Open Biology最新文献

{"title":"Biochemistry and physiology of voltage-gated calcium channel trafficking: a target for gabapentinoid drugs.","authors":"Annette C Dolphin","doi":"10.1098/rsob.250013","DOIUrl":"10.1098/rsob.250013","url":null,"abstract":"<p><p>Voltage-gated calcium channels are multi-pass transmembrane proteins that have key features that are essential for their correct function. For example, the concerted movement of the voltage sensor domains in response to depolarization is required to ensure the channels open over a particular range of voltages, essential for the physiological function of each of the 10 different mammalian calcium channels. Furthermore, their selectivity filter is required to maintain the Ca²⁺ selectivity of these channels. The auxiliary subunits, α₂δ and β, play important roles in aiding the channels to fold, traffic and function correctly. Of therapeutic importance, the α₂δ subunits are a drug target of the gabapentinoid α₂δ ligands, whose mechanism of action is now better understood. However, much is still unknown about how these calcium channels reach and are retained in specific locations, and how these processes are modified by various forms of modulation and synaptic plasticity.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 7","pages":"250013"},"PeriodicalIF":3.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12303104/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144643122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pattern recognition in living cells through the lens of machine learning.","authors":"Frank Britto Bisso, Rodrigo Aguilar, Durga Shree, Yinan Zhu, Mijael Espinoza, Benjamin Diaz, Christian Cuba Samaniego","doi":"10.1098/rsob.240377","DOIUrl":"10.1098/rsob.240377","url":null,"abstract":"<p><p>At a coarse level, pattern recognition within cells involves sensing of environmental signals by surface receptors, and activating downstream signalling pathways that ultimately drive a transcriptome response, enabling biological functions such as differentiation, migration, proliferation, apoptosis or cell-type specification. This kind of decision-making process resembles a classification task that, inspired by machine learning concepts, can be understood in terms of a decision boundary: the combination of inputs relative to the classification region defined by this boundary defines context-specific responses. In this report, we contextualize machine learning concepts within a biological framework to explore the structural and functional similarities (and differences) between artificial neural networks, signalling pathways and gene regulatory networks. We take a preliminary look at neural network architectures that may better suit biological classification tasks, explore how learning fits into this paradigm, and address the role of competitive binding in cellular computation. Altogether, we envision a new research direction at the intersection of systems and synthetic biology, advancing our understanding of the inherent computational capacities of signalling pathways and gene regulatory networks.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 7","pages":"240377"},"PeriodicalIF":3.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12303112/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144643124","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Oxidized phospholipid damage signals as modulators of immunity.","authors":"Joon H Choi, Jonathan C Kagan","doi":"10.1098/rsob.240391","DOIUrl":"10.1098/rsob.240391","url":null,"abstract":"<p><p>Damage-associated molecular patterns (DAMPs) are self-derived molecules released during tissue damage that influence immune responses. Phospholipids, essential to cell membranes and lung surfactants, become oxidized under conditions of cellular stress, forming oxidized phospholipids. Unlike their unoxidized counterparts, oxidized phospholipids function as DAMPs and engage pattern recognition receptors (PRRs) on innate immune cells, activating signalling pathways that regulate immune responses. This activity alters innate immune cells, which in turn modulate the adaptive immune response, ultimately contributing to the pathogenesis of disease. Traditionally considered pro-inflammatory, recent studies reveal a more nuanced role for these lipids, with their effects on immune cells being context dependent. This review examines the mechanisms behind the generation of oxidized phospholipids and their induction in disease. We focus on recent studies that clarify how these lipids affect innate immune cells, leading to downstream effects on adaptive immunity, as well as their direct influence on adaptive immune cells. Finally, we explore therapeutic strategies targeting oxidized phospholipids to regulate immunity, offering insights into their broader role in immune regulation and potential applications in disease prevention.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 7","pages":"240391"},"PeriodicalIF":3.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12307067/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144743514","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Establish a simple and quantitative deep learning-based method to analyse complicated intra- and inter-species social interaction behaviour for four stag beetle species.","authors":"Michael Edbert Suryanto, Petrus Siregar, Tzong-Rong Ger, Chung-Der Hsiao","doi":"10.1098/rsob.250060","DOIUrl":"10.1098/rsob.250060","url":null,"abstract":"<p><p>Stag beetles (Lucanidae) exhibit diverse social behaviours, yet quantifying these interactions remains challenging. Understanding social interactions within and between species is crucial for comprehending their behaviour, ecology and evolution. Stag beetles exhibit diverse social behaviours, including intraspecific competition, courtship and interspecific interactions, often involving complex physical displays and subtle cues. Traditional ethological methods for analysing these behaviours are time-consuming, subjective and limited in their ability to capture the nuances of dynamic interactions. This project aims to develop a simple and quantitative deep learning-based method to analyse complicated intra- and inter-species social interaction behaviour in four stag beetle species. This study utilizes DeepLabCut™ (DLC), a state-of-the-art deep learning-based pose estimation tool, to analyse and compare intra- and inter-species social interactions in four stag beetle species: <i>Phalacrognathus muelleri</i>, <i>Prosopocoilus astacoides</i>, <i>Dorcus titanus</i> and <i>Prosopocoilus inclinatus</i>. High-resolution videos of staged encounters were collected, and DLC was trained to accurately track key body parts of individual beetles. Behavioural parameters such as distance between individuals, orientation angles and movement trajectories were extracted from the pose data. Statistical analyses were conducted to identify species-specific differences in social behaviour, including aggression levels, courtship displays and dominance hierarchies. This study demonstrates the effectiveness of DLC in objectively quantifying complex social interactions in insects, providing valuable insights into the social ecology and evolutionary divergence of stag beetles.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 7","pages":"250060"},"PeriodicalIF":3.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12308235/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144591917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The challenge of measuring mosquito flight performance: going beyond sterile insect technique and into transgenic and gene drive-based approaches.","authors":"Paola Najera, Christian E Ogaugwu, Tyler F Chan, Raja Babu Singh Kushwah, Zach Adelman","doi":"10.1098/rsob.240400","DOIUrl":"10.1098/rsob.240400","url":null,"abstract":"<p><p>Invasive insects inflict global costs of more than 70 billion USD annually by destroying crops and spreading disease-causing pathogens. Sterile insect technique (SIT), an insect population control method, involves the irradiation or chemical sterilization of insects to produce sterile males that are mass-released. SIT has proven effective in reducing populations of the Mediterranean fruit fly, Mexican fruit fly and screwworm fly. In the past decade, efforts to improve SIT with transgenic approaches have increased, including the development of potentially highly invasive gene drive transgenes. Determining flight capability is vital to the success of any insect control programme, and various flight assays can be used to analyse insect dispersal, flight behaviour and the mechanics behind flight. However, traditional flight assays such as mark-release-recapture become more challenging with transgenic or gene drive arthropods due to ecological concerns, while assays such as wind tunnels or flight mills/arenas may not capture the full range of flight abilities. This review seeks to cover current flight assays and their limitations as well as the requirements for flight assays to establish comparative flight ability for genetically modified insects to better prioritize strains prior to any potential field-based releases.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 6","pages":"240400"},"PeriodicalIF":4.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12187402/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144485354","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Glissandra oviformis</i> n. sp.: a novel predatory flagellate illuminates the character evolution within the eukaryotic clade CRuMs.","authors":"Euki Yazaki, Ryo Harada, Ryu Isogai, Kohei Bamba, Ken-Ichiro Ishida, Yuji Inagaki, Takashi Shiratori","doi":"10.1098/rsob.250057","DOIUrl":"10.1098/rsob.250057","url":null,"abstract":"<p><p>Culturing protists offers a powerful approach to exploring eukaryotic diversity, especially for deep-branching lineages. In this study, we cultured and described a novel protist species, named <i>Glissandra oviformis</i> n sp. within the poorly studied and unclassified genus <i>Glissandra</i>. While an SSU rDNA gene phylogeny failed to resolve its phylogenetic placement in the eukaryotic tree, a phylogenomic analysis of 340 proteins indicated <i>G. oviformis</i> as a member of the CRuMs clade. Prior to this study, this clade consisted of diverse heterotrophic amoeba and flagellates, and lacked clear synapomorphies. Ultrastructural observations revealed that <i>G. oviformis</i> shares the characteristics with some CRuMs members, including the pellicle underlying the plasma membrane and an internal sleeve surrounding the central pair of the axoneme at the flagellar transitional region. Our findings suggest potential shared characteristics and synapomorphies for CRuMs and contribute to a deeper understanding of the character evolution within this clade.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 6","pages":"250057"},"PeriodicalIF":4.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12133344/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144216503","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functional characterization of the store-operated calcium entry pathway in naked mole-rat cells.","authors":"Polina Drugachenok, Paulina Urriola-Muñoz, Lanhui Qiu, Zhuang Zhuang Han, Ewan St John Smith, Taufiq Rahman","doi":"10.1098/rsob.250052","DOIUrl":"10.1098/rsob.250052","url":null,"abstract":"<p><p>Naked mole-rats (NMRs, <i>Heterocephalus glaber</i>) are highly unusual rodents exhibiting remarkable adaptations to their subterranean habitat and resistance to developing various age-related diseases such as those related to abnormal cell proliferation or cancer, neurodegeneration and inflammation. In other rodents, as well as humans, a ubiquitous Ca²⁺ influx pathway, namely the store-operated Ca²⁺ entry (SOCE), has been implicated in all these diseases. SOCE is triggered by intracellular Ca²⁺ store depletion resulting in interaction of Stim proteins with Orai proteins, the putative homologues of which appear to be present in the NMR genome, but no functional characterization of SOCE in NMRs has yet been conducted. In this study, we provide the first functional and pharmacological characterization of SOCE in NMR using both excitable and non-excitable cells.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 6","pages":"250052"},"PeriodicalIF":4.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12133337/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144216504","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unravelling axonal transcriptional landscapes: insights from induced pluripotent stem cell-derived cortical neurons and implications for motor neuron degeneration.","authors":"Jishu Xu, Michaela Hörner, Maike Nagel, Perwin Perhat, Milena Korneck, Marvin Noß, Stefan Hauser, Ludger Schoels, Jakob Admard, Nicolas Casadei, Rebecca Schuele","doi":"10.1098/rsob.250101","DOIUrl":"10.1098/rsob.250101","url":null,"abstract":"<p><p>Neuronal function and pathology are deeply influenced by the distinct molecular profiles of the axon and soma. Traditional studies have often overlooked these differences due to the technical challenges of compartment-specific analysis. In this study, we employ a robust RNA-sequencing approach, using microfluidic devices, to generate high-quality axonal transcriptomes from induced pluripotent stem cells-derived cortical neurons (CNs). We achieve high specificity of axonal fractions, ensuring sample purity without contamination. Comparative analysis revealed a unique and specific transcriptional landscape in axonal compartments, characterized by diverse transcript types, including protein-coding mRNAs, RNAs encoding ribosomal proteins, mitochondrial-encoded RNAs and long non-coding RNAs. Previous works have reported the existence of transcription factors (TFs) in the axon. Here, we detect a set of TFs specific to the axon and indicative of their active participation in transcriptional regulation. To investigate transcripts and pathways essential for central motor neuron (MN) degeneration and maintenance we analysed kinesin family member 1C (<i>KIF1C</i>)<i>-</i>knockout <i>(KO</i>) CNs, modelling hereditary spastic paraplegia, a disorder associated with prominent length-dependent degeneration of central MN axons. We found that several key factors crucial for survival and health were absent in <i>KIF1C-KO</i> axons, highlighting a possible role of these also in other neurodegenerative diseases. Taken together, this study underscores the utility of microfluidic devices in studying compartment-specific transcriptomics in human neuronal models and reveals complex molecular dynamics of axonal biology. The impact of <i>KIF1C</i> on the axonal transcriptome not only deepens our understanding of MN diseases but also presents a promising avenue for exploration of compartment-specific disease mechanisms.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 6","pages":"250101"},"PeriodicalIF":4.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12152748/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144266890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unravelling the pathological roles of anastasis in cancer recurrence.","authors":"Ho Man Tang, Ho Lam Tang","doi":"10.1098/rsob.240270","DOIUrl":"10.1098/rsob.240270","url":null,"abstract":"<p><p>Can anastasis contribute to cancer recurrence? Anastasis is a cell recovery mechanism to spare dying cells after the initiation of the cell death process. Emerging studies interrogate anastasis as an unexpected escape tactic for cancer cells to evade cell death-inducing anti-cancer therapy, leading to recurrence. After anastasis, cancer cells display increased invasiveness and genomic instability, which could be associated with the common and fatal features of metastasis and drug resistance at the cancer recurrence. These studies open an encouraging new conceptual avenue for arresting cancer recurrence by targeting anastasis in cancer cells after conventional anti-cancer therapy. Here, we highlight recent findings towards unravelling pathological roles of anastasis in cancer recurrence, for the purpose of stimulating ideas and promoting the development of this new field of cancer research.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 6","pages":"240270"},"PeriodicalIF":4.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12187405/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144485355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reinventing the spermatheca: unveiling a novel sperm storage organ in Epilachninae ladybirds.","authors":"Paulo Henrique Rezende, Glenda Dias, Mauricio da Silva Paulo, Dayvson Ayala-Costa, Ana Clara Pereira Teixeira, José Lino-Neto","doi":"10.1098/rsob.240395","DOIUrl":"10.1098/rsob.240395","url":null,"abstract":"<p><p>This study investigates the reproductive apparatus of <i>Epilachna clandestina</i>, focusing on its secondary spermatheca, first described as a 'seminal node' by Katakura <i>et al</i>. for the Asian Epilachninae. We corroborate their previous findings that highlight this organ as the primary sperm storage site, contrasting with a vestigial typical spermatheca that lacks significant functionality. The functional spermatheca is a dilated, secretory region of the common oviduct filled with sperm. It features a specialized epithelium containing class 3 secretory cells and is lined by a thin chitinous cuticle, indicating that it qualifies as a true spermatheca. This organ seems to optimize sperm storage and maintenance when compared to the vestigial spermatheca. Additionally, we emphasize the close association between sperm and epithelial structures as mechanisms for efficient sperm retention and dosage, which could quantitatively and qualitatively improve reproductive success. Our findings may contribute to a greater understanding of the evolutionary adaptations of reproductive structures in Epilachninae and raise questions regarding the evolutionary history of these organs within ladybirds.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 6","pages":"240395"},"PeriodicalIF":4.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12187400/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144485353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}