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Longitudinal trajectories of brain development from infancy to school age and their relationship to literacy development. 从婴儿期到学龄期大脑发育的纵向轨迹及其与识字发展的关系。
bioRxiv : the preprint server for biology Pub Date : 2025-04-06 DOI: 10.1101/2024.06.29.601366
Ted K Turesky, Elizabeth Escalante, Megan Yf Loh, Nadine Gaab
{"title":"Longitudinal trajectories of brain development from infancy to school age and their relationship to literacy development.","authors":"Ted K Turesky, Elizabeth Escalante, Megan Yf Loh, Nadine Gaab","doi":"10.1101/2024.06.29.601366","DOIUrl":"10.1101/2024.06.29.601366","url":null,"abstract":"<p><p>Reading is one of the most complex skills that we utilize daily, and it involves the early development and interaction of various lower-level subskills, including phonological processing and oral language. These subskills recruit brain structures, which begin to develop long before the skill manifests and exhibit rapid development during infancy. However, how longitudinal trajectories of early brain development in these structures supports long-term acquisition of literacy subskills and subsequent reading is unclear. Children underwent structural and diffusion MRI scanning at multiple timepoints between infancy and second grade and were tested for literacy subskills in preschool and decoding and word reading in early elementary school. We developed and implemented a reproducible pipeline to generate longitudinal trajectories of early brain development to examine associations between these trajectories and literacy (sub)skills. Furthermore, we examined whether familial risk of reading difficulty and home literacy environment, two common literacy-related covariates, influenced those trajectories. Results showed that individual differences in curve features (e.g., intercepts and slopes) for longitudinal trajectories of volumetric, surface-based, and white matter organization measures were linked directly to phonological processing and indirectly to second-grade decoding and word reading skills via phonological processing. Altogether, these findings suggest that the brain bases of phonological processing, previously identified as the strongest behavioral predictor of reading and decoding skills, may already begin to develop early in infancy but undergo further refinement between birth and preschool. The present study underscores the importance of considering academic skill acquisition from the very beginning of life.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11244924/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141618031","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Secreted retropepsin-like enzymes are essential for stress tolerance and biofilm formation in Pseudomonas aeruginosa. 铜绿假单胞菌的渗透胁迫耐受性、抗生素耐药性和生物膜形成需要一类分泌型逆胃蛋白酶样酶。
bioRxiv : the preprint server for biology Pub Date : 2025-04-06 DOI: 10.1101/2025.03.18.643919
Justin D Lormand, Charles H Savelle, Jennifer K Teschler, Eva Lopez, Richard H Little, Jacob Malone, Fitnat H Yildiz, Maria J Garcia-Garcia, Holger Sondermann
{"title":"Secreted retropepsin-like enzymes are essential for stress tolerance and biofilm formation in <i>Pseudomonas aeruginosa</i>.","authors":"Justin D Lormand, Charles H Savelle, Jennifer K Teschler, Eva Lopez, Richard H Little, Jacob Malone, Fitnat H Yildiz, Maria J Garcia-Garcia, Holger Sondermann","doi":"10.1101/2025.03.18.643919","DOIUrl":"10.1101/2025.03.18.643919","url":null,"abstract":"<p><p>Proteases regulate important biological functions. Here we present the structural and functional characterization of three previously uncharacterized aspartic proteases in <i>Pseudomonas aeruginosa</i> . We show that these proteases have structural hallmarks of retropepsin peptidases and play redundant roles for cell survival under hypoosmotic stress conditions. Consequently, we named them retropepsin-like osmotic stress tolerance peptidases (Rlo). Our research shows that while Rlo proteases are homologous to RimB, an aspartic peptidase involved in rhizosphere colonization and plant infection, they contain N-terminal signal peptides and perform distinct biological functions. Mutants lacking all three secreted Rlo peptidases show defects in antibiotic resistance, biofilm formation, and cell morphology. These defects are rescued by mutations in the inactive transglutaminase transmembrane protein RloB and the cytoplasmic ATP-grasp protein RloC, two previously uncharacterized genes in the same operon as one of the Rlo proteases. These studies identify Rlo proteases and <i>rlo</i> operon products as critical factors in clinically relevant processes, making them appealing targets for therapeutic strategies against <i>Pseudomonas</i> infections.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11957051/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143757205","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Fructose-2,6-bisphosphate restores TDP-43 pathology-driven genome repair deficiency in motor neuron diseases. 果糖-2,6-二磷酸恢复运动神经元疾病中TDP-43病理驱动的基因组修复缺陷。
bioRxiv : the preprint server for biology Pub Date : 2025-04-05 DOI: 10.1101/2024.11.13.623464
Anirban Chakraborty, Joy Mitra, Vikas H Malojirao, Manohar Kodavati, Santi M Mandal, Satkarjeet K Gill, Sravan Gopalkrishnashetty Sreenivasmurthy, Velmarini Vasquez, Mikita Mankevich, Balaji Krishnan, Gourisankar Ghosh, Muralidhar Hegde, Tapas Hazra
{"title":"Fructose-2,6-bisphosphate restores TDP-43 pathology-driven genome repair deficiency in motor neuron diseases.","authors":"Anirban Chakraborty, Joy Mitra, Vikas H Malojirao, Manohar Kodavati, Santi M Mandal, Satkarjeet K Gill, Sravan Gopalkrishnashetty Sreenivasmurthy, Velmarini Vasquez, Mikita Mankevich, Balaji Krishnan, Gourisankar Ghosh, Muralidhar Hegde, Tapas Hazra","doi":"10.1101/2024.11.13.623464","DOIUrl":"10.1101/2024.11.13.623464","url":null,"abstract":"<p><p>TAR DNA-binding protein 43 (TDP-43) proteinopathy plays a critical role in neurodegenerative diseases, including amyotrophic lateral sclerosis and frontotemporal dementia (FTD). In our recent discovery, we identified that TDP-43 plays an essential role in DNA double-strand break (DSB) repair via the non-homologous end joining (NHEJ) pathway. Here, we found persistent DNA damage in the brains of ALS/FTD patients, primarily in the transcribed regions of the genome. We further investigated the underlying mechanism and found that polynucleotide kinase 3'-phosphatase (PNKP) activity was severely impaired in the nuclear extracts of both patient brains and TDP-43-depleted cells. PNKP is a key player in DSB repair within the transcribed genome, where its 3'-P termini processing activity is crucial for preventing persistent DNA damage and neuronal death. The inactivation of PNKP in ALS/FTD was due to reduced levels of its interacting partner, phosphofructo-2-kinase fructose 2,6 bisphosphatase (PFKFB3), and its biosynthetic product, fructose-2,6-bisphosphate (F2,6BP), an allosteric modulator of glycolysis. Recent work from our group has shown that F2,6BP acts as a positive modulator of PNKP activity in vivo. Notably, exogenous supplementation with F2,6BP restored PNKP activity in nuclear extracts from ALS/FTD brain samples and patient-derived induced pluripotent stem (iPS) cells harboring pathological mutations. Furthermore, we demonstrate that supplementation of F2,6BP restores genome integrity and partially rescues motor phenotype in a Drosophila model of ALS. Our findings underscore the possibility of exploring the therapeutic potential of F2,6BP or its analogs in TDP-43 pathology-associated motor neuron diseases.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11844424/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143485396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A scoping study of the whole-cell imaging literature: a foundational corpus, potential for data-mining and research synthesis, and a call for standardization of an emerging field. 全细胞成像文献的范围研究:基础语料库,数据挖掘和研究综合的潜力,以及对新兴领域标准化的呼吁。
bioRxiv : the preprint server for biology Pub Date : 2025-04-05 DOI: 10.1101/2025.02.03.636363
Mary Mirvis, Brooke Weingard, Steven Goodman, Wallace F Marshall
{"title":"A scoping study of the whole-cell imaging literature: a foundational corpus, potential for data-mining and research synthesis, and a call for standardization of an emerging field.","authors":"Mary Mirvis, Brooke Weingard, Steven Goodman, Wallace F Marshall","doi":"10.1101/2025.02.03.636363","DOIUrl":"10.1101/2025.02.03.636363","url":null,"abstract":"<p><p>The level of cellular organization bridging the mesoscale and whole-cell scale is coming into focus as a new frontier in cell biology. Great progress has been made in unraveling the complex physical and functional interconnectivity of organelles, but how the entire organelle network is spatially arranged within the cytoplasm is only beginning to be explored. Drawing on cross-disciplinary research synthesis methods, we systematically curated the whole-cell volumetric imaging literature, resulting in a corpus consisting of 89 studies and 118 image datasets. We describe the trajectory and current state of the field between 2004 and 2024. A broad characterization, or 'scoping review', of bibliometrics, study design, and reporting practices shows accelerating technological development and research output. We find high variability in study design and reporting practices, including imaging modality, model organism, cellular contexts, organelles imaged, and analyses. Due to the laborious, low-throughput nature of most volumetric imaging methods, we find trends toward small sample sizes (<10 cells) and small cell types. We describe common quantitative analyses across studies, including volumetric ratios of organelles and inter-organelle contact analyses. This work establishes the initial iteration of a growing dataset of whole-cell imaging literature and data, and motivates a call for standardized whole-cell imaging study design, reporting, and data sharing practices in the context of an emerging sub-field of cell biology. Our curated dataset now provides the basis for a plethora of future aggregate and comparative analyses to reveal larger patterns and generalized hypotheses about the systems behavior and regulation of whole-cell organelle networks. More broadly, we showcase the potential of new rigorous secondary research methods to strengthen cell biology's literature review and reproducibility toolkit, create new avenues for discovery, and promote open research practices that support secondary data-reuse and integration.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11838562/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143461344","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Hyperreflexia after corticospinal tract lesion reflects 1A afferent circuit changes not increased KCC2 hyperexcitability. 皮质脊髓束病变后的高反射反映1A传入回路的改变,而不是KCC2高兴奋性的增加。
bioRxiv : the preprint server for biology Pub Date : 2025-04-05 DOI: 10.1101/2025.02.21.639555
Thelma Bethea, Temitope Adegbenro, John H Martin
{"title":"Hyperreflexia after corticospinal tract lesion reflects 1A afferent circuit changes not increased KCC2 hyperexcitability.","authors":"Thelma Bethea, Temitope Adegbenro, John H Martin","doi":"10.1101/2025.02.21.639555","DOIUrl":"10.1101/2025.02.21.639555","url":null,"abstract":"<p><p>Hyperreflexia is a consequence of spinal cord injury (SCI) and motor system lesions in the brain Two major mechanisms underpinning hyperreflexia have been reported: proprioceptive afferent (PA) circuit changes produced by 1A fiber sprouting, which could enhance reflex signaling, together with reduced GABAergic inhibitory presynaptic regulation (GABApre); and increased intrinsic motor neuron excitability, for example, produced by reduced motor neuron membrane-bound potassium-chloride co-transporter2 (KCC2). Here we examine how selective unilateral CST injury in the medullary pyramid (PTX), which eliminates the CST from one hemisphere, allows for specific investigation of the different mechanisms to determine their contributions to hyperreflexia. We used rate-dependent depression (RDD) of the Hoffmann (H)-reflex for the forelimb and hindlimb 5th-digit abductor muscles to assess hyperreflexia on both the contra- and ipsilesional sides. We compared RDD in naive and unilateral-PTX rats at 7-dpi and 42-dpi, supplemented with additional timepoints to examine hyperreflexia development. Immunohistochemistry was used to identify PA synapses (VGlut1), GABA presynaptic boutons (GABApre), motor neurons (ChAT), and to measure KCC2. Following unilateral PTX, we observed significant hyperreflexia in the contralesional forelimb only. Membrane-bound KCC2 was unchanged in contralesional cervical motor neurons. Whereas both cervical and lumbar motor neurons showed increased PA sprouting contralesionally, there was a concomitant increase in GABApre terminals for the lumbar not cervical cord, which associated with a normal hindlimb H-reflex. Our findings show that KCC2 is disassociated from hyperreflexia in the uniPTX model. Instead, forelimb hyperreflexia can be explained by cervical motor neuron PA sprouting and an uncompensated GABApre regulation.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11870509/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143545552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Effects of in vitro hemolysis and repeated freeze-thaw cycles in protein abundance quantification using the SomaScan and Olink assays. 体外溶血和反复冻融循环对使用SomaScan和Olink测定蛋白质丰度的影响。
bioRxiv : the preprint server for biology Pub Date : 2025-04-05 DOI: 10.1101/2024.09.21.613295
Julián Candia, Giovanna Fantoni, Ruin Moaddel, Francheska Delgado-Peraza, Nader Shehadeh, Toshiko Tanaka, Luigi Ferrucci
{"title":"Effects of in vitro hemolysis and repeated freeze-thaw cycles in protein abundance quantification using the SomaScan and Olink assays.","authors":"Julián Candia, Giovanna Fantoni, Ruin Moaddel, Francheska Delgado-Peraza, Nader Shehadeh, Toshiko Tanaka, Luigi Ferrucci","doi":"10.1101/2024.09.21.613295","DOIUrl":"10.1101/2024.09.21.613295","url":null,"abstract":"<p><p>SomaScan and Olink are affinity-based platforms that aim to estimate the relative abundance of thousands of human proteins with a broad range of endogenous concentrations. In this study, we investigated the effects of in vitro hemolysis and repeated freeze-thaw cycles in protein abundance quantification across 10,776 (11K SomaScan) and 1472 (Olink Explore 1536) analytes, respectively. Using SomaScan, we found two distinct groups, each one consisting of 4% of all aptamers, affected by either hemolysis or freeze-thaw cycles. Using Olink, we found 6% of analytes affected by freeze-thaw cycles and nearly half of all measured probes significantly impacted by hemolysis. Moreover, we observed that Olink probes affected by hemolysis target proteins with a larger number of annotated protein-protein interactions. We found that Olink probes affected by hemolysis were significantly associated with the erythrocyte proteome, whereas SomaScan probes were not. Given the extent of the observed nuisance effects, we propose that unbiased, quantitative methods of evaluating hemolysis, such as the hemolysis index successfully implemented in many clinical laboratories, should be adopted in proteomics studies. We provide detailed results for each SomaScan and Olink probe in the form of extensive Supplementary Data files to be used as resources for the growing user communities of both platforms.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956925/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143757323","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Molecular Crowding Suppresses Mechanical Stress-Driven DNA Strand Separation. 分子拥挤抑制机械应力驱动的DNA链分离。
bioRxiv : the preprint server for biology Pub Date : 2025-04-03 DOI: 10.1101/2024.12.11.628023
Parth Rakesh Desai, John F Marko
{"title":"Molecular Crowding Suppresses Mechanical Stress-Driven DNA Strand Separation.","authors":"Parth Rakesh Desai, John F Marko","doi":"10.1101/2024.12.11.628023","DOIUrl":"10.1101/2024.12.11.628023","url":null,"abstract":"<p><p>Molecular crowding influences DNA mechanics and DNA - protein interactions and is ubiquitous in living cells. Quantifying the effects of molecular crowding on DNA supercoiling is essential to relating in-vitro experiments to in-vivo DNA supercoiling. We use single molecule magnetic tweezers to study DNA supercoiling in the presence of dehydrating or crowding co-solutes. To study DNA supercoiling, we apply a stretching force of 0.8 pN to the DNA and then rotate one end of the DNA to induce supercoiling. In a 200 mM NaCl buffer without co-solutes, negatively supercoiled DNA absorbs some of the torsional stress by forming locally melted DNA regions. The base pairs in these locally melted regions are believed to adopt a configuration where nucleotide base pairing is disrupted. We find that the presence of a dehydrating co-solute like glycerol further destabilizes base-pairs in negatively supercoiled DNA. The presence of polyethylene glycol, commonly used as a crowding agent, suppresses local strand separation and results in plectoneme formation even when DNA is negatively supercoiled. The results presented in this letter suggest further directions for studies of DNA supercoiling and supercoiled DNA-protein interactions in molecular conditions that approximate in-vivo molecular composition.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11661227/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142879078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
BASELINE: A CRISPR Base Editing Platform for Mammalian-Scale Single-Cell Lineage Tracing. 基线:用于哺乳动物单细胞谱系追踪的CRISPR碱基编辑平台。
bioRxiv : the preprint server for biology Pub Date : 2025-04-03 DOI: 10.1101/2025.03.19.644238
Evan Winter, Francesco Emiliani, Aidan Cook, Asma Abderrahim, Aaron Henrik McKenna
{"title":"BASELINE: A CRISPR Base Editing Platform for Mammalian-Scale Single-Cell Lineage Tracing.","authors":"Evan Winter, Francesco Emiliani, Aidan Cook, Asma Abderrahim, Aaron Henrik McKenna","doi":"10.1101/2025.03.19.644238","DOIUrl":"10.1101/2025.03.19.644238","url":null,"abstract":"<p><p>A cells fate is shaped by its inherited state, or lineage, and the ever-shifting context of its environment. CRISPR-based recording technologies are a promising solution to map the lineage of a developing system, yet challenges remain regarding single-cell recovery, engineering complexity, and scale. Here, we introduce BASELINE, which uses base editing to generate high-resolution lineage trees in conjunction with single-cell profiling. BASELINE uses the Cas12a adenine base editor to irreversibly edit nucleotides within 50 synthetic target sites, which are integrated multiple times into a cells genome. We show that BASELINE accumulates lineage-specific marks over a wide range of biologically relevant intervals, recording more than 4300 bits of information in a model of pancreatic cancer, a 50X increase over existing technologies. Single-cell sequencing reveals high-fidelity capture of these recorders, recovering lineage reconstructions up to 40 cell divisions deep, within the estimated range of mammalian development. We expect BASELINE to apply to a wide range of lineage-tracing projects in development and disease, especially in which cellular engineering makes small, more distributed systems challenging.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11957144/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143757225","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Human differentiated adipocytes can serve as surrogate mature adipocytes for adipocyte-derived extracellular vesicle analysis. 人分化脂肪细胞可作为成熟脂肪细胞的替代品,用于脂肪细胞来源的细胞外囊泡分析。
bioRxiv : the preprint server for biology Pub Date : 2025-04-03 DOI: 10.1101/2025.02.05.636729
Mangesh Dattu Hade, Bradley L Butsch, Paola Loreto Palacio, Kim Truc Nguyen, Dharti Shantaram, Sabrena Noria, Stacy A Brethauer, Bradley J Needleman, Willa Hsueh, Eduardo Reategui, Setty M Magana
{"title":"Human differentiated adipocytes can serve as surrogate mature adipocytes for adipocyte-derived extracellular vesicle analysis.","authors":"Mangesh Dattu Hade, Bradley L Butsch, Paola Loreto Palacio, Kim Truc Nguyen, Dharti Shantaram, Sabrena Noria, Stacy A Brethauer, Bradley J Needleman, Willa Hsueh, Eduardo Reategui, Setty M Magana","doi":"10.1101/2025.02.05.636729","DOIUrl":"10.1101/2025.02.05.636729","url":null,"abstract":"<p><p>Obesity is a growing global health concern, contributing to diseases such as cancer, autoimmune disorders, and neurodegenerative conditions. Adipose tissue dysfunction, characterized by abnormal adipokine secretion and chronic inflammation, plays a key role in these conditions. Adipose-derived extracellular vesicles (ADEVs) have emerged as critical mediators in obesity-related diseases. However, the study of mature adipocyte-derived EVs (mAdipo-EVs) is limited due to the short lifespan of mature adipocytes in culture, low EV yields, and the low abundance of these EV subpopulations in the circulation. Additionally, most studies rely on rodent models, which have differences in adipose tissue biology compared to humans. To overcome these challenges, we developed a standardized approach for differentiating human preadipocytes (preAdipos) into mature differentiated adipocytes (difAdipos), which produce high-yield, human adipocyte EVs (Adipo-EVs). Using visceral adipose tissue from bariatric surgical patients, we isolated the stromal vascular fraction (SVF) and differentiated preAdipos into difAdipos. Brightfield microscopy revealed that difAdipos exhibited morphological characteristics comparable to mature adipocytes (mAdipos) directly isolated from visceral adipose tissue, confirming their structural similarity. Additionally, qPCR analysis demonstrated decreased preadipocyte markers and increased mature adipocyte markers, further validating successful differentiation. Functionally, difAdipos exhibited lipolytic activity comparable to mAdipos, supporting their functional resemblance to native adipocytes. We then isolated preAdipo-EVs and difAdipo-EVs using tangential flow filtration and characterized them using bulk and single EV analysis. DifAdipo-EVs displayed classical EV and adipocyte-specific markers, with significant differences in biomarker expression compared to preAdipo-EVs. These findings demonstrate that difAdipos serve as a reliable surrogate for mature adipocytes, offering a consistent and scalable source of adipocyte-derived EVs for studying obesity and its associated disorders. Keywords: extracellular vesicles, adipocyte, adipose, adipocyte-derived extracellular vesicles, obesity.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11839020/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143461602","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Trikafta rescues F508del-CFTR by tightening specific phosphorylation-dependent interdomain interactions. Trikafta 通过加强特定的磷酸化依赖性域间相互作用来挽救 F508del-CFTR 。
bioRxiv : the preprint server for biology Pub Date : 2025-04-03 DOI: 10.1101/2024.11.20.624197
Guangyu Wang
{"title":"Trikafta rescues F508del-CFTR by tightening specific phosphorylation-dependent interdomain interactions.","authors":"Guangyu Wang","doi":"10.1101/2024.11.20.624197","DOIUrl":"10.1101/2024.11.20.624197","url":null,"abstract":"<p><p>Trikafta is well-known for correcting thermal and gating defects caused by the most common cystic fibrosis mutation F508del in the human cystic fibrosis transmembrane conductance regulator even at a physiological temperature. However, the exact correction pathway is still unclear. Here, noncovalent interactions among two transmembrane domains (TMD1 and TMD2), the regulatory (R) domain and two nucleotide binding domains (NBD1 and NBD2) were analyzed. The thermal stability of NBD1 was also evaluated through its tertiary constrained noncovalent interaction networks or thermoring structures. The results demonstrated that Trikafta binding to flexible TMD1 and TMD2 rearranged their interactions with the R domain upon phosphorylation, coupling tightened cytoplasmic TMD1-TMD2 interactions to tightened Mg/ATP-dependent NBD1-NBD2 dimerization, which stabilized NBD1 above human body temperature. Overall, although the deletion of F508 induces the primary thermal defect in NBD1 and then the gating defect at the TMD1-TMD2 interface, Trikafta rescued them in a reverse manner allosterically. These mechanistic insights into the precise correction pathway of this misfolded channel facilitate optimizing cystic fibrosis treatment.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11601583/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142742274","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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