Biology Open最新文献

{"title":"Ccn2a acts downstream of cx43 to influence joint formation during zebrafish fin regeneration.","authors":"Victoria Hyland, M Kathryn Iovine","doi":"10.1242/bio.061674","DOIUrl":"10.1242/bio.061674","url":null,"abstract":"<p><p>This study provides new insights into the molecular pathways dictating skeletal patterning during zebrafish fin regeneration. Connexin43 (Cx43) is known to influence skeletal patterning by inhibiting evx1 expression and thereby regulating the timing of joint formation. Here, we demonstrate that cellular communication network factor 2 (ccn2a) also contributes to this pathway. We find that Ccn2a appears to act downstream of Cx43 and similarly inhibits joint formation by inhibiting evx1 expression. Pharmacological inhibition of β-catenin demonstrates that ccn2a is likely regulated by β-catenin. Additionally, this paper provides evidence that Yap signaling contributes to joint formation through regulating ccn2a. These findings provide novel insights into the role of Ccn2a during skeletal patterning.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143439919","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The combinatorial binding syntax of transcription factors in forebrain-specific enhancers.","authors":"Fatima Batool, Huma Shireen, Muhammad Faizan Malik, Muhammad Abrar, Amir Ali Abbasi","doi":"10.1242/bio.061751","DOIUrl":"https://doi.org/10.1242/bio.061751","url":null,"abstract":"<p><p>Tissue-specific gene regulation in mammals involves the coordinated binding of multiple transcription factors (TFs). Using the forebrain as a model, we investigated the syntax of TF occupancy to determine tissue-specific enhancer regions. We analyzed forebrain-exclusive enhancers from the VISTA Enhancer Browser and a curated set of 23 TFs relevant to forebrain development and disease. Our findings revealed multiple distinct patterns of combinatorial TF binding, with the HES5-FOXP2-GATA3 triad being the most frequent in forebrain-specific enhancers. This syntactic structure was detected in 2614 enhancers from a genome-wide catalog of 25,000 predicted human forebrain enhancers. Notably, this catalog represents a computationally predicted dataset, distinct from the in vivo validated set of enhancers obtained from the VISTA Enhancer Browser. The shortlisted 2614 enhancers were further analyzed using genome-wide epigenetic data and evaluated for evolutionary conservation and disease relevance. Our findings highlight the value of these 2614 enhancers in forebrain-specific gene regulation and provide a framework for discovering tissue-specific enhancers, enhancing the understanding of enhancer function.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":"14 2","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143457056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A high-resolution bovine mitochondrial co-expression network.","authors":"Pâmela A Alexandre, Kate Keogh, Antonio Reverter, Nicholas J Hudson","doi":"10.1242/bio.061630","DOIUrl":"10.1242/bio.061630","url":null,"abstract":"<p><p>The mitochondrion is a sophisticated, versatile, and dynamic organelle whose function is incompletely understood. Intending to provide a framework for mitochondrial visualisation and interpretation of genome-wide molecular data, we reverse-engineered a co-expression network whose final structure represented mRNA encoding more than half of the entire mitochondrial proteome. We drew upon 723 RNA-seq data sets representing 91 tissues and cell types from 441 individual cattle. A mitochondrial landscape was formed comprising a main network and many smaller sub-networks. One of the discrete sub-networks contains all 13 mRNA (e.g. MT-ND1, MT -CYTB, MT -COX2, MT -ATP8) plus 15/22 tRNA (e.g. MT-TT) encoded by the mt-genome itself, indicating some independent regulation from the nuclear genome with whom it must cooperate. Intriguingly, this mtDNA sub-network also contains a single nuclear-encoded gene, that of PDHA1. PDHA1 encodes a subunit of the pyruvate dehydrogenase complex that governs the conversion of pyruvate to Acetyl CoA. This enzyme is extremely influential, representing the fundamental cellular connection between the ancient, conserved pathway of glycolysis that occurs exclusively in the cytoplasm, and the TCA cycle that occurs within the mitochondrial matrix. To demonstrate the downstream utility of our approach, we overlaid Longissimus dorsi muscle transcriptome data from differentially feed efficient Charolais and Holstein Friesian cattle. This approach highlighted expression patterns sensitive to both breed and diet in a complex manner. An analytic advantage of this approach is that relatively subtle (<2-fold) but coordinated changes that may be overlooked by conventional gene-by-gene significance testing become readily apparent. Finally, intending to understand the transcriptional regulation of mitochondrial function more thoroughly, we engineered a network built with transcription factors in addition to those mRNA encoding mitochondrial proteins. Here, a set of influential nuclear hormone receptors (e.g. PPARA) are enriched among the most highly and/or well-connected TF.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":"14 2","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11832118/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078620","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impairment of proteasome-associated deubiquitinating enzyme Uchl5/UBH-4 affects autophagy.","authors":"Sweta Jha, Johanna Pispa, Carina I Holmberg","doi":"10.1242/bio.061644","DOIUrl":"10.1242/bio.061644","url":null,"abstract":"<p><p>The autophagy-lysosomal pathway (ALP) and the ubiquitin-proteasome system (UPS) are the two major intracellular proteolytic systems that mediate protein turnover in eukaryotes. Although a crosstalk exists between these two systems, it is still unclear how UPS and ALP interact in vivo. Here, we investigated how impaired function of the proteasome-associated deubiquitinating enzyme (DUB) Uchl5/UBH-4 affects autophagy in human cells and in a multicellular organism. We show that downregulation of Uchl5 by siRNA reduces autophagy by partially blocking the fusion of autophagosomes with the lysosomes in HeLa cells, which is similar to a previously reported role of the proteasome-associated DUB Usp14 on autophagy. However, exposure of Caenorhabditis elegans to ubh-4 or usp-14 RNAi, or to their pharmacological inhibitors, results in diverse effects on numbers of autophagosomes and autolysosomes, without blocking the lysosomal fusion, in the intestine, hypodermal seam cells and the pharynx. Our results reveal that impairment of Uchl5/UBH-4 and Usp14 affects autophagy in a tissue context manner. A deeper insight into the interplay between UPS and ALP in various tissues in vivo has the potential to promote development of therapeutic approaches for disorders associated with proteostasis dysfunction.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":"14 2","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11832120/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143254714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"LRRC56 deletion causes primary ciliary dyskinesia in mice characterized by dynein arms defects.","authors":"Ruolan Wu, Huilong Li, Pingyun Wu, Qi Yang, Xueting Wan, Yuan Wu","doi":"10.1242/bio.061846","DOIUrl":"10.1242/bio.061846","url":null,"abstract":"<p><p>Leucine Rich Repeat Containing protein 56 (LRRC56), also known as DNAAF12, is a member of the LRRC superfamily, whose dysfunction is associated with mucociliary clearance and laterality defects in humans. Here, we generated LRRC56-knockout mice using the CRISPR/Cas9 nuclease system to specifically target exons 4-5 of the LRRC56 gene. We observed that homozygous LRRC56 gene deletion is definitely deleterious, as 27.8% of LRRC56-/- mice died before adulthood. Among the surviving LRRC56-/- mice, the most prominent phenotypes included hydrocephalus, situs inversus, male infertility, and bronchiectasis. Transmission electron microscopy revealed defects in dynein arms of cilia and disorganized axonemal structure in flagella. Immunofluorescence analysis similarly revealed the absence of inner and outer dynein arm markers DNALI1 and DNAI2 in the cilia. Heterozygous LRRC56+/- mice developed normally, without exhibiting any symptoms of primary ciliary dyskinesia. In conclusion, the knockout of the LRRC56 gene in mice leads to a range of conditions consistent with primary ciliary dyskinesia. The absence of DNALI1 and DNAI2 signaling in knockout mouse cilia supports the critical role of the LRRC56 gene in dynein arm assembly.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":"14 2","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11832119/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143254716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A larval zebrafish model of traumatic brain injury: optimizing the dose of neurotrauma for discovery of treatments and aetiology.","authors":"Laszlo F Locskai, Taylor Gill, Samantha A W Tan, Alexander H Burton, Hadeel Alyenbaawi, Edward A Burton, W Ted Allison","doi":"10.1242/bio.060601","DOIUrl":"10.1242/bio.060601","url":null,"abstract":"<p><p>Traumatic brain injuries (TBI) are diverse with heterogeneous injury pathologies, which creates challenges for the clinical treatment and prevention of secondary pathologies such as post-traumatic epilepsy and subsequent dementias. To develop pharmacological strategies that treat TBI and prevent complications, animal models must capture the spectrum of TBI severity to better understand pathophysiological events that occur during and after injury. To address such issues, we improved upon our recent larval zebrafish TBI paradigm emphasizing titrating to different injury levels. We observed coordination between an increase in injury level and clinically relevant injury phenotypes including post-traumatic seizures (PTS) and tau aggregation. This preclinical TBI model is simple to implement, allows dosing of injury levels to model diverse pathologies, and can be scaled to medium- or high-throughput screening.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":"14 2","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143398111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A CRISPR mis-insertion in the Zic3 5'UTR inhibits in vivo translation and is predicted to result in formation of a mRNA stem-loop hairpin.","authors":"Helen M Bellchambers, Maria B Padua, Stephanie M Ware","doi":"10.1242/bio.061677","DOIUrl":"https://doi.org/10.1242/bio.061677","url":null,"abstract":"<p><p>Zic3 loss of function is associated with a range of congenital defects, including heterotaxy and isolated heart defects in humans, as well as neural tube defects, situs anomalies, and tail kinks in model organisms. Here, we describe a novel Zic3ins5V mouse line generated due to a mis-insertion during the CRISPR genome editing process which altered the Zic3 5'UTR structure. Mice with this insertion developed similar phenotypes to Zic3LacZ null mice, including heterotaxy, isolated heart defects, neural tube defects and tail kinks. Surprisingly, gene expression analysis revealed that the novel Zic3ins5V line displays higher levels of Zic3 mRNA, but western blot analysis confirmed that levels of ZIC3 were greatly reduced in vivo. RNAfold, a RNA secondary structure prediction tool, showed that this mis-insertion may cause the formation of a large stem-loop hairpin incorporating some of the 5'UTR and first exon of Zic3, and the insertion of similar hairpins in a cell-based assay caused the loss of ZIC3. Thus, this mouse line displays a loss of ZIC3 protein consistent with the inhibitory effects of 5'UTR stem-loop hairpin structures.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143254749","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enteropathogenic E. coli effector Map interacts with Rab13 and regulates the depletion of the tight junction proteins occludin and claudins via cathepsin B-mediated mechanisms.","authors":"Anupam Mandal, Pangertoshi Walling, Shirin Qureshi, Kritika Kansal, Saima Aijaz","doi":"10.1242/bio.061794","DOIUrl":"https://doi.org/10.1242/bio.061794","url":null,"abstract":"<p><p>Infections by Enteropathogenic E. coli cause acute diarrheal disease in infants accounting for severe morbidity and mortality. One of the underlying causes of the disease is the break-down of the intestinal barrier maintained by the tight junctions (TJs). EPEC uses a type 3 secretion system to translocate more than twenty effectors into infected cells which disrupt several functions of the host cells. The effectors EspF, Map, EspG1/G2 and NleA have been reported to disrupt the TJs causing the leakage of charged ions and uncharged molecules through the barrier. We reported earlier that EspF and Map cause the depletion of TJ proteins claudin-1, claudin-4 and occludin through both transcriptional and post-transcriptional mechanisms. Here we show that the inhibition of the lysosomal protease cathepsin B, in cells expressing the EPEC effector Map, reduces the depletion of claudin-1, claudin-4 and occludin. Further, we show that the expression of a mutant Map protein lacking the mitochondrial targeting sequence inhibits the depletion of occludin and its delocalization from the TJs and partially rescues claudin-4 levels and its junctional localization. We also identified a novel interaction of Map with the GTPase Rab13. Rab13 has been reported to mediate the recycling of occludin to the plasma membrane. Since occludin regulates the passage of macromolecules through the intestinal TJ barrier, the interaction of Map with Rab13 may have important implications for the loss of TJ integrity and excessive leakage through the intestinal barrier in EPEC pathogenesis.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143254760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Air-liquid interface culture combined with differentiation factors reproducing intestinal cell structure formation in vitro.","authors":"Isamu Ogawa, Takaaki Nakai, Takahiro Iwao, Tamihide Matsunaga","doi":"10.1242/bio.061612","DOIUrl":"10.1242/bio.061612","url":null,"abstract":"<p><p>Reproducing intestinal cells in vitro is important in pharmaceutical research and drug development. Caco-2 cells and human iPS cell-derived intestinal epithelial cells are widely used, but few evaluation systems can mimic the complex crypt-villus-like structure. We attempted to generate intestinal cells mimicking the three-dimensional structure from human iPS cells. After inducing the differentiation of iPS cells into intestinal organoids, these were dispersed into single cells and cultured two-dimensionally. An air-liquid interface culture was used, with CHIR99021, forskolin, and A-83-01 used as key compounds. Long-term culture was also performed by adding Wnt3a, Noggin, and RSPO1, which are frequently used in organoid culture. The air-liquid interface culture combined several compounds that successfully induced the formation of a crypt-villus-like structure, which grew rapidly at around day 6. The expression of pharmacokinetic genes such as CYP3A4 was also enhanced. The intestinal stem cells were efficiently maintained by the addition of Wnt3a, Noggin, and RSPO1. We were able to construct a crypt-villus-like structure on cell culture inserts, which is considered a very simple culture platform. This structure had characteristics extremely similar to living intestinal tissues and may have a superior homeostatic mechanism.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":"14 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11789277/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143000468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gene expression and DNA methylation changes in response to hypoxia in toxicant-adapted Atlantic killifish (Fundulus heteroclitus).","authors":"Neelakanteswar Aluru, Yaamini R Venkataraman, Christopher S Murray, Veronica DePascuale","doi":"10.1242/bio.061801","DOIUrl":"10.1242/bio.061801","url":null,"abstract":"<p><p>Coastal fish populations are threatened by multiple anthropogenic impacts, including the accumulation of industrial contaminants and the increasing frequency of hypoxia. Some populations of the Atlantic killifish (Fundulus heteroclitus), like those in New Bedford Harbor (NBH), Massachusetts, USA, have evolved a resistance to dioxin-like polychlorinated biphenyls (PCBs) that may influence their ability to cope with secondary stressors. To address this question, we compared hepatic gene expression and DNA methylation patterns in response to mild or severe hypoxia in killifish from NBH and Scorton Creek (SC), a reference population from a relatively pristine environment. We hypothesized that NBH fish would show altered responses to hypoxia due to trade-offs linked to toxicant resistance. Our results revealed substantial differences between populations. SC fish demonstrated dose-dependent changes in gene expression in response to hypoxia, while NBH fish exhibited a muted transcriptional response to severe hypoxia. Interestingly, NBH fish showed significant DNA methylation changes in response to hypoxia, while SC fish did not exhibit notable epigenetic alterations. These findings suggest that toxicant-adapted killifish may face trade-offs in their molecular response to environmental stress, potentially impacting their ability to survive severe hypoxia in coastal habitats. Further research is needed to elucidate the functional implications of these epigenetic modifications and their role in adaptive stress responses.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":"14 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11744052/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142930620","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}