bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell-specific delivery of GJB2 restores auditory function in mouse models of DFNB1 deafness and mediates appropriate expression in NHP cochlea
Authors: Ivanchenko Maryna V. , Booth Kevin T.A. , Karavitaki K. Domenica , Antonellis Larisa M. , Nagy M. Aurel , Peters Cole W. , Price Spencer , Li Yaqiao , Lytvyn Anton , Ward Andrew , Griffith Eric C. , Hrvatin Sinisa , Greenberg Michael E. , Corey David P. 
Published: December 2024

AbstractMutations in theGJB2gene cause the most common form of human hereditary hearing loss, known as DFNB1.GJB2is expressed in two cell groups of the cochlea—epithelial cells of the organ of Corti and fibrocytes of the inner sulcus and lateral wall—but not by sensory hair cells or neurons. Attempts to treat mouse models of DFNB1 with AAV vectors mediating nonspecificGjb2expression have not substantially restored function, perhaps because inappropriate expression in hair cells and neurons could compromise their electrical activity. Here, we used genomic chromatin accessibility profiling to identify candidate gene regulatory elements (GREs) that could drive cell-type-specific expression ofGjb2in the cochlea. HA-tagged GJB2, delivered to a conditional knockout model in an AAV vector with GRE control of expression, was localized to the appropriate cell types, prevented the cochlear degeneration observed in untreated knockout mice, and partially rescued hearing sensitivity. In aGjb2partial knockdown mouse model, such exogenous GJB2 prevented degeneration and completely restored hearing sensitivity. We tested control of expression by these GREs in nonhuman primate cochleas and found that vector-delivered human GJB2.HA was located in the appropriate cell types and caused little or no reduction in hearing sensitivity. Together, these findings suggest that GRE-mediated expression ofGJB2could prevent hearing loss in DFNB1 patients.
Elucidation of gene clusters underlying withanolide biosynthesis in ashwagandha through yeast metabolic engineering
Authors: Reynolds Erin , Trauger Marena , Li Fu-Shuang , Huang Jonathan , Moss Trevor , Christ Bastien , Xu Menglong , Knoch Eva , Weng Jing-Ke 
Published: December 2024

AbstractWithanolides are medicinally relevant steroidal lactones produced byWithania somnifera(ashwagandha) amongst other Solanaceae family plants. However, the biosynthetic pathway to withanolides is largely unknown, preventing scale-up and hindering pharmaceutical applications. We sequenced the genome ofW. somniferaand identified two biosynthetic gene clusters exhibiting a segmented tissue-specific expression pattern. We characterized the cluster enzymes through stepwise pathway reconstitution in yeast and transient expression inNicotiana benthamiana, leading to the identification of three cytochrome P450s (CYP87G1, CYP88C7, and CYP749B2) and a short-chain dehydrogenase that produce a lactone ring- containing intermediate when co-expressed. A fourth cytochrome P450 (CYP88C10) and a sulfotransferase convert this into an intermediate with the characteristic withanolide A-ring structure, featuring a C1ketone and C2-C3unsaturation. The discovery of the sulfotransferase as a core pathway enzyme challenges the conventional paradigm of sulfotransferases as tailoring enzymes. These insights pave the way for an efficient biomanufacturing process for withanolides and future development of withanolide-derived drugs.
Multi-omics analysis of long-term cultured human islets
Authors: Sun Guihua , Qi Meirigeng , Sun Olivia , Lizhar Elizabeth M. , Hussey Deborah , Shi Yanhong , Riggs Arthur D. 
Published: December 2024

Abstractβ-cell dysfunction in pancreatic islets, characterized as either the loss of β-cell mass or the resistance of β-cell to glucose, is the leading cause of progression to diabetes. Islet transplantation became a promising approach to replenish functional β-cell mass. However, not much known about changes in islets used for transplantation after isolation. We have subjected human islets into long-termin vitroculture (LTC) and characterized those survived islets. While most of the dysregulated genes were downregulated during LTC, specific groups of mRNA or miRNA were upregulated, and they are involved in specific pathways. In general, α-cells and β-cells of LTC-islets have elevated expressions ofMAFBandMAFAgenes, respectively. We also found that exocrine cells were eliminated faster than endocrine cells, and β-cells were lost at a higher rate than α-cells. Interestingly, one specific group of cells that have characteristics of immature α-cells or β-cells, were enriched in LTC-islets, revealing the possibility of transdifferentiation of α-cells to β-cells, or dedifferentiation of β-cells to α -cells, underin vitroculture. Our results suggest that there are intrinsic cellular and molecular mechanisms in pancreatic cells that are associated with their maturity and correlated with their survival ability under unfavorable living conditions.
Phages-bacteria interactions underlying the dynamics of polyhydroxyalkanoates-producing mixed microbial cultures via meta-omics study
Authors: Yao Jian , Zeng Yan , Hong Xia , Wang Meng , Zhang Quan , Chen Yating , Gou Min , Xia Zi-Yuan , Tang Yue-Qin 
Published: December 2024

AbstractThe dynamics of the structure of polyhydroxyalkanoates-producing mixed microbial cultures (PHA-MMCs) during enrichment and maintenance is an unsolved problem. The effect of phages has been proposed as a cause of dynamic changes in community structure, but evidence is lacking. To address this question, we enriched five PHA-MMCs and sampled temporally to study the interactions between phage and prokaryotic members by combining metagenomics and metatranscriptomics. 963 metagenome-assemble genomes and 4294 phage operational taxonomic units were assembled from bulk metagenomic data. There were complex interactions between the phages in Casadabanvirus and Unclassified Hendrixvirinae and the dominant species inAzomonas,Paracoccus,ThaueraandBreundimonas. The dynamic change of the structure of phage and prokaryotic communities were remarkably consistent. Further structural equation modeling analysis showed that phage communities could significantly affect the activity and community structure of prokaryotic microorganisms. In addition, seven key auxiliary metabolic genes (phaC, fadJ, acs, ackA, phbB, acdAB and fadD) in the PHA synthesis pathway were identified from phage sequences. Importantly, these auxiliary metabolic genes were expressed at the transcriptional level, indicating that they were in an active functional state. This meta-analysis provides the first catalog of phages in PHA-MMCs and the auxiliary metabolic genes they carry, as well as how they play a role in the dynamic changes of prokaryotic communities. This study provides a reference for subsequent studies on understanding and regulating the microbial community structure of artificial open microbial systems.ImportanceThe synthesis of biodegradable plastic PHA from organic waste through mixed microbial cultures (MMCs), with extremely low cost, has the potential for expanded production. However, there is a gap of understanding of the dynamics of dominant species in MMCs to better control community structure. Our results demonstrate for the first time the impact of phages on the structure of prokaryotic communities in the MMCs. There are complex interactions between the PHA producers (Azomonas,Paracoccus,Thauera) and phages (Casadabanvirus and Unclassified Hendrixvirinae). Phage communities can negatively regulate the activity and structure of prokaryotic communities. In addition, the auxiliary metabolic genes in the PHA synthesis pathways carried by phages may promote the PHA synthesis ability of prokaryotic members. This study highlights the impact of phages on prokaryotic community structure, suggesting that phages have the potential to become a tool for better controlling the microbial community structure of PHA-MMCs.
Global and genetic regulation of gene expression in human endothelial and vascular smooth muscle cells
Authors: Liu Pengyuan , Ray Atrayee , Liu Yong , Mishra Manoj K. , Qiu Qiongzi , Pandey Rajan , Therani Bhavika , Huang Jing , Ren Jiayi , Stelloh Cary , Bai Xiaowen , Greene Andrew S. , Cowley Allen W. , Geurts Aron M. , Rao Sridhar , Liang Mingyu 
Published: December 2024

AbstractBackgroundThe understanding of genetic and epigenetic regulation of gene expression in endothelial and vascular smooth muscle cells remains fragmented with limited experimental validation.MethodsChromatin conformation (Micro-C), DNA methylation (RRBS), chromatin accessibility (ATAC-seq), and transcriptome profiles (RNA-seq) were mapped in human induced pluripotent stem cell (hiPSC)-derived, isogenic endothelial and vascular smooth muscle cells (iECs and iVSMCs). CTCF and RAD21 were depleted to assess the functional relevance of chromatin architecture, and genome editing was used to evaluate the allelic effect of a blood pressure-associated single nucleotide polymorphism (SNP).ResultsSignificant correlations were identified between gene expression levels and chromatin interactions, chromatin accessibility, and DNA methylation in iECs and iVSMCs, with chromatin interactions showing the strongest association. Chromatin contact regions displayed distinct epigenetic landscapes depending on the types of regulatory element interactions involved. Perturbation of CTCF and RAD21 revealed their differential regulatory effects, particularly on the expression of genes overlapping chromatin contacts, with RAD21 exhibiting a broader regulatory impact. SNPs associated with several vascular traits were enriched in chromatin loops or accessible regions in iECs or iVSMCs. Precise genome editing demonstrated allele-dependent effects of SNP rs9833313 on the expression ofSHOX2located 247.4 kbp away but within the same chromatin loops as the SNP.ConclusionThis study provides an extensive epigenetic landscape of vascular cells that may drive novel research on the role of genetic and epigenetic mechanisms of vascular function and disease as demonstrated by our targeted experiments.
A vestibulospinal pathway for context-dependent motor control of the mouse tail
Authors: Lacava Salvatore Andrea , Isilak Necmettin , Ranawat Nishtha , Katzke Julian , Hugo Hoedemaker Johannes Frederik , Yoshida Yutaka , Uusisaari Marylka Yoe 
Published: December 2024

ABSTRACTThe tail movement is critical for maintaining balance during locomotion in many animal species, yet its underlying neuro-muscular control remains poorly understood. In this study we investigated what are the neuronal substrates responsible for tail control in mice. Using high-resolution microCT scans and retrograde labeling, we lay out the neuro-muscular organization of the tail and identified distinct pools of motoneurons in the spinal cord that innervate proximal and distal muscles. We further show that the spinal vestibular nucleus (SpVN) in the brainstem sends direct projections to the same spinal cord segments where tail motoneurons are located. The activation of these vestibulospinal neurons using optogenetics results in more accurate tail movements during challenging balance tasks. Our results reveal that the vestibular system’s influence on tail control is context-dependent, enhancing balance performance under uncertain sensory conditions. These findings provide novel insights into the neural circuits responsible for maintaining balance, highlighting the role of the vestibulospinal pathway in context-dependent modulation of tail movement to maintain stability during complex locomotor tasks.
A single-cell map of hypertension
Authors: Qiu Qiongzi , Liu Yong , Xue Hong , Pandey Rajan , He Lishu , Liu Jing , Liu Pengyuan , Therani Bhavika , Kumar Vinod , Huang Jing , Guenther Maya , Usa Kristie , Grzybowski Michael , Vanden Avond Mark A. , Greene Andrew S. , Cowley Allen W. , Rao Sridhar , Geurts Aron M. , Liang Mingyu 
Published: December 2024

AbstractHypertension is a leading risk factor for disease burden and death worldwide. Several organ systems are involved in the development of hypertension, which contributes to stroke, heart disease, and kidney disease. Despite the broad health relevance, our understanding of the molecular landscape in hypertension is limited and lags other major diseases. Here we report an extensive analysis of the molecular landscape in hypertension and its end-organ damage and uncover novel mechanisms linking human genetic variants to the development of these diseases. We obtained single-nucleus RNA-seq (612,984 nuclei), single-nucleus ATAC-seq (179,637 nuclei), or spatial transcriptome data from five organs (hypothalamus, kidney, heart, 3rdorder mesenteric artery, middle cerebral artery) in three mouse and rat models under twelve experimental conditions. More than one third of all hypertension research in animal models involves these three models. We identified both model-specific and convergent responses in cell types, genes, and pathways. By integrating our data with human genomic data, we partitioned the blood pressure and end-organ damage traits into cell type-specific transcriptional contributions and cell types common across multiple traits. Using genomic editing in animal models and human induced pluripotent stem cells, we extended key findings and identified new mechanisms linking human genetic variants to the development of hypertension and related renal injury. We anticipate that our rich data sets and findings will broadly drive forward the research of hypertension and hypertensive end-organ damage. Our approach of integrating multi-model and multi-tissue single-cell analysis with human genetic data and in vivo and in vitro genome editing can be applied to investigate other complex traits.
Candida albicansinduce hypoxia response via activating EGFR to promote colorectal cancer progression
Authors: Wang Wanqiu , Li Haihuang , Gong FangLei , Zhang Zhenyu , Ma Yanping , Zhao Yu , Du Changzheng , Li Ningning , He Guiwei , Sun Kun 
Published: December 2024

AbstractColorectal cancer (CRC) is one of the leading causes of cancer-related mortality worldwide. Gut microbiota, including fungi, are considered to associate with CRC progression, while their functions and underlying mechanisms remain largely elusive. Here, we assessed the engagement ofCandida albicans(C. albicans), a common fungus, in CRC progression. Using a cell-fungi co-culture system, we found thatC. albicanscould activate critical pro-metastatic genes and pathways, including MAPK and NF-κB, to up-regulate the expression of transcription factor, c-Jun, and c-Myc. Subsequently, c-Jun and c-Myc provoked hypoxia inducible factor 1α (HIF-1α) stabilization at normoxia, which further promote angiogenesis and tumor progression. Loss-of-function investigation showed that during this procedure, the virulence factor candidalysin secreted byC. albicanswas essential for eliciting cancer cell responses through inducing the phosphorylation of epidermal growth factor receptor (EGFR) and Toll-like Receptors (TLRs) in the tumor cell, preferably in a species and cancer cell-dependent manner. The activation of hypoxia pathway byC. albicanswas reinforced in colon organoids derived from CRC specimens. Hence, our results demonstrated thatC. albicansactivated the EGFR/TLR2 – ERK/NF-κB – HIF-1α signaling pathway and induced a hypoxia response to promote cancer progression, thereby presenting a potential therapeutic target for CRC treatment.
Universality of representation in biological and artificial neural networks
Authors: Hosseini Eghbal , Casto Colton , Zaslavsky Noga , Conwell Colin , Richardson Mark , Fedorenko Evelina 
Published: December 2024

AbstractMany artificial neural networks (ANNs) trained with ecologically plausible objectives on naturalistic data align with behavior and neural representations in biological systems. Here, we show that this alignment is a consequence of convergence onto the same representations by high-performing ANNs and by brains. We developed a method to identify stimuli that systematically vary the degree of inter-model representation agreement. Across language and vision, we then showed that stimuli from high-and low-agreement sets predictably modulated model-to-brain alignment. We also examined which stimulus features distinguish high-from low-agreement sentences and images. Our results establish representation universality as a core component in the model-to-brain alignment and provide a new approach for using ANNs to uncover the structure of biological representations and computations.
Structure-based mechanistic principles for the paradoxical effects of pathological RET mutations
Authors: Fassler Bakhman Anna , Cohen Michal , Kolodny Rachel , Kosloff Mickey 
Published: December 2024

ABSTRACTThe RET receptor is a transmembrane protein that belongs to the receptor tyrosine kinase family. RET activates signaling pathways regulating cell growth, differentiation and survival in diverse tissues that include the thyroid and enteric nervous system. Mutations that reduce RET levels or function can cause Hirschsprung’s (HSCR) disease, characterized by abnormal distal colon innervation in the developing embryo. In contrast, mutations that constitutively activate RET can lead to tumorigenesis, most notably in multiple endocrine neoplasia type 2 (MEN2) syndromes usually identified in the thyroid. Paradoxically, some RET mutations can both reduce RET activity in enteric ganglia, and increase signaling in other tissues, resulting in co-occurrence of both HSCR and MEN2A. Although extensive research has been conducted on RET mutations, the structural and mechanistic bases underlying these paradoxical effects remain unclear. Here, we assimilated data on 70 positions in RET extracellular domains where point-mutations were associated with HSCR, MEN2A, or both. Using 3D structure-based approaches, we predict the potential structural effects of mutations in these positions. Our analysis suggests that approximately 90% of positions associated with HSCR disease can, upon mutation, disrupt intramolecular interactions that stabilize RET tertiary structure: residues buried in the protein core, calcium-binding sites, or residues participating in stabilizing intramolecular electrostatic/covalent bonds. A smaller subset of mutations involves substitutions to/from glycines or prolines in key positions. Only a small minority of HSCR-associated positions affect protein-protein interactions needed for signal activation. On the other hand, our analysis showed that ∼75% of mutations in positions that cause MEN2A lead to an unpaired cysteine that can form an intermolecular disulfide bond between two RET monomers. Other mutations that cause MEN2A are also predicted to enhance RET homodimerization via extracellular domains that are proximal to the membrane. Importantly, a substitution leading to an unpaired cysteine that concurrently destabilizes RET tertiary structure is predicted to cause the paradoxical co-occurrence of MEN2A and HSCR. Our findings suggest a mechanistic basis for almost all identified pathological mutations in RET and that therapeutic strategies for targeting RET activity in HSCR and MEN2A may need to be orthogonal.
Ectopic gene conversion causing quantitative trait variation
Authors: Pfalz Marina , Naadja Seïf-Eddine , Shykoff Jacqui Anne , Kroymann Juergen 
Published: December 2024

AbstractWhy is there so much non-neutral genetic variation segregating in natural populations? We dissect function and evolution of a near-cryptic quantitative trait locus (QTL) for defense metabolites in Arabidopsis using the CRISPR/Cas9 system and nucleotide polymorphism patterns. The QTL is explained by genetic variation in a family of four tightly linked indole-glucosinolateO-methyltransferase genes. Some of this variation appears to be maintained by balancing selection, some appears to be generated by non-reciprocal transfer of sequence, also known as ectopic gene conversion (EGC), between functionally diverged gene copies. Here we elucidate how EGC, as an inevitable consequence of gene duplication, could be a general mechanism for generating genetic variation for fitness traits.
McsB regulates CtsR thermosensing through periphery arginine phosphorylation
Authors: Cai Huahuan , Hua Boyang , Guo Yeting , Xia Xing-Hua , Zhao Yufen 
Published: December 2024

AbstractPost-translational protein modifications (PTMs) are a ubiquitous phenomenon that exists in all domains of life. The bacterial transcription repressor CtsR becomes phosphorylated by the arginine kinase McsB when cells sense an elevated temperature in the environment. Here, we perform single-molecule experiments based on the protein-induced fluorescence enhancement (PIFE) effect to monitor the DNA-CtsR-McsB interaction. Our single-molecule analysis reveals that CtsR binds rapidly and stably to the cognate DNA, and that McsB transiently interacts with the DNA-bound CtsR. We determined the binding kinetics between McsB and the DNA-bound CtsR by single-molecule real-time binding assays, withkonandkoffof 0.80 μM-1s-1and 0.14 s-1, respectively. Through this interaction, McsB does not remove CtsR from the DNA, but instead alters its thermosensing behavior, lowering the temperature threshold for CtsR dissociation. Phosphorylation of several periphery arginine residues on CtsR underlies a plausible molecular mechanism for this effect. Taken together, these results provide insights into how CtsR might integrate inputs from different environment stresses and regulate the initiation of the heat-shock response when cells are faced with complex environment conditions.
MethylQUEEN: A Methylation Encoded DNA Foundation Model
Authors: Li Mingyang , Gu Ruichu , Fan Shiyu , Fan Yu , He Bo , Yang Jinmin , Chen Yuting , Xin Mengling , Wen Han , Yi Chengqi 
Published: December 2024

AbstractDNA 5-methylcytosine (5mC) modification plays a pivotal role in many biological processes, yet 5mC information and pattern hidden behind remains to be explored. Here, we developMethylation Language Model based onQuintupleBidirectional Transformer (MethylQUEEN), a novel pre-trained DNA methylation foundation model capable of sensing methylation states and covering the genome-wide methylation landscape. Through tailored methylation-prone pre-training, MethylQUEEN effectively captured epigenetics information hidden within the DNA sequences: it accurately traces DNA’s tissue-of-origin, and successfully recovers the expression profile through methylation states. Integrative analysis on MethylQUEEN’s attention scores also enables us to reveal the unique methylation status of a tissue for precise disease detection, and identifying key regulatory 5mC sites for disease intervention. As a result, MethylQUEEN signifies a new paradigm in methylation analysis for various biological problems. Besides, our study demonstrates the effectiveness of directly integrating methylation information into pre-training, offering new perspectives and methodologies for a range of methylation-related biological processes. It serves as an initial exploration for the development of more comprehensive epigenomic models.