Biology Open最新文献

{"title":"da_Tracker: Automated workflow for high throughput single cell and single phagosome tracking in infected cells.","authors":"Jacques Augenstreich, Anushka Poddar, Ashton T Belew, Najib M El-Sayed, Volker Briken","doi":"10.1242/bio.060555","DOIUrl":"10.1242/bio.060555","url":null,"abstract":"<p><p>Time-lapse microscopy has emerged as a crucial tool in cell biology, facilitating a deeper understanding of dynamic cellular processes. While existing tracking tools have proven effective in detecting and monitoring objects over time, the quantification of signals within these tracked objects often faces implementation constraints. In the context of infectious diseases, the quantification of signals at localized compartments within the cell and around intracellular pathogens can provide even deeper insight into the interactions between the pathogen and host cell organelles. Existing quantitative analysis at a single-phagosome level remains limited and dependent on manual tracking methods. We developed a near-fully automated workflow that performs with limited bias, high-throughput cell segmentation and quantitative tracking of both single cell and single bacterium/phagosome within multi-channel, z-stack, time-lapse confocal microscopy videos. We took advantage of the PyImageJ library to bring Fiji functionality into a Python environment and combined deep-learning-based segmentation from Cellpose with tracking algorithms from Trackmate. The 'da_tracker' workflow provides a versatile toolkit of functions for measuring relevant signal parameters at the single-cell level (such as velocity or bacterial burden) and at the single-phagosome level (i.e. assessment of phagosome maturation over time). Its capabilities in both single-cell and single-phagosome quantification, its flexibility and open-source nature should assist studies that aim to decipher for example the pathogenicity of bacteria and the mechanism of virulence factors that could pave the way for the development of innovative therapeutic approaches.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11423910/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142035305","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":"foxg1a is required for hair cell development and regeneration in the zebrafish lateral line.","authors":"Jon M Bell, Emily M Turner, Cole Biesemeyer, Madison M Vanderbeck, Roe Hendricks, Hillary F McGraw","doi":"10.1242/bio.060580","DOIUrl":"10.1242/bio.060580","url":null,"abstract":"<p><p>Mechanosensory hair cells located in the inner ear mediate the sensations of hearing and balance. If damaged, mammalian inner ear hair cells are unable to regenerate, resulting in permanent sensory deficits. Aquatic vertebrates like zebrafish (Danio rerio) have a specialized class of mechanosensory hair cells found in the lateral line system, allowing them to sense changes in water current. Unlike mammalian inner ear hair cells, lateral line hair cells can robustly regenerate following damage. In mammals, the transcription factor Foxg1 functions to promote normal development of the inner ear. Foxg1a is expressed in lateral line sensory organs in zebrafish larvae, but its function during lateral line development and regeneration has not been investigated. Our study demonstrates that mutation of foxg1a results in slower posterior lateral line primordium migration and delayed neuromast formation. In developing and regenerating neuromasts, we find that loss of Foxg1a function results in reduced hair cell numbers, as well as decreased proliferation of neuromast cells. Foxg1a specifically regulates the development and regeneration of Islet1-labeled hair cells. These data suggest that Foxg1 may be a valuable target for investigation of clinical hair cell regeneration.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":"13 9","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11423914/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142280444","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":"Membrane structures and functional correlates in the bi-segmented eye lens of the cephalopod.","authors":"Justyn W Regini, Naoto Yagi, Robert D Young, Hidetoshi Tanioka, Shigeru Kinoshita, Masato Hoshino, Kentaro Uesugi, Keith M Meek, Andy T Augousti, Carlo Knupp, Barbara K Pierscionek, Andrew J Quantock, Gerald F Elliott","doi":"10.1242/bio.060445","DOIUrl":"10.1242/bio.060445","url":null,"abstract":"<p><p>The cephalopod eye lens is unique because it has evolved as a compound structure with two physiologically distinct segments. However, the detailed ultrastructure of this lens and precise optical role of each segment are far from clear. To help elucidate structure-function relationships in the cephalopod lens, we conducted multiple structural investigations on squid. Synchrotron x-ray scattering and transmission electron microscopy disclose that an extensive network of structural features that resemble cell membrane complexes form a substantial component of both anterior and posterior lens segments. Optically, the segments are distinct, however, and Talbot interferometry indicates that the posterior segment possesses a noticeably higher refractive index gradient. We propose that the hitherto unrecognised network of membrane structures in the cephalopod lens has evolved to act as an essential conduit for the internal passage of ions and other metabolic agents through what is otherwise a highly dense structure owing to a very high protein concentration.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11381927/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141916107","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":"Lower-limb coordination changes following a 6-week training intervention that elicited enhancements to maximum velocity sprint performance.","authors":"Daniel Lenthall, Adam Brazil, Adrián Castaño-Zambudio, Harry Lightfoot, Jurdan Mendiguchia, Pedro Jiménez-Reyes, Steffi L Colyer","doi":"10.1242/bio.060589","DOIUrl":"10.1242/bio.060589","url":null,"abstract":"<p><p>Alterations to intra- and inter-limb coordination with improved maximal velocity performance remain largely unexplored. This study quantified within-day variability in lower-limb segmental coordination profiles during maximal velocity sprinting and investigated the modifications to coordination strategies in 15 recreationally active males following a 6-week period comprised of a multimodal training programme [intervention group (INT); n=7] or continued participation in sports (control group; n=8). The INT demonstrated a large decrease (effect size=-1.54) in within-day coordination profile variability, suggesting potential skill development. Thigh-thigh coordination modifications for the INT were characterised by an earlier onset of trail thigh reversal in early swing (26 versus 28% stride) and lead thigh reversal in late swing (76 versus 79% stride), rather than increases in overall time spent in anti-phase. Moreover, an increase in backward rotation of thigh relative to shank (effect size, 95% CIs: 0.75, 0.17 to 1.33) and shank relative to foot (0.76, -0.17 to 1.68) during late swing likely facilitated more aggressive acceleration of the limb, contributing to reduced touchdown distance and more favourable lower-limb configuration at initial ground contact. These novel findings provide empirical support for the role of longitudinal coordination modifications in improving maximal velocity performance.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11381917/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141892879","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":"Theoretical model of impact mitigation mechanisms inherent to the North American bison skull.","authors":"Andrea Karen Persons, Youssef Hammi, Steven H Elder, Lauren B Priddy, Matthew W Priddy, Ryan Butler, Avery Schemmel, Elizabeth Whitehurst, Nayeon Lee, Mark F Horstemeyer","doi":"10.1242/bio.060517","DOIUrl":"10.1242/bio.060517","url":null,"abstract":"<p><p>North American bison (Bovidae: Bison bison) incur blunt impacts to the interparietal and frontal bones when they engage in head-to-head fights. To investigate the impact mitigation of these bones, a finite element analysis (FEA) of the skull under loading conditions was performed. Based on anatomical and histological studies, the interparietal and frontal bones are both comprised of a combination of haversian and plexiform bone and are both underlain by bony septa. Additionally, the interparietal bone is thicker than the frontal bone. Data regarding the mechanical properties of bison bone are scarce, but the results of a phylogenetic analysis infer that the material properties of the closely related domestic cow bone are a suitable proxy for use in the FEA. Results of the FEA suggest that the thickness of the interparietal bone in conjunction with the bony septa may prevent fracture stresses by helping to absorb and disperse the blunt impact energy throughout the skull. Monotonic stress levels of 294 MPa, which are below the compressive strength of bone were exhibited in the simulated bison head impacts indicating no fracture of the bones.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":"13 9","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11423911/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142280446","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":"Development of germline progenitors in larval queen honeybee ovaries.","authors":"Georgia Cullen, Erin Delargy, Peter K Dearden","doi":"10.1242/bio.060511","DOIUrl":"10.1242/bio.060511","url":null,"abstract":"<p><p>Honeybees (Apis mellifera) are a keystone species for managed pollination and the production of hive products. Eusociality in honeybees leads to much of the reproduction in a hive driven by the queen. Queen bees have two large active ovaries that can produce large numbers of eggs if conditions are appropriate. These ovaries are also active throughout the long lives of these insects, up to 5 years in some cases. Recent studies have indicated that the germline precursors of the adult honeybee queen ovary are organized into 8-cell clusters, joined together by a polyfusome; a cytoplasmic bridge. To understand the origin of these clusters, and trace the development of the honeybee queen ovary, we examined the cell types and regionalization of the developing larval and pupal queen ovaries. We used established (nanos and castor), and novel (odd skipped) gene expression markers to determine regions of the developing ovary. Primordial germline cells develop in the honeybee embryo and are organized into ovary structures before the embryo hatches. The ovary is regionalized by larval stage 3 into terminal filaments and germaria. At this stage, clusters of germline cells in the germaria are joined by fusomes and are dividing synchronously. The origin of the 8-cell clusters in the adult germarium is therefore during larval stages. On emergence, the queen ovary has terminal filaments and germaria but has not yet developed any vitellaria, which are produced after the queen embarks on a nuptial flight. The lack of germaria, and the storing of germline progenitors as clusters, may be adaptions for queen bees to endure the metabolic demands of a nuptial flight, as well as rapidly lay large numbers of eggs to establish a hive.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":"13 9","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11413931/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142280443","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":"Interspecific hybridisation provides a low-risk option for increasing genetic diversity of reef-building corals.","authors":"Annika M Lamb, Lesa M Peplow, Ashley M Dungan, Sophie N Ferguson, Peter L Harrison, Craig A Humphrey, Guy A McCutchan, Matthew R Nitschke, Madeleine J H van Oppen","doi":"10.1242/bio.060482","DOIUrl":"10.1242/bio.060482","url":null,"abstract":"<p><p>Interspecific hybridisation increases genetic diversity and has played a significant role in the evolution of corals in the genus Acropora. In vitro fertilisation can be used to increase the frequency of hybridisation among corals, potentially enhancing their ability to adapt to climate change. Here, we assessed the field performance of hybrids derived from the highly cross-fertile coral species Acropora sarmentosa and Acropora florida from the Great Barrier Reef. Following outplanting to an inshore reef environment, the 10-month survivorship of the hybrid offspring groups was intermediate between that of the purebred groups, although not all pairwise comparisons were statistically significant. The A. florida purebreds, which had the lowest survivorship, were significantly larger at 10 months post-deployment compared to the other three groups. The four offspring groups harboured the same intracellular photosymbiont communities (Symbiodiniaceae), indicating that observed performance differences were due to the coral host and not photosymbiont communities. The limited differences in the performance of the groups and the lack of outbreeding depression of the F1 hybrids in the field suggest that interspecific hybridisation may be a useful method to boost the genetic diversity, and as such increase the adaptive capacity, of coral stock for restoration of degraded and potentially genetically eroded populations.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":"13 9","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11381923/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142104472","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A larval zebrafish model of cardiac physiological recovery following cardiac arrest and myocardial hypoxic damage.","authors":"Warren Burggren, Regina Abramova, Naim M Bautista, Regina Fritsche Danielson, Ben Dubansky, Avi Gupta, Kenny Hansson, Neha Iyer, Pudur Jagadeeswaran, Karin Jennbacken, Katarina Rydén-Markinhutha, Vishal Patel, Revathi Raman, Hersh Trivedi, Karem Vazquez Roman, Steven Williams, Qing-Dong Wang","doi":"10.1242/bio.060230","DOIUrl":"10.1242/bio.060230","url":null,"abstract":"<p><p>Contemporary cardiac injury models in zebrafish larvae include cryoinjury, laser ablation, pharmacological treatment and cardiac dysfunction mutations. Although effective in damaging cardiomyocytes, these models lack the important element of myocardial hypoxia, which induces critical molecular cascades within cardiac muscle. We have developed a novel, tractable, high throughput in vivo model of hypoxia-induced cardiac damage that can subsequently be used in screening cardioactive drugs and testing recovery therapies. Our potentially more realistic model for studying cardiac arrest and recovery involves larval zebrafish (Danio rerio) acutely exposed to severe hypoxia (PO2=5-7 mmHg). Such exposure induces loss of mobility quickly followed by cardiac arrest occurring within 120 min in 5 days post fertilization (dpf) and within 40 min at 10 dpf. Approximately 90% of 5 dpf larvae survive acute hypoxic exposure, but survival fell to 30% by 10 dpf. Upon return to air-saturated water, only a subset of larvae resumed heartbeat, occurring within 4 min (5 dpf) and 6-8 min (8-10 dpf). Heart rate, stroke volume and cardiac output in control larvae before hypoxic exposure were 188±5 bpm, 0.20±0.001 nL and 35.5±2.2 nL/min (n=35), respectively. After briefly falling to zero upon severe hypoxic exposure, heart rate returned to control values by 24 h of recovery. However, reflecting the severe cardiac damage induced by the hypoxic episode, stroke volume and cardiac output remained depressed by ∼50% from control values at 24 h of recovery, and full restoration of cardiac function ultimately required 72 h post-cardiac arrest. Immunohistological staining showed co-localization of Troponin C (identifying cardiomyocytes) and Capase-3 (identifying cellular apoptosis). As an alternative to models employing mechanical or pharmacological damage to the developing myocardium, the highly reproducible cardiac effects of acute hypoxia-induced cardiac arrest in the larval zebrafish represent an alternative, potentially more realistic model that mimics the cellular and molecular consequences of an infarction for studying cardiac tissue hypoxia injury and recovery of function.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":"13 9","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11413934/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142280440","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":"The role of cilia in the development, survival, and regeneration of hair cells.","authors":"Hope Boldizar, Amanda Friedman, Tess Stanley, María Padilla, Jennifer Galdieri, Arielle Sclar, Tamara M Stawicki","doi":"10.1242/bio.061690","DOIUrl":"10.1242/bio.061690","url":null,"abstract":"<p><p>Mutations impacting cilia genes lead to a class of human diseases known as ciliopathies. This is due to the role of cilia in the development, survival, and regeneration of many cell types. We investigated the extent to which disrupting cilia impacted these processes in lateral line hair cells of zebrafish. We found that mutations in two intraflagellar transport (IFT) genes, ift88 and dync2h1, which lead to the loss of kinocilia, caused increased hair cell apoptosis. IFT gene mutants also have a decreased mitochondrial membrane potential, and blocking the mitochondrial uniporter causes a loss of hair cells in wild-type zebrafish but not mutants, suggesting mitochondria dysfunction may contribute to the apoptosis seen in these mutants. These mutants also showed decreased proliferation during hair cell regeneration but did not show consistent changes in support cell number or proliferation during hair cell development. These results show that the loss of hair cells seen following disruption of cilia through either mutations in anterograde or retrograde IFT genes appears to be due to impacts on hair cell survival but not necessarily development in the zebrafish lateral line.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":"13 9","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11413933/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142280445","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":"Optimization of an in situ liver perfusion method to evaluate hepatic function of juvenile American alligators (Alligator mississippiensis).","authors":"Yu Umeki, David Hala, Lene Hebsgaard Petersen","doi":"10.1242/bio.060532","DOIUrl":"10.1242/bio.060532","url":null,"abstract":"<p><p>American alligators (Alligator mississippiensis) are a sentinel species whose health is representative of environmental quality. However, their susceptibility to various natural or anthropogenic stressors is yet to be comprehensively studied. Understanding hepatic function in such assessments is essential as the liver is the central organ in the metabolic physiology of an organism, and therefore influences its adaptive capability. In this study, a novel liver perfusion system was developed to study the hepatic physiology of juvenile alligators. First, a cannulation procedure was developed for an in situ liver perfusion preparation. Second, an optimal flow rate of 0.5 ml/min/g liver was determined based on the oxygen content in the effluent perfusate. Third, the efficacy of the liver preparation was tested by perfusing the liver with normoxic or hypoxic Tyrode's buffer while various biomarkers of hepatic function were monitored in the effluent perfusate. Our results showed that in the normoxic perfusion, the aspartate transferase (AST) and lactate/pyruvate ratio in the perfusate remained stable and within an acceptable physiological range for 6 h. In contrast, hypoxia exposure significantly increased the lactate/pyruvate ratio in the perfusate after 2 h, indicating an induction of anaerobic metabolism. These results suggest that the perfused liver remained viable during the perfusion period and exhibited the expected physiological response under hypoxia exposure. The liver perfusion system developed in this study provides an experimental framework with which to study the basic hepatic physiology of alligators and elucidate the effects of environmental or anthropogenic stressors on the metabolic physiology of this sentinel species.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":"13 8","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11381930/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142072044","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}