Biology OpenPub Date : 2025-08-15Epub Date: 2025-08-01DOI: 10.1242/bio.062014
Linda Serra, Anna Nordin, Mattias Jonasson, Carolina Marenco, Guido Rovelli, Annika Diebels, Francesca Gullo, Sergio Ottolenghi, Federico Zambelli, Michèle Studer, Giulio Pavesi, Claudio Cantù, Silvia K Nicolis, Sara Mercurio
{"title":"SOX2 and NR2F1 coordinate the gene expression program of the early postnatal visual thalamus.","authors":"Linda Serra, Anna Nordin, Mattias Jonasson, Carolina Marenco, Guido Rovelli, Annika Diebels, Francesca Gullo, Sergio Ottolenghi, Federico Zambelli, Michèle Studer, Giulio Pavesi, Claudio Cantù, Silvia K Nicolis, Sara Mercurio","doi":"10.1242/bio.062014","DOIUrl":"10.1242/bio.062014","url":null,"abstract":"<p><p>The thalamic dorsolateral geniculate nucleus (dLGN) receives visual input from the retina via the optic nerve, and projects to the cortical visual area, where eye-derived signals are elaborated. The transcription factors SOX2 and NR2F1 are directly involved in the differentiation of dLGN neurons, based on mouse work and patient mutations leading to vision defects. However, whether they regulate each other, or control common targets is still unclear. By RNA-seq analysis of neonatal dLGN from thalamo-specific Sox2 and Nr2f1 mouse mutants, we found a striking overlap of deregulated genes. Among them, Vgf, encoding a cytokine transported along thalamic-cortical axons is strongly downregulated in both mutants. Direct SOX2 binding to some of these genes was confirmed by CUT&RUN, which identified a SOX2 chromatin-binding pattern characteristic of the dLGN. Collectively, our genetic and molecular analyses on the SOX2 and NR2F1-coregulated genes contribute to our understanding of the gene regulatory network driving the differentiation and connectivity of thalamic neurons, and the vision impairments caused by mutations in these genes.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2025-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144590477","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}
Biology OpenPub Date : 2025-08-15Epub Date: 2025-07-29DOI: 10.1242/bio.061992
Will Scott, Vitaliia Polutranko, Jakub Milczarek, Ian Hands-Portman, Mohan K Balasubramanian
{"title":"Fluorescent protein tags for human tropomyosin isoform comparison.","authors":"Will Scott, Vitaliia Polutranko, Jakub Milczarek, Ian Hands-Portman, Mohan K Balasubramanian","doi":"10.1242/bio.061992","DOIUrl":"10.1242/bio.061992","url":null,"abstract":"<p><p>Tropomyosin is an important actin cytoskeletal protein underpinning processes such as muscle contraction, cell shape and cell division. Defects in tropomyosin function can lead to diseases, including some myopathies and allergies. In cells, tropomyosin molecules form coiled-coil dimers, which then polymerise end-to-end with other dimers for actin association. Tropomyosin is challenging to tag for in vivo fluorescence microscopy without perturbing its polymerisation interfaces. We recently developed a fluorescent tag comprising a 40-amino acid flexible linker capable of detecting tropomyosin in S. pombe actin cables and the actomyosin ring, and in patch-like structures that were previously unappreciated. We also used this strategy successfully to tag human TPM2.2, a prominent human muscle isoform. Here, we expanded this tool to visualise eight other human tropomyosin isoforms, using mNeonGreen, mCherry, mStayGold(E138D) and mScarlet3-H tags. All showed typical tropomyosin fluorescence, no signs of cytotoxicity and are compatible with super-resolution microscopy. These tools singly or in combination should aid detailed mechanistic investigations of tropomyosin isoforms.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2025-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144599487","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}
Biology OpenPub Date : 2025-08-15Epub Date: 2025-07-31DOI: 10.1242/bio.062091
Md Tangigul Haque, Shatabdi Paul, Md Kawsar Khan
{"title":"Heatwaves reduce mating frequency in an aquatic insect.","authors":"Md Tangigul Haque, Shatabdi Paul, Md Kawsar Khan","doi":"10.1242/bio.062091","DOIUrl":"10.1242/bio.062091","url":null,"abstract":"<p><p>Heatwaves are becoming more frequent and intense across the globe due to global warming. Heatwaves - unusual daytime and nighttime high temperatures over three consecutive days - can disrupt physiological functions of organisms, reducing fitness. Insects are stressed because of the increasing frequency and intensity of temperature extremes. While many studies have focused on insect behaviour during heatwaves in laboratory settings, the impact of natural heatwaves in the wild remains understudied. Here, we investigated the impact of natural heatwaves on mating behaviour, flight activity, and local abundance in the damselfly, Xanthagrion erythroneurum. We found that damselfly mating frequency decreased, while flight number and net population abundance remained unchanged during natural heatwaves. The decreased mating frequency may suggest a sex-specific decoupling of mate-searching efforts under thermal stress. Heatwave driven disruptions in mating behaviours and the occurrence of more frequent and acute heatwaves in the future may have long-term consequences for damselfly populations. Our results provide crucial data of the behaviour of thermally sensitive insects to heatwaves, which could assist in developing effective conservation strategies for maintaining biodiversity in a warming world.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2025-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144625386","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}
Biology OpenPub Date : 2025-07-28DOI: 10.1242/bio.061986
Jenna N Duttenhefner, Rahul R Singh, Katherine Schmidt, Katie M Reindl
{"title":"Multiomics analysis of GSTP1 knockdown pancreatic cancer cells reveals key regulators of redox and metabolic homeostasis.","authors":"Jenna N Duttenhefner, Rahul R Singh, Katherine Schmidt, Katie M Reindl","doi":"10.1242/bio.061986","DOIUrl":"https://doi.org/10.1242/bio.061986","url":null,"abstract":"<p><p>Glutathione S transferase pi-1 (GSTP1) is a detoxification enzyme essential for oxidative homeostasis. In cancer, GSTP1 has been implicated in tumorigenicity, cell cycle progression, and chemoresistance. While GSTP1 depletion has been associated with decreased cancer growth in various models, the mechanism remains poorly understood. This study investigates GSTP1 as a therapeutic target for pancreatic ductal adenocarcinoma (PDAC) using inducible knockdown models. We demonstrate that GSTP1 loss disrupts redox balance, impairs cell survival, and induces metabolic adaptations. Multiomics analysis characterized the global impact of inducible GSTP1 knockdown on the transcriptome and proteome of PDAC cells, identifying 550 differentially expressed genes and 62 proteins. Notably, 43 of these showed consistent regulation at both the mRNA and protein levels. We identify dysregulation of key stress response proteins, including dimethylarginine dimethylaminohydrolase 1 (DDAH1), involved in nitric oxide metabolism, and protein disulfide isomerase A6 (PDIA6), which maintains protein homeostasis. The interplay between GSTP1, DDAH1, and PDIA6 highlights the complexity of redox regulation in pancreatic cancer and suggests that targeting GSTP1 may offer a new therapeutic approach for PDAC.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144728047","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}
Biology OpenPub Date : 2025-07-28DOI: 10.1242/bio.062128
Satheeja Santhi Velayudhan, Chih-Wen Chu, Keiji Itoh, Sergei Y Sokol
{"title":"Mechanosensitive localization of Diversin highlights its function in vertebrate morphogenesis and planar cell polarity.","authors":"Satheeja Santhi Velayudhan, Chih-Wen Chu, Keiji Itoh, Sergei Y Sokol","doi":"10.1242/bio.062128","DOIUrl":"https://doi.org/10.1242/bio.062128","url":null,"abstract":"<p><p>Diversin is a vertebrate homolog of the core planar cell polarity (PCP) protein Diego. Here we studied the function of Diversin in Xenopus embryo morphogenesis and its subcellular localization at different locations in superficial ectoderm cells. Depletion of Diversin in the neuroectoderm inhibited apical domain size and neural tube closure and disrupted the polarized localization of endogenous Vangl2, another PCP protein. Whereas Diversin puncta were randomly distributed in early ectoderm, they acquired planar polarity in the neuroectoderm in a stage- and position-specific manner. We find that Diversin is accumulated at the cell junctions adjacent to apically constricting cells at the Xenopus neural plate border and the gastrula blastopore lip. Moreover, Diversin cytoplasmic puncta redistributed in the direction of the pulling forces from the cells with constricting apical domains, suggesting a mechanosensitive process. PCP complexes of Dishevelled (Dvl2) and Diversin or the mechanosensitive adaptor ADIP exhibited planar polarity in the neural plate and the wound edge and promoted wound healing. We propose that Diversin- and Dvl2-containing PCP complexes control morphogenesis in a tension-dependent manner.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144728046","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}
Biology OpenPub Date : 2025-07-28DOI: 10.1242/bio.062145
Lily A Kelleher, Manuela O Ramalho
{"title":"Impact of rising temperatures on the bacterial communities of Aphaenogaster ants.","authors":"Lily A Kelleher, Manuela O Ramalho","doi":"10.1242/bio.062145","DOIUrl":"https://doi.org/10.1242/bio.062145","url":null,"abstract":"<p><p>Studies have shown that biodiversity will be impacted by global climate change, with the effect on ants just beginning to be documented. However, this influence on ant symbiotic bacterial communities remains understudied. Aphaenogaster Mayr, 1853, are seed dispersing ants in deciduous forests and their bacterial communities have just been uncovered; however, much is unknown. We aim to determine the impact that warming temperatures will have on Aphaenogaster survival and on their bacterial communities. Ants from four colonies were collected from West Chester, Pennsylvania, USA and entire colonies were subjected to a control temperature (22 °C). After 6-12 months the same colonies were subjected to an experimental temperature (32 °C). DNA was then extracted from ants of all development stages and the 16S rRNA gene was amplified and sequenced following the NGS amplicon approach. The findings revealed that Aphaenogaster ant mortality rates increased, and their symbiotic bacterial communities changed in warmer temperatures. This resulted in a decrease in the presence of Wolbachia spp. and an increase in the presence of Corynebacterium sp. This study reveals important information about the impact of warming temperature on Aphaenogaster ants, and we suggested methods to help protect these ants and other insects in the future.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144728045","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}
Biology OpenPub Date : 2025-07-28DOI: 10.1242/bio.061904
Justin Wheelan, Melissa Spigelman, Angelo Cirinelli, James Reilly, Carlos A Molina
{"title":"Phosphorylation Deficient Inducible cAMP Early Repressor (ICER) Modulates Tumorigenesis and Survival in a Transgenic Zebrafish (Danio rerio) Model of Melanoma.","authors":"Justin Wheelan, Melissa Spigelman, Angelo Cirinelli, James Reilly, Carlos A Molina","doi":"10.1242/bio.061904","DOIUrl":"https://doi.org/10.1242/bio.061904","url":null,"abstract":"<p><p>Melanoma, the most lethal form of skin cancer, is commonly associated by mutations in the BRAF gene, particularly BRAFV600E, which drives tumor proliferation via ERK1/2 signaling cascade. While BRAF inhibitors initially demonstrate efficacy, therapeutic resistance remains a significant challenge. Emerging evidence implicates the cAMP signaling pathway, particularly the cAMP response element-binding protein (CREB) and its repressor, Inducible cAMP Early Repressor (ICER), in melanoma progression and drug resistance. ICER, a transcriptional repressor regulated via Ras/MAPK-mediated phosphorylation and ubiquitination, is degraded in melanoma, undermining its tumor-suppressive role. In a brafV600E; p53(loss of function) transgenic zebrafish (Danio rerio) model, we investigated the role of a ubiquitin-resistant ICER mutant (S35-41A-ICER) in tumor progression. Transgenic fish expressing S35-41A-ICER exhibited extended survival and reduced tumor invasiveness compared to wild-type ICER. RNA sequencing revealed dysregulation of CREB/CREM targets and compensatory pathways, including Rap1 and PI3K/AKT signaling, as well as candidate gene targets of ICER regulation, including the Protein Kinase A catalytic subunit prkacaa. Our findings suggest that a ubiquitin resistant ICER mitigates melanoma progression and represses oncogenic pathways in a brafV600E melanoma context.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144728048","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}
Biology OpenPub Date : 2025-07-15Epub Date: 2025-07-18DOI: 10.1242/bio.061970
Mohamed Jemaà, Amine Bourzam, Marwen Ben Fdilen, Mariem Sellami
{"title":"From Primary Cell to Organoid: the proliferative fate international conference and workshop.","authors":"Mohamed Jemaà, Amine Bourzam, Marwen Ben Fdilen, Mariem Sellami","doi":"10.1242/bio.061970","DOIUrl":"10.1242/bio.061970","url":null,"abstract":"<p><p>Cell culture is an essential tool for basic, biomedical and translational research. This can be as routine as growing cell lines for toxicity assays, as specific and personalised as patient-derived cell culture, or it can mimic physiological conditions such as organoid culture. In order to train and promote collaborative research among North African researchers in the field of cell culture, a consortium formed by the Faculty of Sciences of Tunis, Tunisia, the Laboratory of Neurophysiology, Cellular Physiopathology and Valorisation of Biomolecules, the Merck Group and Learn and Win decided to organise a North African conference and workshop on complex cell culture, from primary cells to organoids. For 1 week, from 18 to 23 November 2024, more than 500 young researchers and students in the life sciences and more than 30 international speakers and trainers met at the Faculty of Sciences in Tunis, Tunisia, to discuss cell culture technology and protocols, from primary cell culture to organoids, with a strong focus on technologies and discoveries. This meeting review describes the scientific event and highlights the main results of both the conferences and the practical sessions.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":"14 7","pages":""},"PeriodicalIF":1.7,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12309900/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144658482","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}
Biology OpenPub Date : 2025-07-15Epub Date: 2025-07-28DOI: 10.1242/bio.062079
Rahul Kumar, Ritika Mukherji, Kamakshi Singh
{"title":"Reflections on the EMBO Workshop: Neuroscience of Sleep 2025.","authors":"Rahul Kumar, Ritika Mukherji, Kamakshi Singh","doi":"10.1242/bio.062079","DOIUrl":"10.1242/bio.062079","url":null,"abstract":"<p><p>The inaugural EMBO workshop on the neuroscience of sleep took place from 11th-13th March 2025 at the India Habitat Centre in New Delhi, India, and marked a milestone for the global sleep research community. It overlapped with the 25th anniversary of the discovery of sleep in Drosophila, and the meeting celebrated the scientific advances in recognising sleep as a deeply conserved and biologically vital process. With around 85 participants from across the globe, the workshop brought together scientists to explore the biological, molecular, and computational dimensions of sleep across scales. The conference program included keynote lectures from the pioneers in sleep research, exciting new studies on sleep's role in regulating neural computation, metabolism, and plasticity, and reflected the increasing interest in the field for sleep studies in non-model organisms in natural settings. In addition to the science, the conference involved thoughtful talks and conversations around women in science, gender equity, and varied career paths, with many participants sharing their own experiences. The meeting being hosted in India allowed space for meaningful exchange, collaboration, and mentorship among researchers of the Global South. This Meeting Review captures an overview of the scientific discussions that made this event a success.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":"14 7","pages":""},"PeriodicalIF":1.7,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144728050","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}
Biology OpenPub Date : 2025-07-15Epub Date: 2025-07-09DOI: 10.1242/bio.062057
Mariam Duhaini, Habiba S Shamroukh, Zhi Zhang, Kalyan C Kondapalli
{"title":"Astrocyte secretome remodeling under iron deficiency: potential implications for brain iron homeostasis.","authors":"Mariam Duhaini, Habiba S Shamroukh, Zhi Zhang, Kalyan C Kondapalli","doi":"10.1242/bio.062057","DOIUrl":"10.1242/bio.062057","url":null,"abstract":"<p><p>The brain is the most metabolically active organ in the body and has a high demand for iron. Iron deficiency impairs brain function and is linked to various neurological disorders. To maintain iron homeostasis, astrocytes respond to iron levels and signal brain microvascular endothelial cells (BMVECs), which regulate iron import into the brain. However, the specific signaling molecules released by astrocytes remain largely unknown. In this study, we addressed this by performing a global proteomic analysis of the secretome of primary mouse astrocytes cultured under iron-deficient conditions. Quantitative mass spectrometry demonstrated significant remodeling of the astrocyte secretome in response to iron deficiency, affecting critical pathways related to metabolic reprogramming, stress responses, and cellular communication. We identified specific secreted factors with potential roles in paracrine signaling, with their secretion supported by prediction analysis. Our analysis also revealed novel condition-specific proteins. These findings provide new insights into astrocyte communication under iron stress and its potential influence on iron availability at the blood-brain barrier. This study establishes a foundation for future investigations into astrocyte-secreted factors and their roles in neurological diseases associated with iron dysregulation.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12309891/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538950","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}