAS solutions were less affected by LD and robust with source of expression that identified known genes related to traits from different development stages and tissues. A novel gene named pod colorL2was identified via TWAS and functionally validated by genome editing. Our introduction of the new exon proportion feature significantly improves the capture of expression variations resulting from structural variations and alternative splicing. As a result, the genes identified by our TWAS approach exhibited a diverse range of causal variations, including SNP, insertion/deletion, gene fusion, copy number variation, and alternative splicing. Using our TWAS approach, we identified genes associated with flowering time, including both previously known candidates and novel genes that had not been linked to this trait before, providing complementary insights with GWAS. In summary, this study supports the application of TWAS for candidate gene identification in species with low rates of LD decay.
Intradisciplinary Growth of Sustainability-Minded Engineers through Conservation Technology
Authors: Schulz Andrew , Shriver Cassie , Patka Anika , Greiner Caroline , Seleb Benjamin , Hull Rebecca Watts , Subiño Sullivan Carol , Sonnenberg-Klein Julia M. , Moore Roxanne 
Published: July 2023

AbstractBackgroundThe need for sustainability-minded engineers prepared to address complex societal challenges has grown exponentially in recent years. Frameworks like the United Nations (UN) Sustainable Development Goals (SDGs) have begun to drive structural changes in engineering education, including new ABET accreditation focused on sustainability. The new field of conservation technology allows engineers to develop sustainability competencies and identities as conservationists and environmentalists.PurposeThis manuscript describes an assessment of student identity development in conservation and environmentalism in the GaTech4Wildlife Vertically Integrated Project (VIP) course at Georgia Tech. The course uses the principles of Human-Centered Design along with the UN Sustainable Development Goals and project-based learning to solve conservation-oriented, real-world problems and develop sustainability-minded engineers.Design/MethodUndergraduate students participated in the course and utilizing both in-person interviews and post-course assessment, students were assessed for course themes and identities. The sample consisted of students from the College of Engineering and the College of Computing.ResultsSince 2019, over 50 students have participated in this Tech4Wildlife course. Based on surveys and interviews of nearly 20 of the most recent students, students transitioned from identifying as engineers and coders with no sustainability knowledge to nearly doubling their identity measures as conservationists and environmentalists after only one semester.ConclusionsTo teach the next generation of sustainability-minded engineers, interdisciplinary, project-based courses grounded in Sustainable Development Goals may offer a meaningful pathway for students to develop both technical skills and conservationist identities.
Nanobead-based single-molecule pulldown for single cells
Authors: Zhao Qirui , Shen Yusheng , Li Xiaofen , Li Yulin , Tian Fang , Yu Xiaojie , Liu Zhengzhao , Tong Rongbiao , Park Hyokeun , Yobas Levent , Huang Pingbo 
Published: July 2023

AbstractInvestigation of cell-to-cell variability holds critical physiological and clinical implications. Thus, numerous new techniques have been developed for studying cell-to-cell variability, and these single-cell techniques can also be used to investigate rare cells. Moreover, for studying protein-protein interactions (PPIs) in single cells, several techniques have been developed based on the principle of the single-molecule pulldown (SiMPull) assay. However, the applicability of these single-cell SiMPull (sc-SiMPull) techniques is limited because of their high technical barrier and special requirements for target cells and molecules. Here, we report a highly innovative nanobead-based approach for sc-SiMPull that is based on our recently developed microbead-based, improved version of SiMPull for cell populations. In our sc-SiMPull method, single cells are captured in microwells and lysed in situ, after which commercially available, pre-surface-functionalized magnetic nanobeads are placed in the microwells to specifically capture proteins of interest together with their binding partners from cell extracts; subsequently, the PPIs are examined under a microscope at the single-molecule level. Relative to previously published methods, nanobead-based sc-SiMPull is considerably faster, easier to use, more reproducible, and more versatile for distinct cell types and protein molecules, and yet provides similar sensitivity and signal-to-background ratio. These crucial features should enable universal application of our method to the study of PPIs in single cells.Statement of SignificanceHeterogeneity between single cells holds critical physiological and clinical implications. Characterization of protein-protein interactions (PPIs) and identification of the interacting partners of a specific protein are critical for elucidating the function and regulation of the protein. However, the applicability of the currently available techniques for studying PPIs in single cells is limited by their high technical barrier and special requirements for cell/proteins types. Our single-cell single-molecule pulldown (sc-SiMPull) assay in this study is not only substantially simpler and faster than existing sc-SiMPull methods, but also considerably more widely applicable—to all cell types and to both soluble and transmembrane proteins. These two crucial features should enable universal application of our method to the study of PPIs in single cells.
Aberrant regulation of the Rap1 small GTPase in response to escalating, intermittent stress produces hippocampal synaptic and cognitive dysfunction
Authors: Bjornson Kathryn J. , Vanderplow Amanda M. , Yang Yezi , Kermath Bailey A. , Cahill Michael E. 
Published: July 2023

SummaryThe effects of repeated stress on cognitive impairment are thought to be mediated, at least in part, by reductions in the stability of dendritic spines in brain regions critical for proper learning and memory, including the hippocampus. Small GTPases are particularly potent regulators of dendritic spine formation, stability, and morphology in hippocampal neurons. Through the use of small GTPase protein profiling in mice, we identify increased levels of synaptic Rap1 in the hippocampal CA3 region in response to escalating, intermittent stress. We then demonstrate that increased Rap1 in the CA3 is sufficient in and of itself to produce stress-relevant dendritic spine and cognitive phenotypes. Further, using super-resolution imaging, we investigate how the pattern of Rap1 trafficking to synapses likely underlies its effects on the stability of select dendritic spine subtypes. These findings illuminate the involvement of aberrant Rap1 regulation in the hippocampus in contributing to the psychobiological effects of stress.
A CRISPR-based genetic screen inBacteroides thetaiotaomicronreveals a small RNA modulator of bile susceptibility
Authors: Prezza Gianluca , Liao Chunyu , Reichardt Sarah , Beisel Chase L. , Westermann Alexander J. 
Published: July 2023

AbstractMicrobiota-centric interventions are limited by our incomplete understanding of the gene functions of many of its constituent species. This applies in particular to small RNAs (sRNAs), which are emerging as important regulators in microbiota species, yet tend to be missed by traditional functional genomics approaches. Here, we establish CRISPR interference (CRISPRi) in the abundant microbiota memberBacteroides thetaiotaomicronfor genome-wide sRNA screens. By assessing the abundance of different protospacer-adjacent motifs, we identify thePrevotella bryantiiB14 Cas12a as a suitable nuclease for CRISPR screens in these bacteria and generate an inducible Cas12a expression system. Using a luciferase reporter strain, we infer guide design rules and use this knowledge to assemble a computational pipeline for automated gRNA design. By subjecting the resulting guide library to a phenotypic screen, we uncover the previously uncharacterized sRNA BatR to increase susceptibility to bile salts, likely through the regulation of genes involved inBacteroidescell surface structure. Our study lays the groundwork for unlocking the genetic potential of these major human gut mutualists and, more generally, for discovering hidden functions of bacterial sRNAs.
Unifying design principles of endocrine gland mass and its regulatory circuits
Authors: Raz Moriya , Milo Tomer , Kohanim Yael Korem , Karin Omer , Tendler Avichai , Bar Alon , Glass David S. , Mayo Avi , Alon Uri 
Published: July 2023

AbstractHormones are regulatory molecules that impact physiological functions. Much is known about individual hormones, but general rules that connect the regulatory logic of different hormone systems are limited. In this study, we analyzed a range of human hormone systems using a mathematical approach to integrate knowledge on endocrine cells, target tissues and regulation, to uncover unifying principles and regulatory circuits. We find that the number of cells in an endocrine gland is proportional to the number of cells in its target tissues, as one single endocrine cell serves approximately 2000 target cells. We identified five classes of regulatory circuits, each has specific regulatory functions such as homeostasis or allostasis. The most complex class includes an intermediate gland, the pituitary, which can otherwise be considered redundant and exposes to fragilities. We suggest a tradeoff: with the price of fragilities comes advantages -amplification, buffering of hypersecreting tumors, and faster response times. By elucidating these unifying principles and circuits, this study deepens our understanding of the control of endocrine processes and builds the foundation for systems endocrinology.
NOTCH3 signalling controls human trophoblast stem cell expansion and differentiation
Authors: Dietrich Bianca , Victoria Kunihs , Lackner Andreas I. , Meinhardt Gudrun , Koo Bon-Kyoung , Pollheimer Jürgen , Haider Sandra , Knöfler Martin 
Published: July 2023

ABSTRACTFailures in growth and differentiation of the early human placenta are associated with severe pregnancy disorders such as preeclampsia and fetal growth restriction. However, regulatory mechanisms controlling development of its epithelial cells, the trophoblasts, remain poorly elucidated. Using trophoblast stem cells (TSCs), trophoblast organoids (TB-ORGs) and primary cytotrophoblasts (CTBs) of early pregnancy, we herein show that autocrine NOTCH3 signalling controls human placental expansion and differentiation. NOTCH3 receptor was specifically expressed in proliferative CTB progenitors and its active form, the nuclear NOTCH3 intracellular domain (NOTCH3-ICD), interacted with the transcriptional co-activator Mastermind-like 1 (MAML1). Doxycyclin-inducible expression of dominant-negative MAML1 in TSC lines provoked cell fusion and upregulation of genes specific for multinucleated syncytiotrophoblasts, the differentiated hormone-producing cell type of the placenta. However, progenitor expansion and markers of trophoblast stemness and proliferation were suppressed. Accordingly, inhibition of NOTCH3 signalling diminished growth of TB-ORGs whereas overexpression of NOTCH3-ICD in primary CTBs and TSCs showed opposite effects. In conclusion, the data suggest that canonical NOTCH3 signalling plays a key role in human placental development promoting self-renewal of CTB progenitors.
Circulating MicroRNAs indicative of sex and stress in the European seabass (Dicentrarchus labrax): toward the identification of new biomarkers
Authors: Houdelet Camille , Blondeau-Bidet Eva , Estevez-Villar Mathilde , Mialhe Xavier , Hermet Sophie , Ruelle François , Dutto Gilbert , Bajek Aline , Bobe Julien , Geffroy Benjamin 
Published: July 2023

AbstractMicroRNAs (miRNAs) constitute a new category of biomarkers. Studies on miRNAs in non-mammalian species have drastically increased in the last few years. Here, we explored the use of miRNAs as potential, poorly-invasive markers, to identify sex and characterize acute stress in fish. The European seabass (Dicentrarchus labrax) was chosen as model because of its rapid response to stress and its specific sex determination system, devoid of sexual chromosomes. We performed a small RNA-sequencing analysis in the blood plasma of males and females’ European seabass (mature and immature) as well as in the blood plasma of juveniles submitted to an acute stress and sampled throughout the recovery period (at 0h, 0.5h, 1.5h and 6h). In immature individuals, both miR-1388-3p and miR-7132a-5p were up-regulated in females, while miR-499a-5p was more abundant in males. However, no miRNAs were found to be differentially expressed between sexes in the blood plasma of mature individuals. For the acute stress analysis, five miRNAs (miR-155-5p, miR-200a-3p, miR-205-1-5p, miR-143-3p and miR-223-3p) followed cortisol production over time. All miRNAs identified were tested and validated by RT-qPCR on sequenced samples. A complementary analysis on the 3’UTR sequences of the European seabass allowed to predict potential mRNA targets, some of them being particularly relevant regarding stress regulation, e.g. the glucocorticoid and the mineralocorticoid receptor. The present study provides new avenues and recommendations on the use of miRNAs as biomarkers of sex or stress of the European seabass, with potential application on other fish species.
Deep immunophenotyping reveals circulating activated lymphocytes in individuals at risk for rheumatoid arthritis
Authors: Inamo Jun , Keegan Joshua , Griffith Alec , Ghosh Tusharkanti , Horisberger Alice , Howard Kaitlyn , Pulford John , Murzin Ekaterina , Hancock Brandon , Jonsson Anna Helena , Seifert Jennifer , Feser Marie L. , Norris Jill M. , Cao Ye , Apruzzese William , Louis Bridges S. , Bykerk Vivian , Goodman Susan , Donlin Laura , Firestein Gary S. , Perlman Harris , Bathon Joan M. , Hughes Laura B. , Tabechian Darren , Filer Andrew , Pitzalis Costantino , Anolik Jennifer H. , Moreland Larry , Guthridge Joel M. , James Judith A. , Brenner Michael B. , Raychaudhuri Soumya , Sparks Jeffrey A. ,   The Accelerating Medicines Partnership RA/SLE Network, Michael Holers V. , Deane Kevin D. , Lederer James A. , Rao Deepak A. , Zhang Fan 
Published: July 2023

AbstractRheumatoid arthritis (RA) is a systemic autoimmune disease with currently no universally highly effective prevention strategies. Identifying pathogenic immune phenotypes in ‘At-Risk’ populations prior to clinical disease onset is crucial to establishing effective prevention strategies. Here, we applied mass cytometry to deeply characterize the immunophenotypes in blood from At-Risk individuals identified through the presence of serum antibodies to citrullinated protein antigens (ACPA) and/or first-degree relative (FDR) status (n=52), as compared to established RA (n=67), and healthy controls (n=48). We identified significant cell expansions in At-Risk individuals compared with controls, including CCR2+CD4+ T cells, T peripheral helper (Tph) cells, type 1 T helper cells, and CXCR5+CD8+ T cells. We also found that CD15+ classical monocytes were specifically expanded in ACPA-negative FDRs, and an activated PAX5lownaïve B cell population was expanded in ACPA-positive FDRs. Further, we developed an “RA immunophenotype score” classification method based on the degree of enrichment of cell states relevant to established RA patients. This score significantly distinguished At-Risk individuals from controls. In all, we systematically identified activated lymphocyte phenotypes in At-Risk individuals, along with immunophenotypic differences among both ACPA+ and ACPA-FDR At-Risk subpopulations. Our classification model provides a promising approach for understanding RA pathogenesis with the goal to further improve prevention strategies and identify novel therapeutic targets.
Traditional Norwegian Kveik Yeast: An Ancient Sister Group to DomesticatedSaccharomyces cerevisiae
Authors: Dondrup Michael , Eiken Hans Geir , Martinussen Atle Ove , Haugland Lisa Karine , Holdhus Rita , Dolan David , Grellscheid Sushma , Hagen Snorre , Elameen Abdelhameed , Myking Tor 
Published: July 2023

AbstractKveik is the common name of yeast that has been used in traditional farmhouse brewing of western Norway for generations. Its fast fermentation, increased flocculation, temperature tolerance, and rich flavor profile have led to growing interest in recent years. Previous genetic analyses have shown that kveik forms a distinct group within theSaccharomyces cerevisiaetree and placed its origins within the Beer I clade of industrial brewing yeasts, although with signs of mixed ancestry.In this study, we revisited the phylogenetic position of kveik within theS. cerevisiaetree. We searched for traditional farm breweries in western Norway and collected ten samples of potential kveik yeast.Using Illumina whole genome shotgun sequencing, we reconstructed the phylogenetic tree of kveik based onde novogenome assemblies and variant calls of our new kveik samples, along with published wild and domesticatedS. cerevisiaestrains. We calibrated and used sequential computational experiments at different thresholds to determine the most probable phylogenetic position of kveik yeast.Previously sequenced kveik genotypes form a clade with our new samples clustering partially by place of origin. Our results indicate that kveik is indeed a compact clade withinS. cerevisiaewith significantly reduced polymorphism compared to common brewing yeasts and wild strains. Contrary to what was previously thought, our analyses support a more ancient divergence of kveik and place it closer to the root of theS. cerevisiaetree.In conclusion, our genetic analyses suggest that kveik is a unique and ancient yeast group, distinct from other domesticatedS. cerevisiaestrains. Considering a possible far east origin of kveik yeast, the apparent endemism to western Norway remains as a big paradox These findings have important implications for the understanding of yeast domestication and the use of kveik in modern brewing practices.
Modeling Stress-Induced Responses: Plasticity in Continuous State Space and Gradual Clonal Evolution
Authors: Bukkuri Anuraag 
Published: July 2023

AbstractMathematical models of cancer and bacterial evolution have generally stemmed from a gene-centric framework, assuming clonal evolution via acquisition of resistance-conferring mutations and selection of their corresponding subpopulations. More recently, the role of phenotypic plasticity has been recognized and models accounting for phenotypic switching between discrete cell states (e.g. epithelial and mesenchymal) have been developed. However, seldom do models incorporate both plasticity and mutationally-driven resistance, particularly when the state space is continuous and resistance evolves in a continuous fashion. In this paper, we develop a framework to model plastic and mutational mechanisms of acquiring resistance in a continuous, gradual fashion. We use this framework to examine ways in which cancer and bacterial populations can respond to stress and consider implications for therapeutic strategies. Although we primarily discuss our framework in the context of cancer and bacteria, it applies broadly to any system capable of evolving via plasticity and genetic evolution.
Activity-Induced MeCP2 Phosphorylation Regulates Retinogeniculate Synapse Refinement
Authors: Tzeng Christopher P. , Whitwam Tess , Boxer Lisa D. , Li Emmy , Silberfeld Andrew , Trowbridge Sara , Mei Kevin , Lin Cindy , Shamah Rebecca , Griffith Eric C. , Renthal William , Chen Chinfei , Greenberg Michael E. 
Published: July 2023

ABSTRACTMutations inMECP2give rise to Rett syndrome (RTT), an X-linked neurodevelopmental disorder that results in broad cognitive impairments in females. While the exact etiology of RTT symptoms remains unknown, one possible explanation for its clinical presentation is that loss of MeCP2 causes miswiring of neural circuits due to defects in the brain’s capacity to respond to changes in neuronal activity and sensory experience. Here we show that MeCP2 is phosphorylated at four residues in the brain (S86, S274, T308, and S421) in response to neuronal activity, and we generate a quadruple knock-in (QKI) mouse line in which all four activity-dependent sites are mutated to alanines to prevent phosphorylation. QKI mice do not display overt RTT phenotypes or detectable gene expression changes in two brain regions. However, electrophysiological recordings from the retinogeniculate synapse of QKI mice reveal that while synapse elimination is initially normal at P14, it is significantly compromised at P20. Notably, this phenotype is distinct from that previously reported forMecp2null mice, where synapses initially refine but then regress after the third postnatal week. We thus propose a model in which activity-induced phosphorylation of MeCP2 is critical for the proper timing of retinogeniculate synapse maturation specifically during the early postnatal period.SIGNIFICANCE STATEMENTRett syndrome (RTT) is an X-linked neurodevelopmental disorder that predominantly affects girls. RTT is caused by loss of function mutations in a single gene MeCP2. Girls with RTT develop normally during their first year of life, but then experience neurological abnormalities including breathing and movement difficulties, loss of speech, and seizures. This study investigates the function of the MeCP2 protein in the brain, and how MeCP2 activity is modulated by sensory experience in early life. Evidence is presented that sensory experience affects MeCP2 function, and that this is required for synaptic pruning in the brain. These findings provide insight into MeCP2 function, and clues as to what goes awry in the brain when the function of MeCP2 is disrupted.