Biology Open最新文献

{"title":"Kinetic properties of optogenetic site-specific DNA recombination by LiCre-loxP.","authors":"Alice Dufour, Hélène Duplus-Bottin, Thomas Boukéké-Lesplulier, Eliane Casassa, Gérard Triqueneaux, Léo Tarbouriech, Camille Darthenay-Kiennemann, Agnès Dumont, Catherine Moali, Franck Vittoz, Daniel Jost, Gaël Yvert","doi":"10.1242/bio.062381","DOIUrl":"10.1242/bio.062381","url":null,"abstract":"<p><p>Advances in optogenetics now allow specific modifications to the DNA of live cells with light. However, successfully using these technologies requires knowing their properties in terms of sensitivity, efficiency, kinetics and mechanism. We previously developed an optogenetic tool made of a single chimeric protein called LiCre that enables the induction of specific changes in the genome with blue light via DNA recombination between loxP sites ( Duplus-Bottin et al., 2021). Here, we used in vitro and in vivo experiments combined with kinetic modeling to provide a deeper characterization of the photoactivated LiCre-loxP recombination reaction. We find that LiCre binds DNA with high affinity in the absence of a light stimulus and that this binding is cooperative, although not as much as for the Cre recombinase from which LiCre was derived. In yeast, the addition of riboflavin to the culture medium had no effect on LiCre's efficiency, even when cells over-expressed riboflavin kinase, suggesting that the abundance of the flavin mononucleotide cofactor is not limiting for the reaction. However, LiCre's efficiency in yeast gradually increased when raising the temperature from 20°C to 37°C. The recombination kinetics observed in live cells are best explained by a model where the photoactivation of two or more DNA-bound LiCre units (happening in seconds) can produce (in several minutes) a functional recombination synapse. This model was able to capture the effect of a point mutation altering LiCre's light cycle. This deeper understanding of the LiCre-loxP system provides additional knowledge for designing experiments where specific genetic changes are induced in live cells with light.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":"15 5","pages":""},"PeriodicalIF":1.8,"publicationDate":"2026-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13225215/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147926570","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":"Low oxygen environment alters transcripts related to energy metabolism without altering the pluripotency core of bovine embryonic stem cells.","authors":"Ramon C Botigelli, Rachel Braz Arcanjo, Carly Guiltinan, Amanda J Morton, Justin M Smith, Anna C Denicol","doi":"10.1242/bio.062352","DOIUrl":"10.1242/bio.062352","url":null,"abstract":"<p><p>Stem cell pluripotency is shaped by culture microenvironment. Growth factors, cytokines, and oxygen tension are key regulators of self-renewal and pluripotency state. Here we evaluated the adaptation of bovine embryonic stem cells (bESC) derived on mouse embryonic fibroblasts (MEF) to feeder-free conditions and the effects of low oxygen (5% O2) on their molecular profile. Primed bESC established on MEF and 21% O2 (high oxygen) were adapted to 5% O2 (low oxygen) and to feeder-free conditions in vitronectin to generate four culture conditions: high and low O2 tension in MEF and feeder-free. Adaptation to feeder-free upregulated transcripts related to cell differentiation in bESC cultured in high compared to low oxygen. Transition of bESC on MEF from normoxia to 5% O2 did not alter cell morphology or growth. Interestingly, colony morphology was maintained when transitioning bESC from MEF into feeder-free in low oxygen. Furthermore, there were fewer transcriptomic changes in bESC grown on MEF compared to feeder-free in low compared to high oxygen. While low oxygen tension did not alter the pluripotency profile of bESC, it promoted transcriptional changes related to energetic metabolism and increased mitochondrial membrane potential. These findings emphasize the importance of oxygen tension for derivation, maintenance, and performance of ESC.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2026-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13225197/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147762604","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":"AXL receptor tyrosine kinase regulates Golgi organization and function via an adhesion-Arf1 signalling axis in breast and lung cancer cell lines.","authors":"Prachi Joshi, Arnav Saha, Radhika Malaviya, Debiprasad Panda, Grishma Mehta, Manojeet Pattanayak, Vibha Singh, Nagaraj Balasubramanian","doi":"10.1242/bio.062581","DOIUrl":"10.1242/bio.062581","url":null,"abstract":"<p><p>Cell-matrix adhesion regulates membrane trafficking, Golgi organization, and function. Altered Golgi organization in cancer cells may influence trafficking and cargo processing. A simple screen revealed distinct, adhesion-dependent differences in Golgi organization across breast (MDAMB231 versus MCF7) and lung (A549 versus CaLu1) cancer cell lines. To identify regulators driving these differences, we performed an in silico analysis of differentially expressed genes in the Cancer Cell Line Encyclopedia dataset, integrating Golgi-associated functions from interaction networks and literature. This analysis highlighted AXL as a putative Golgi regulator. AXL is prominently localized to the Golgi and is displaced upon inhibition with R428, which disrupts Golgi organization. AXL knockdown also does the same. AXL-mediated regulation of the Golgi is adhesion dependent. Mechanistically, AXL controls Arf1 activation through an AMPK-GBF1 pathway. Targeting of AMPK activation thus significantly reverses R428-mediated Golgi disorganization. Loss of adhesion promotes AMPK and reduces Arf1 activity, displacing AXL and Arf1 from the Golgi, driving its disorganization. This impacts Golgi-associated functions, tubulin acetylation in MDAMB231 cells, and cell-surface glycosylation in A549 cells. Together, our findings identify an adhesion-AXL-AMPK-GBF1-Arf1 pathway governing Golgi organization and function in cancer cells.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":"15 5","pages":""},"PeriodicalIF":1.8,"publicationDate":"2026-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13225716/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147970661","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":"Background colour preference in juvenile European lobster (Homarus gammarus).","authors":"Matt E Bell, Nicholas Kuvaldin, Erik Romero Frontaura, Felix K A Kuebutornye, Paula Costa Domech, Carlos Espírito-Santo, Rodrigo O A Ozório, Alex H L Wan","doi":"10.1242/bio.062203","DOIUrl":"10.1242/bio.062203","url":null,"abstract":"<p><p>The European lobster (Homarus gammarus) is a commercially valuable species facing increasing anthropogenic pressure. As hatchery-based restocking and aquaculture expand, optimising artificial rearing conditions, particularly environmental factors like habitat colouration are essential for improving welfare. The present study investigated background colour preference in juvenile (poststage V) lobsters. Custom triangle segments were 3D printed with different-coloured filaments and assembled into hexagonal chambers. In sub-trial 1, each chamber contained six colour: black, red, blue, green, white, and yellow. Lobster behavioural responses were measured using three metrics: time spent (duration), number of incidental movements, and final colour settlement. These metrics had five behavioural parameters: mean duration, total duration, colour preference ratio, final colour settlement and incidental movement. An assessment of these metrics and behavioural parameters revealed that lobsters had a similarly significant preference for black and red background colours. To discern whether there is a higher preference for one colour over the other, sub-trial 2 was performed, using equal black and red segments. Sub-trial 2 indicates that the preference for red is marginally greater than black under the same metrics. These findings contribute to a better understanding of lobster environmental preference and can inform the design of aquaculture systems to enhance animal welfare.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2026-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13225228/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147572299","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":"Separating the generational effects of temperature and viscosity on the body size of a freshwater Mesocyclops copepod.","authors":"Zachary Wagner, Griffin Wagner, David M Fields, Jeannette Yen","doi":"10.1242/bio.062549","DOIUrl":"10.1242/bio.062549","url":null,"abstract":"<p><p>Copepods are small crustacean zooplankton that closely follow Bergmann's rule, which states that larger organisms will be found at higher latitudes. While thermally driven metabolic effects and food availability are often stated to be the major drivers behind this trend, temperature affects multiple variables within the copepod and its environment, a key variable to copepod ecology being viscosity. To test the effects of viscosity on copepod body size, two lineages of subtropical, freshwater Mesocyclops sp. copepods were grown for five generations in cultures of differing temperatures, 30°C and 18°C, and viscosities, natural and altered to mimic 18°C while at 30°C. Copepods grown at 30°C were, on average, 13.20% smaller than those grown at 18°C, regardless of viscosity. Copepods grown in 30°C cultures with a viscosity of 18°C had no body size differences when compared to copepods grown at 30°C and a natural viscosity. Copepods reached sexual maturity after 10 days while grown at 30°C and after 13 days while grown at 18°C, with viscosity playing no role in maturation time. As such, this study provides further support for temperature driving copepod body size, with the viscosity of the environment playing no discernible role in the body size of these small organisms.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2026-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13225232/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147697677","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":"Profiling cell proliferation after whole-genome duplication in human cells.","authors":"Guang Yang, Masaya Inoko, Kaito Ogura, Sumire Ishida-Ishihara, Yuki Tsukada, Akira Funahashi, Masanao Sato, Ryota Uehara","doi":"10.1242/bio.062568","DOIUrl":"10.1242/bio.062568","url":null,"abstract":"<p><p>Though whole-genome duplication (WGD) contributes to cancer progression, the mechanism of post-WGD cell proliferation remains unclear. Here, using 6-day live-imaging, we analyzed the proliferation dynamics of more than 150 post-WGD HCT116 cell lineages. A quantitative comparison of mitotic patterns and cell fates between proliferative and non-proliferative lineages revealed that multipolar chromosome segregation in early mitosis is a potential key factor limiting the proliferative capacity of post-WGD progenies. Multipolar chromosome segregation correlated with suppressed post-WGD cell viability, particularly when accompanied by drastic chromosome loss or when it repeatedly occurred. Tracing proliferative lineages elucidated that they proliferated mainly by imposing the risk of multipolar chromosome segregation on one of two sub-lineages that formed after the first bipolar division. Meanwhile, a considerable proportion of proliferative lineages consisted entirely of progeny of early multipolar chromosome segregation events. Our results highlight key cellular events that determine the proliferation dynamics and diversity of post-WGD progenies, providing a fundamental reference for understanding WGD-associated biological processes.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2026-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13267767/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147866921","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":"Uncoupling of nutrient sensing and cell size control by specific defects in ceramide structure.","authors":"José Ignacio Quesada-Márquez, Ana Serrano, María Alcaide-Gavilán, Rafael Lucena","doi":"10.1242/bio.062633","DOIUrl":"10.1242/bio.062633","url":null,"abstract":"<p><p>Ceramides are essential structural lipids whose chemical diversity arises from variations in acyl-chain length and sphingoid-base modifications, yet how these structural features couple metabolic state to growth regulation remains unclear. In Saccharomyces cerevisiae, the target of rapamycin complex 2 (TORC2)-Ypk1/2 signaling axis coordinates plasma membrane homeostasis with cellular growth; however, the lipid-derived signals modulating this pathway are not fully defined. Here, we establish that the elongation of very long-chain fatty acids (VLCFAs), specifically to C26, is a critical determinant of the nutrient-dependent regulation of TORC2 activity. Based on a molecular caliper model for acyl-chain determination, we show that the TORC2-Ypk1 axis is specifically tuned to detect the successful completion of C26-VLCFA synthesis. Disrupting VLCFA elongation (elo3Δ) triggers constitutive TORC2 hyperactivation and a failure to reduce cell size in response to nutrient limitation. By expressing mammalian ceramide synthases (CerS1-CerS4), we demonstrate that TORC2 nutrient sensing is specifically tuned to acyl-chain length. While CerS1, CerS3, and CerS4 restore the rapid, nutrient-induced downregulation of TORC2, CerS2 expression phenocopies the elo3Δ mutant, exhibiting a total kinetic failure to inhibit TORC2 signaling upon nutrient shift. Notably, cells producing C18 ceramides (GhLag1) maintained size control despite elevated TORC2 activity, revealing that ceramide-dependent signaling intensity and the physical execution of size regulation can be uncoupled. We further demonstrate that while sphingoid-base hydroxylation is required for the execution of size remodeling, it is dispensable for nutrient sensing; sur2Δ mutants exhibited severe size defects despite maintaining statistically normal, nutrient-responsive TORC2 signaling. Overall, our findings reveal a functional hierarchy where the protein-mediated caliper measurement of VLCFA length serves as the primary sensor for TORC2 nutrient responsiveness, while subsequent lipid modifications govern the biophysical execution of cell size control.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2026-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13267774/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147833862","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":"Isolation, validation, and long-term culture of mouse ear fibroblasts.","authors":"Katie L Barnes, Nicole M Davis, Billy J Erazo, Katie M Cataldo, Emmaly H Bertges, Laura J Knoll","doi":"10.1242/bio.062483","DOIUrl":"10.1242/bio.062483","url":null,"abstract":"<p><p>Primary fibroblasts are essential cell culture models for studying cellular homeostasis, disease mechanisms, and host-pathogen interactions. Primary cells offer physiological relevance that immortalized cell lines cannot recapitulate. However, existing protocols for isolating and culturing primary fibroblasts lack standardization for long-term applications. Contamination by non-fibroblast cell types, variable media formulations, and poorly monitored passage numbers remain critical challenges for reproducibility. Here, we present a streamlined, cost-optimized protocol for isolating and culturing mouse ear fibroblasts (MEarFs) suitable for extended passages. We demonstrate that enriched media (Advanced DMEM/F-12+15% FBS) consistently promoted adipocyte-like cell contamination in long-term MEarF cultures. In contrast, minimal media (DMEM+10% FBS) proved sufficient for both isolation and long-term cultures, with fibroblast gene expression confirmed through passage 9. Cells displayed characteristic fibroblast morphology, expressed the mesenchymal marker vimentin, and maintained fibroblast-associated transcripts with minimal epithelial and adipocyte marker expression throughout the culture. Bulk RNA sequencing revealed that 17% of mapped genes exhibited differential abundance between passage 3 and passage 9, with enrichment in functional categories related to cell cycle regulation and paracrine signaling. This protocol provides an accessible primary fibroblast cell culture model with broad research applications, emphasizing reproducibility and resource-conscious practices.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2026-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13225709/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147762460","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":"Live-cell tracking of biliverdin trafficking reveals metabolic exchange between plastids and peroxisomes.","authors":"Mone Shibata, Keiji Yoshida, Hitomi Takahashi, Yutaka Kodama","doi":"10.1242/bio.062435","DOIUrl":"10.1242/bio.062435","url":null,"abstract":"<p><p>Metabolite trafficking between organelles is widespread, yet many trafficking routes remain poorly understood. Biliverdin (BV), a tetrapyrrolic pigment, is involved in redox and light signaling in animal and plant cells. To visualize the inter-organelle trafficking of BV in living cells, we used small ultrared fluorescent protein (smURFP), a BV-induced far-red fluorescent protein typically used for deep-tissue imaging in animals. Upon targeting smURFP to various organelles in plant cells, we detected fluorescence from BV-bound smURFP in plastids and peroxisomes. Enhanced BV biosynthesis in plastids led to greater smURFP fluorescence in peroxisomes and vice versa, indicating bidirectional trafficking of BV between these organelles. We also observed trafficking of BV between the cytosol and both plastids and peroxisomes, suggesting that bidirectional trafficking of BV between plastids and peroxisomes occurs via the cytosol. These findings provide a dynamic model for organelle-level metabolite trafficking.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2026-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13225713/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147833764","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":"Shifting paradigms: phosphatases from basic biology to druggable targets.","authors":"Catia L Pierotti, Marian Brenner, Yamini Chand, Fabrice Krier, Melina Lappe, Franziska Schedel, Malgorzata Trebacz","doi":"10.1242/bio.062400","DOIUrl":"10.1242/bio.062400","url":null,"abstract":"<p><p>The EMBO Workshop 'Phosphatases: from basic research to translation' (27 to 31 July 2025, Würzburg, Germany) brought together researchers from academia and industry for a deep dive into the rapidly evolving world of phosphatase biology. Over five days, participants explored the interplay of phosphatase structure, function, regulation, and signalling, while also uncovering their expanding influence in cancer, immunology, neurological disorders, and cardiometabolic health. The central focus of the meeting was the accelerating progress in phosphatase drug discovery, an enzyme class historically considered undruggable. This Meeting Review summarises the key findings and novel insights presented at the meeting and reflects the progress being made in the field.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":"15 5","pages":""},"PeriodicalIF":1.8,"publicationDate":"2026-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13225212/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147833848","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}