Biology Open最新文献_第10页

Distinct features of the regenerating heart uncovered through comparative single-cell profiling. 通过比较单细胞图谱发现再生心脏的不同特征。

IF 2.4 4区生物学

Biology Open Pub Date : 2024-04-15 Epub Date: 2024-04-05 DOI: 10.1242/bio.060156

Clayton M Carey, Hailey L Hollins, Alexis V Schmid, James A Gagnon

{"title":"Distinct features of the regenerating heart uncovered through comparative single-cell profiling.","authors":"Clayton M Carey, Hailey L Hollins, Alexis V Schmid, James A Gagnon","doi":"10.1242/bio.060156","DOIUrl":"10.1242/bio.060156","url":null,"abstract":"Adult humans respond to heart injury by forming a permanent scar, yet other vertebrates are capable of robust and complete cardiac regeneration. Despite progress towards characterizing the mechanisms of cardiac regeneration in fish and amphibians, the large evolutionary gulf between mammals and regenerating vertebrates complicates deciphering which cellular and molecular features truly enable regeneration. To better define these features, we compared cardiac injury responses in zebrafish and medaka, two fish species that share similar heart anatomy and common teleost ancestry but differ in regenerative capability. We used single-cell transcriptional profiling to create a time-resolved comparative cell atlas of injury responses in all major cardiac cell types across both species. With this approach, we identified several key features that distinguish cardiac injury response in the non-regenerating medaka heart. By comparing immune responses to injury, we found altered cell recruitment and a distinct pro-inflammatory gene program in medaka leukocytes, and an absence of the injury-induced interferon response seen in zebrafish. In addition, we found a lack of pro-regenerative signals, including nrg1 and retinoic acid, from medaka endothelial and epicardial cells. Finally, we identified alterations in the myocardial structure in medaka, where they lack primordial layer cardiomyocytes and fail to employ a cardioprotective gene program shared by regenerating vertebrates. Our findings reveal notable variation in injury response across nearly all major cardiac cell types in zebrafish and medaka, demonstrating how evolutionary divergence influences the hidden cellular features underpinning regenerative potential in these seemingly similar vertebrates.","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11007736/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140206370","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}

引用次数: 0

Clearance rates of sand-burrowed and laterally pressed unburrowed Pismo clam Tivela stultorum (Mawe 1823) in a laboratory open-flow system. 在实验室开流系统中，沙壤土和聚氯乙烯压制的无壤土 Pismo 蚌 Tivela stultorum (Mawe 1823) 的清除率。

IF 2.4 4区生物学

Biology Open Pub Date : 2024-04-15 Epub Date: 2024-03-28 DOI: 10.1242/bio.060268

Enrique Zepeda, Zaul Garcia-Esquivel, Marco A González-Gómez, Fernando Díaz, Sheila Castellanos-Martinez

{"title":"Clearance rates of sand-burrowed and laterally pressed unburrowed Pismo clam Tivela stultorum (Mawe 1823) in a laboratory open-flow system.","authors":"Enrique Zepeda, Zaul Garcia-Esquivel, Marco A González-Gómez, Fernando Díaz, Sheila Castellanos-Martinez","doi":"10.1242/bio.060268","DOIUrl":"10.1242/bio.060268","url":null,"abstract":"Pismo clam extraction is currently banned in Mexico to help the recovery of natural populations. Thus, the primary objective of this study was to gain insight on its basic biology and husbandry protocols. Growth and clearance rate (CR) of sand-burrowed and sediment-free, laterally pressed adult Pismo clams were quantified in the laboratory as a function of burrowing condition, flow, temperature, and microalgal concentration using open-flow chambers. After 40 days, clams remained healthy regardless of burrowing condition and showed a hyperbolic CR response pattern to increased flow, with CR directly proportional to flows lower than 1000 ml min-1. Maximal asymptotic CR values (300 to 400 ml min-1 org-1) were observed from 1000 to 2000 ml min-1. No significant CR differences were observed between burrowed and laterally pressed clams, yet microalgal concentration effects were detected, with constant maximal CRs of ∼250 ml min-1 in the range of 50 to 200 cells µl-1 and decline at higher concentrations. Maintenance protocols of laterally pressed organisms were validated in the laboratory with both weight and CR data. To our knowledge, this is the first study providing whole-body physiological data translated into effective husbandry protocols for Pismo clams. This approach represents a fresh perspective to traditional research areas, opening the possibility for continued experimentation under controlled conditions.","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10997049/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140118829","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}

引用次数: 0

P2X7 regulates ependymo-radial glial cell proliferation in adult Danio rerio following spinal cord injury. P2X7 可调控脊髓损伤后成年小白鼠上皮神经胶质细胞的增殖。

IF 2.4 4区生物学

Biology Open Pub Date : 2024-04-15 Epub Date: 2024-04-11 DOI: 10.1242/bio.060270

Eva E Stefanova, Julian Vincent T Dychiao, Mavis C Chinn, Matin Borhani, Angela L Scott

{"title":"P2X7 regulates ependymo-radial glial cell proliferation in adult Danio rerio following spinal cord injury.","authors":"Eva E Stefanova, Julian Vincent T Dychiao, Mavis C Chinn, Matin Borhani, Angela L Scott","doi":"10.1242/bio.060270","DOIUrl":"10.1242/bio.060270","url":null,"abstract":"In contrast to mammals, zebrafish undergo successful neural regeneration following spinal cord injury. Spinal cord ependymo-radial glia (ERG) undergo injury-induced proliferation and neuronal differentiation to replace damaged cells and restore motor function. However, the molecular cues driving these processes remain elusive. Here, we demonstrate that the evolutionarily conserved P2X7 receptors are widely distributed on neurons and ERG within the zebrafish spinal cord. At the protein level, the P2X7 receptor expressed in zebrafish is a truncated splice variant of the full-length variant found in mammals. The protein expression of this 50 kDa isoform was significantly downregulated at 7 days post-injury (dpi) but returned to basal levels at 14 dpi when compared to naïve controls. Pharmacological activation of P2X7 following SCI resulted in a greater number of proliferating cells around the central canal by 7 dpi but did not affect neuronal differentiation at 14 dpi. Our findings suggest that unlike in mammals, P2X7 signaling may not play a maladaptive role following SCI in adult zebrafish and may also work to curb the proliferative response of ERG following injury.","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11033521/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140206371","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}

引用次数: 0

Machine learning models reveal distinct disease subgroups and improve diagnostic and prognostic accuracy for individuals with pathogenic SCN8A gain-of-function variants. 机器学习模型揭示了不同的疾病亚群，并提高了对 SCN8A 功能增益变异致病个体的诊断和预后准确性。

IF 2.4 4区生物学

Biology Open Pub Date : 2024-04-15 Epub Date: 2024-04-24 DOI: 10.1242/bio.060286

Joshua B Hack, Joseph C Watkins, Michael F Hammer

{"title":"Machine learning models reveal distinct disease subgroups and improve diagnostic and prognostic accuracy for individuals with pathogenic SCN8A gain-of-function variants.","authors":"Joshua B Hack, Joseph C Watkins, Michael F Hammer","doi":"10.1242/bio.060286","DOIUrl":"10.1242/bio.060286","url":null,"abstract":"Distinguishing clinical subgroups for patients suffering with diseases characterized by a wide phenotypic spectrum is essential for developing precision therapies. Patients with gain-of-function (GOF) variants in the SCN8A gene exhibit substantial clinical heterogeneity, viewed historically as a linear spectrum ranging from mild to severe. To test for hidden clinical subgroups, we applied two machine-learning algorithms to analyze a dataset of patient features collected by the International SCN8A Patient Registry. We used two research methodologies: a supervised approach that incorporated feature severity cutoffs based on clinical conventions, and an unsupervised approach employing an entirely data-driven strategy. Both approaches found statistical support for three distinct subgroups and were validated by correlation analyses using external variables. However, distinguishing features of the three subgroups within each approach were not concordant, suggesting a more complex phenotypic landscape. The unsupervised approach yielded strong support for a model involving three partially ordered subgroups rather than a linear spectrum. Application of these machine-learning approaches may lead to improved prognosis and clinical management of individuals with SCN8A GOF variants and provide insights into the underlying mechanisms of the disease.","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11070785/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140093473","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}

引用次数: 0

DeepLabCut-based daily behavioural and posture analysis in a cricket. 基于 DeepLabCut 的蟋蟀日常行为和姿势分析。

IF 2.4 4区生物学

Biology Open Pub Date : 2024-04-15 Epub Date: 2024-04-23 DOI: 10.1242/bio.060237

Shota Hayakawa, Kosuke Kataoka, Masanobu Yamamoto, Toru Asahi, Takeshi Suzuki

{"title":"DeepLabCut-based daily behavioural and posture analysis in a cricket.","authors":"Shota Hayakawa, Kosuke Kataoka, Masanobu Yamamoto, Toru Asahi, Takeshi Suzuki","doi":"10.1242/bio.060237","DOIUrl":"10.1242/bio.060237","url":null,"abstract":"Circadian rhythms are indispensable intrinsic programs that regulate the daily rhythmicity of physiological processes, such as feeding and sleep. The cricket has been employed as a model organism for understanding the neural mechanisms underlying circadian rhythms in insects. However, previous studies measuring rhythm-controlled behaviours only analysed locomotive activity using seesaw-type and infrared sensor-based actometers. Meanwhile, advances in deep learning techniques have made it possible to analyse animal behaviour and posture using software that is devoid of human bias and does not require physical tagging of individual animals. Here, we present a system that can simultaneously quantify multiple behaviours in individual crickets - such as locomotor activity, feeding, and sleep-like states - in the long-term, using DeepLabCut, a supervised machine learning-based software for body keypoints labelling. Our system successfully labelled the six body parts of a single cricket with a high level of confidence and produced reliable data showing the diurnal rhythms of multiple behaviours. Our system also enabled the estimation of sleep-like states by focusing on posture, instead of immobility time, which is a conventional parameter. We anticipate that this system will provide an opportunity for simultaneous and automatic prediction of cricket behaviour and posture, facilitating the study of circadian rhythms.","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11070783/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140292874","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}

引用次数: 0

SRRM2 splicing factor modulates cell fate in early development. SRRM2 剪接因子在早期发育过程中调节细胞命运。

IF 2.4 4区生物学

Biology Open Pub Date : 2024-04-15 Epub Date: 2024-04-24 DOI: 10.1242/bio.060415

Silvia Carvalho, Luna Zea-Redondo, Tsz Ching Chloe Tang, Philipp Stachel-Braum, Duncan Miller, Paulo Caldas, Alexander Kukalev, Sebastian Diecke, Stefanie Grosswendt, Ana Rita Grosso, Ana Pombo

{"title":"SRRM2 splicing factor modulates cell fate in early development.","authors":"Silvia Carvalho, Luna Zea-Redondo, Tsz Ching Chloe Tang, Philipp Stachel-Braum, Duncan Miller, Paulo Caldas, Alexander Kukalev, Sebastian Diecke, Stefanie Grosswendt, Ana Rita Grosso, Ana Pombo","doi":"10.1242/bio.060415","DOIUrl":"10.1242/bio.060415","url":null,"abstract":"Embryo development is an orchestrated process that relies on tight regulation of gene expression to guide cell differentiation and fate decisions. The Srrm2 splicing factor has recently been implicated in developmental disorders and diseases, but its role in early mammalian development remains unexplored. Here, we show that Srrm2 dosage is critical for maintaining embryonic stem cell pluripotency and cell identity. Srrm2 heterozygosity promotes loss of stemness, characterised by the coexistence of cells expressing naive and formative pluripotency markers, together with extensive changes in gene expression, including genes regulated by serum-response transcription factor (SRF) and differentiation-related genes. Depletion of Srrm2 by RNA interference in embryonic stem cells shows that the earliest effects of Srrm2 heterozygosity are specific alternative splicing events on a small number of genes, followed by expression changes in metabolism and differentiation-related genes. Our findings unveil molecular and cellular roles of Srrm2 in stemness and lineage commitment, shedding light on the roles of splicing regulators in early embryogenesis, developmental diseases and tumorigenesis.","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11070786/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140855987","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}

引用次数: 0

Hotter deserts and the impending challenges for the Spiny-tailed Lizard in India. 更炎热的沙漠和印度刺尾蜥即将面临的挑战。

IF 2.4 4区生物学

Biology Open Pub Date : 2024-04-15 Epub Date: 2024-04-02 DOI: 10.1242/bio.060150

Avichal Tatu, Sutirtha Dutta, Maria Thaker

{"title":"Hotter deserts and the impending challenges for the Spiny-tailed Lizard in India.","authors":"Avichal Tatu, Sutirtha Dutta, Maria Thaker","doi":"10.1242/bio.060150","DOIUrl":"10.1242/bio.060150","url":null,"abstract":"Ectotherms are particularly vulnerable to climate change, especially those living in extreme areas, such as deserts, where species are already thermally constrained. Using the vulnerable herbivorous lizard Saara hardwickii as a model system, we used a multi-pronged approach to understand the thermal ecology of a desert agamid and potential impacts of rising temperatures. Our data included field-based measures of operative temperatures, body temperatures, and activity, as well as lab-based measures of thermal limits, preferences, and sprint speed. As expected, the temperature dependence of locomotor performance and foraging activity were different, and in the worst-case global warming scenario (SSP5-8.5), potential sprint speed may decrease by up to 14.5% and foraging activity may decrease by up to 43.5% by 2099. Burrows are essential thermal refuges, and global warming projections suggest that S. hardwickii may be restricted to burrows for up to 9 h per day by 2099, which would greatly limit critical activities, like foraging and seeking mating opportunities. Overall, we show that key information on thermal ecology, including temperature-sensitive behaviours in the wild, is necessary to understand the multiple ways in which increasing temperatures may influence ectothermic vertebrates, especially for species like S. hardwickii that are already vulnerable to environmental change.","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11007731/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140093472","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}

引用次数: 0

10th European Calcium Society symposium: The Ca2+-signaling toolkit in cell function, health and disease. 第 10 届欧洲钙学会研讨会：细胞功能、健康和疾病中的 Ca2+ 信号工具包。

IF 2.4 4区生物学

Biology Open Pub Date : 2024-04-15 DOI: 10.1242/bio.060357

Femke Speelman-Rooms, Maarten Vanmunster, Aled Coughlan, Macarena Hinrichs, Ilaria Pontisso, Solene Barbeau, Thibaud Parpaite, G. Bultynck, Malene Brohus

{"title":"10th European Calcium Society symposium: The Ca2+-signaling toolkit in cell function, health and disease.","authors":"Femke Speelman-Rooms, Maarten Vanmunster, Aled Coughlan, Macarena Hinrichs, Ilaria Pontisso, Solene Barbeau, Thibaud Parpaite, G. Bultynck, Malene Brohus","doi":"10.1242/bio.060357","DOIUrl":"https://doi.org/10.1242/bio.060357","url":null,"abstract":"The 10th European Calcium Society symposium, organized in Leuven, Belgium on November 15-17, 2023, focused on the role of Ca2+ signaling in cell function, health and disease. The symposium featured six scientific sessions, 16 invited speakers - of whom two were postdoctoral researchers - and 14 short talks. The talks covered various aspects of intracellular Ca2+ signaling and its implications in pathology. Each session was opened by one or more invited speakers, followed by a series of presentations from speakers selected from submitted abstracts. Through short talks, poster presentations, awards, and sustainable travel fellowships, the symposium also fostered opportunities for the active participation of early-career researchers. At least half of the short talks were allocated to early-career researchers, thereby offering a platform for the presentation of ongoing work and unpublished results. Presentations were also broadcast in real-time for online attendees. In this Meeting Review, we aim to capture the spirit of the meeting and discuss the main take-home messages that emerged during the symposium.","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140701217","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}

引用次数: 0

First person – Joshua Hack 第一人称 - 约书亚-哈克

IF 2.4 4区生物学

Biology Open Pub Date : 2024-04-15 DOI: 10.1242/bio.060410

引用次数: 0

Seed preference is only weakly linked to seed-type-specific feeding performance in a songbird. 在鸣禽中，种子偏好与种子类型特异性喂食表现的联系很弱。

IF 1.8 4区生物学

Biology Open Pub Date : 2024-04-15 Epub Date: 2024-04-11 DOI: 10.1242/bio.060353

Tim Andries, Wendt Müller, Sam Van Wassenbergh

{"title":"Seed preference is only weakly linked to seed-type-specific feeding performance in a songbird.","authors":"Tim Andries, Wendt Müller, Sam Van Wassenbergh","doi":"10.1242/bio.060353","DOIUrl":"10.1242/bio.060353","url":null,"abstract":"The dehusking of seeds by granivorous songbirds is a complex process that requires fast, coordinated and sensory-feedback-controlled movements of beak and tongue. Hence, efficient seed handling requires a high degree of sensorimotoric skill and behavioural flexibility, since seeds vary considerably in size, shape and husk structure. To deal with this variability, individuals might specialise on specific seed types, which could result in greater seed handling efficiency of the preferred seed type, but lower efficiency for other seed types. To test this, we assessed seed preferences of canaries (Serinus canaria) through food choice experiments and related these to data of feeding performance, seed-handling skills and beak kinematics during feeding on small, spindle-shaped canary seeds and larger, spheroid-shaped hemp seeds. We found great variety in seed preferences among individuals: some had no clear preference, while others almost exclusively fed on hemp seeds, or even prioritized novel seed types (millet seed). Surprisingly, we only observed few and weak effects of seed preference on feeding efficiency. This suggests either that the ability to handle seeds efficiently can be readily applied across various seed types, or alternatively, that achieving high levels of seed-specific handling skills does not require extensive practice.","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11033522/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140854241","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}

引用次数: 0