Biology Open最新文献

{"title":"Primed bovine embryonic stem cell lines can be derived at diverse stages of blastocyst development with similar efficiency and molecular characteristics.","authors":"Carly Guiltinan, Ramon C Botigelli, Juliana I Candelaria, Justin M Smith, Rachel B Arcanjo, Anna C Denicol","doi":"10.1242/bio.061819","DOIUrl":"10.1242/bio.061819","url":null,"abstract":"<p><p>In this study, we established bovine embryonic stem cell (bESC) lines from early (eBL) and full (BL) blastocysts to determine the efficiency of bESC derivation from an earlier embryonic stage and compare the characteristics of the resulting lines. Using established medium and protocols for derivation of primed bESCs from expanded blastocysts, we derived bESC lines from eBLs and BLs with the same efficiency (4/12 each, 33%). Regardless of original blastocyst stage, bESC lines had a similar phenotype, including differentiation capacity, stable karyotype, and pluripotency marker expression over feeder-free transition and long-term culture. Transcriptome and functional analyses indicated that eBL- and BL-derived lines were in primed pluripotency. We additionally compared RNA-sequencing data from our lines to bovine embryos and stem cells from other recent reports, finding that base medium was the predominant source of variation among cell lines. In conclusion, our results show that indistinguishable bESC lines can be readily derived from eBL and BL, widening the pool of embryos available for bESC establishment. Finally, our investigation points to sources of variation in cell phenotype among recently reported bESC conditions, opening the door to future studies investigating the impact of factors aside from signaling molecules on ESC derivation, maintenance, and performance.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11911636/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143432428","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":"Fast & Fair peer review: a bold experiment in scientific publishing.","authors":"Daniel A Gorelick, Alejandra Clark","doi":"10.1242/bio.061982","DOIUrl":"https://doi.org/10.1242/bio.061982","url":null,"abstract":"","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":"14 3","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699693","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":"From fossils to future - Jane Francis on polar exploration and changing climates.","authors":"Katie Pickup","doi":"10.1242/bio.061973","DOIUrl":"10.1242/bio.061973","url":null,"abstract":"<p><p>Professor Dame Jane Francis is a palaeoclimatologist whose research has focused on studying fossil plants, particularly from polar regions, to understand past biodiversity and climate. She is the Director of the British Antarctic Survey (BAS) and Chancellor of the University of Leeds, UK. She was awarded the Polar Medal for her contributions to British polar research in 2002, only the fourth woman to receive this recognition at that time. Throughout her career, Jane has conducted numerous Antarctic and Arctic expeditions, camping in remote and extreme environments to collect data about the polar regions from the days of the dinosaurs when Antarctica and the Arctic were warmer and covered in forests. We met at the BAS headquarters in Cambridge, UK, sitting alongside her collection of petrified fossil wood. Here, we discuss what these fossil plants can tell us about climate, the importance of Antarctic research in understanding our changing world, and the benefits of open science in promoting collaboration and even reducing carbon emissions.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":"14 3","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699696","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":"Deciphering the flapping frequency allometry: unveiling the role of sustained body attitude in the aerodynamic scaling of normal hovering animals.","authors":"Jeremy Pohly, Chang-Kwon Kang, Hikaru Aono","doi":"10.1242/bio.061932","DOIUrl":"10.1242/bio.061932","url":null,"abstract":"<p><p>Hovering flight helps facilitate feeding, pollination, and courtship. Observed only in smaller flying animals, hover kinematic characteristics are diverse except for the decreasing flapping frequency with the animal size. Although studies have shown that these wing patterns enable distinct unsteady aerodynamic mechanisms, the role of flapping frequency scaling remains a source of disagreement. Here we show that negative allometry of the flapping frequency is required to sustain body attitude during hovering, consistent with experimental data of hovering animals, from fruit flies to hummingbirds, reported in the literature. The derived scaling model reveals that the lift coefficient and reduced frequency remain invariant with mass, enabling leading-edge vortex formation and wake-capture for a wide range of fliers to hover.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11928051/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143457060","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":"Neurogenetic disorders associated with mutations in the FERRY complex: a novel disease class?","authors":"R Madison Riffe, Gerald B Downes","doi":"10.1242/bio.061808","DOIUrl":"10.1242/bio.061808","url":null,"abstract":"<p><p>The five-subunit endosomal Rab5 and RNA/ribose intermediary (FERRY) complex is a newly described protein complex consisting of TBCK, PPP1R21, FERRY3 (previously C12orf4), CRYZL1, and GATD1. The FERRY complex is proposed to function as a Rab5 effector to shuttle mRNA to the cell periphery for local translation, a process especially important in cells with far reaching processes. Interestingly, three members of the FERRY complex are associated with ultra-rare neurogenetic disorders. Mutation of TBCK causes TBCK syndrome, mutation of PPP1R21 is associated with PPP1R21-related intellectual disability, and mutation of FERRY3 results in an autosomal recessive intellectual disability. Neurologic disorders have yet to be associated with mutation of GATD1 or CRYZL1. Here, we provide a review of each FERRY complex-related neurologic disorder and draw clinical comparisons between the disease states. We also discuss data from the current cellular and animal models available to study these disorders, which is notably disparate and scattered across different cell types and systems. Taken together, we explore the possibility that these three diseases may represent one shared disease class, which could be further understood by combining and comparing known information about each individual disease. If true, this could have substantial implications on our understanding of the cellular role of the FERRY complex and on treatment strategies for affected individuals, allowing researchers, clinicians, and patient organizations to maximize the utility of research efforts and resources to support patients with these disorders.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":"14 3","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11928052/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143584557","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 CRISPR mis-insertion in the Zic3 5'UTR inhibits in vivo translation and is predicted to result in formation of an mRNA stem-loop hairpin.","authors":"Helen M Bellchambers, Maria B Padua, Stephanie M Ware","doi":"10.1242/bio.061677","DOIUrl":"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, an 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 expression. 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":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11957448/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of vessel noise on beluga (Delphinapterus leucas) call type use: ultrasonic communication as an adaptation to noisy environments?","authors":"Valeria Vergara, Marie-Ana Mikus, Clément Chion, Dominic Lagrois, Marianne Marcoux, Robert Michaud","doi":"10.1242/bio.061783","DOIUrl":"10.1242/bio.061783","url":null,"abstract":"<p><p>Animal vocalizations can evolve structural features as long-term adaptations to noisy environments. Using such signals, cetaceans could mitigate masking from vessel noise. This study investigates whether beluga whales (Delphinapterus leucas) use ultrasonic high-frequency burst pulse (HFBP) calls to communicate in noisy conditions. We identified HFBP calls in three populations: St Lawrence Estuary, Eastern High Arctic-Baffin Bay, and Western Hudson Bay. Focusing on the industrialized St Lawrence, we investigated the effects of vessel noise on HFBP call rates compared to other call types. Ultrasonic calls, spanning a bandwidth of 36.4±6.5 to 144 kHz (Nyquist frequency), comprised 13% of the St Lawrence beluga repertoire (n=25,435). Noise events (n=21) were defined as periods when at least one vessel was visible within 2 km of the hydrophone while belugas were within 500 m. Sound pressure levels were measured before, during, and after exposure. Generalized linear mixed models revealed consistent HFBP call rates before, during, and after vessel noise exposure, while contact calls and other call types declined during exposure (n=4528). These findings suggest that ultrasonic signals that evolved in the Arctic - where ice-associated noise may have created a need for high-frequency communication - remain a viable communication channel in vessel noise, allowing belugas to exploit these signals to maintain communication. Understanding how belugas use signals in noisy environments can inform conservation strategies for noise-impacted marine mammals.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11957452/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143490681","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":"Zebrafish ETS transcription factor Fli1b functions upstream of Scl/Tal1 during embryonic hematopoiesis.","authors":"Valentina Laverde, Luiza Loges, Saulius Sumanas","doi":"10.1242/bio.061948","DOIUrl":"https://doi.org/10.1242/bio.061948","url":null,"abstract":"<p><p>During embryonic development vascular endothelial and hematopoietic cells are thought to originate from a common precursor, the hemangioblast. An evolutionarily conserved ETS transcription factor FLI1 has been previously implicated in the hemangioblast formation and hematopoietic and vascular development. However, its role in regulating hemangioblast transition into hematovascular lineages is still incompletely understood. Its zebrafish paralog Fli1b functions partially redundantly with an ETS transcription factor Etv2 / Etsrp during vasculogenesis and angiogenesis. However, its role in embryonic hematopoiesis has not been previously investigated. Here we show that zebrafish fli1b mutants have a reduced formation of primitive erythrocytes and hematopoietic stem and progenitor cells, and display reduced expression of key regulators of hematopoiesis, including scl / tal1, gata1 and runx1. Expression of scl / tal1 was sufficient to partially rescue defects in erythroid differentiation in fli1b mutants, arguing that scl functions downstream of fli1b during primitive erythropoiesis. In addition, myelopoiesis was strongly misregulated in fli1b mutants. While the formation of the earliest myeloid progenitors, neutrophils and macrophages, was greatly reduced in fli1b mutants, this was compensated by the increased emergence of the myeloid cells from the alternative hematopoietic site, the endocardium. Intriguingly, myeloid cells in fli1b mutants retained vascular endothelial marker expression, suggesting that they are present in hemangioblast-like state. In summary, our results demonstrate a novel role of fli1b transcription factor in regulating embryonic hematopoiesis.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143613450","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":"Differential effect of ubiquitous and germline depletion of Integrator complex function on C. elegans physiology.","authors":"Brandon M Waddell, Alice Ronita Roy, Carlos Zapien Verdugo, Cheng-Wei Wu","doi":"10.1242/bio.061930","DOIUrl":"https://doi.org/10.1242/bio.061930","url":null,"abstract":"<p><p>The Integrator is a metazoan-conserved protein complex with endonuclease activity that functions to cleave various RNA substrates to shape transcriptome homeostasis by coordinating small nuclear RNA biogenesis to premature transcription termination. Depletion of Integrator results in developmental defects across different model systems and has emerged as a causative factor in human neurodevelopmental syndromes. Here, we use the model system Caenorhabditis elegans to enable studying the temporal effects of Integrator depletion on various physiological parameters with the auxin-inducible degron system that permitted depletion of INTS-4 (Integrator subunit) catalytic subunit of the protein complex. We found that Integrator activity is critical and required for C. elegans development within the L1 larval stage, but becomes dispensable for development and lifespan after the animals have reached the L2/L3 stage. Depletion of INTS-4 only shortened lifespan if auxin was introduced at the L1 stage, suggesting that the previously described lifespan reduction by Integrator inhibition is linked to developmental growth defects. We also found that while germline-specific degradation of Integrator results in the accumulation of misprocessed snRNA transcript, it did not impair the development or lifespan but surprisingly increased progeny production. Together, our study illustrates a temporal, and a potential tissue-specific requirement of the Integrator complex function in shaping whole organism development, aging, and reproduction.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143603497","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":"Metabolic depression and non-specific immune response during hibernation of common Asian toad, Duttaphrynus melanostictus.","authors":"Debadas Sahoo, Sibakalyani Acharya","doi":"10.1242/bio.061789","DOIUrl":"https://doi.org/10.1242/bio.061789","url":null,"abstract":"<p><p>To assess metabolic depression and non-specific immune response during hibernation in the common Asian toad, Duttaphrynus melanostictus, we measured activities of different enzymes of both aerobic (Oxygen-dependent) and anaerobic (Oxygen-independent) metabolic pathways in liver tissue and some non-specific immune responses in blood and liver tissue by obtaining hibernating toads directly from their hibernaculum in nature. Though decreased activities of enzymes and suppressions of non-specific immune responses were hypothesised, some contrasting results were found. Activities of citrate synthase (CS) and isocitrate dehydrogenase (ICDH) enzymes of aerobic metabolic pathways showed a significant decrease in their activities during hibernation up to 29% and 61% respectively of their active period value. Contrary to our hypothesis enzymes of oxygen-independent metabolic pathways i.e. pyruvate kinase (PK) and lactate dehydrogenase (LDH) showed no significant changes in their activities during hibernation compared to the active period. This shows aerobic metabolic depression during normoxic hibernation in common Asian toads and maintenance of vital activities at a minimum level with utilisation of energy (ATP) generated from the oxygen-independent metabolic pathway. Likewise, the non-specific immune response comprising total leucocyte count, individual leucocytes like neutrophil, eosinophil, basophil, lymphocyte and monocytes showed a significant decrease in their count during hibernation along with a reduction in complement proteins indicated by serum bacteria-killing ability, compared to active period. In contrast, the levels of reactive oxygen species (ROS) in liver tissue resulting in oxidative stress in terms of TBARS formed and GSSG/GSH ratio were significantly higher during hibernation, suggesting some components of non-specific immunity remain elevated. So, we conclude that, though there is suppression of non-specific immune response during hibernation to a maximum extent to conserve energy, some components of it in terms of oxidative stress are still in an active state to provide the signal to adaptive immunity for a quick response that is expected during post hibernation phase. Further, it indicates that non-specific immune response during hibernation is variable and tissue-specific.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143432425","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}