Cells Tissues Organs最新文献

{"title":"Assessing Combinatorial Diversity of Aureochrome Basic Leucine Zippers through Genome-Wide Screening.","authors":"Madhurima Khamaru, Deep Nath, Devrani Mitra, Soumen Roy","doi":"10.1159/000527593","DOIUrl":"10.1159/000527593","url":null,"abstract":"<p><p>Aureochromes are unique blue light-responsive light-oxygen-voltage (LOV) photoreceptors cum basic leucine zipper (bZIP) transcription factors (TFs), present exclusively in photosynthetic marine stramenopiles. Considering the availability of the complete genome sequence, this study focuses on aureochromes from Ectocarpus siliculosus. Aureochromes mediate light-regulated developmental responses in these brown photosynthetic algae. Both the LOV sensor and the bZIP effector show overall sequence-structure conservation. The structurally similar LOV + bZIP modules of aureochrome homologs/paralogs prefer a dimeric state. Besides a heterogeneous linker connecting the sensor-effector and a flexible N-terminal region, the sequence composition of both domains is vital. Aureochromes execute diverse cellular responses in different photosynthetic stramenopiles - though their activities can vary even within a given algal species. Therefore, it is important to understand whether aureochromes select dimerization partners from the same family or interact with other bZIPs as well. To regulate multifarious biological activities, it is possible that aureochromes activate the global TF interaction network. Following homo/heterodimer modeling, we address the compatibility of dimerization partners by screening through heptad repeats. We evaluate the dimer interface area in terms of gain in solvation energy and the number of hydrogen bonds/salt bridge interactions. We further explore the relative stability of these structures from a graph-theoretic perspective through well-studied measures such as the energy of the graph, average participation coefficient, and betweenness centrality. Furthermore, we also conduct an information-theoretic analysis using hitherto understudied measures such as network information centrality and Kullback-Leibler divergence. We find that all our investigations into the relative stability of the dimers using diverse methods from bioinformatics, network science, and information theory are in harmonious agreement. Coupling preferences of monomers in aureochromes can be further translated to design novel optogenetic tools useful for understanding human development and disease.</p>","PeriodicalId":9717,"journal":{"name":"Cells Tissues Organs","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40342974","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}

{"title":"Using Optogenetics to Investigate the Shared Mechanisms of Apical-Basal Polarity and Mitosis.","authors":"Helena A Crellin, Clare E Buckley","doi":"10.1159/000528796","DOIUrl":"10.1159/000528796","url":null,"abstract":"<p><p>The initiation of apical-basal (AB) polarity and the process of mitotic cell division are both characterised by the generation of specialised plasma membrane and cortical domains. These are generated using shared mechanisms, such as asymmetric protein accumulation, Rho GTPase signalling, cytoskeletal reorganisation, vesicle trafficking, and asymmetric phosphoinositide distribution. In epithelial tissue, the coordination of AB polarity and mitosis in space and time is important both during initial epithelial development and to maintain tissue integrity and ensure appropriate cell differentiation at later stages. Whilst significant progress has been made in understanding the mechanisms underlying cell division and AB polarity, it has so far been challenging to fully unpick the complex interrelationship between polarity, signalling, morphogenesis, and cell division. However, the recent emergence of optogenetic protein localisation techniques is now allowing researchers to reversibly control protein activation, localisation, and signalling with high spatiotemporal resolution. This has the potential to revolutionise our understanding of how subcellular processes such as AB polarity are integrated with cell behaviours such as mitosis and how these processes impact whole tissue morphogenesis. So far, these techniques have been used to investigate processes such as cleavage furrow ingression, mitotic spindle positioning, and in vivo epithelial morphogenesis. This review describes some of the key shared mechanisms of cell division and AB polarity establishment, how they are coordinated during development and how the advance of optogenetic techniques is furthering this research field.</p>","PeriodicalId":9717,"journal":{"name":"Cells Tissues Organs","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10480677","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}

{"title":"Prediction of Golgi Polarity in Collectively Migrating Epithelial Cells Using Graph Neural Network.","authors":"Purnati Khuntia, Tamal Das","doi":"10.1159/000528354","DOIUrl":"10.1159/000528354","url":null,"abstract":"<p><p>In the stationary epithelium, the Golgi apparatus assumes an apical position, above the cell nucleus. However, during wound healing and morphogenesis, as the epithelial cells start migrating, it relocalizes closer to the basal plane. On this plane, the position of Golgi with respect to the cell nucleus defines the organizational polarity of a migrating epithelial cell, which is crucial for an efficient collective migration. Yet, factors influencing the Golgi polarity remain elusive. Here, we constructed a graph neural network-based deep learning model to systematically analyze the dependency of Golgi polarity on multiple geometric and physical factors. In spite of the complexity of a migrating epithelial monolayer, our simple model was able to predict the Golgi polarity with 75% accuracy. Moreover, the model predicted that Golgi polarity predominantly correlates with the orientation of maximum principal stress. Finally, we found that this correlation operates locally since progressive coarsening of the stress field over multiple cell-lengths reduced the stress polarity-Golgi polarity correlation as well as the predictive accuracy of the neural network model. Taken together, our results demonstrate that graph neural networks could be a powerful tool toward understanding how different physical factors influence collective cell migration. They also highlight a previously unknown role of physical cues in defining the intracellular organization.</p>","PeriodicalId":9717,"journal":{"name":"Cells Tissues Organs","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40456512","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}

{"title":"Nuclear Biophysical Changes during Human Melanoma Plasticity.","authors":"Maria Chiara Lionetti, Maria Rita Fumagalli, Caterina A M La Porta","doi":"10.1159/000528601","DOIUrl":"10.1159/000528601","url":null,"abstract":"<p><p>Tumor plasticity is an emerging property of tumor cells which allows them to change their phenotype in dependence on the environment. The epithelial-mesenchymal transition plays a crucial role in helping cells acquire a more aggressive phenotype when they are in the mesenchymal state. Herein, we investigated the biophysical changes occurring during phenotypic switching in human melanoma cells, considering the blebbiness of the nuclei, their stiffness, and the involvement of polycombs with lamins. We show that the formation of cellular heterogeneity involves many crucial nuclear changes including the interaction between different types of polycombs with lamins and chromosome accessibility. Altogether, our results shed new light on the molecular mechanisms involved in the formation of a heterogeneous cell population during phenotypic switching. In particular, our results show that phenotypic switching in melanoma involves chromatin remodeling changing the transcriptional activity of cells and consequently their phenotype.</p>","PeriodicalId":9717,"journal":{"name":"Cells Tissues Organs","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10393933","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}

{"title":"Differentiation of Myoblasts in Culture: Focus on Serum and Gamma-Aminobutyric Acid.","authors":"Guzel Sibgatullina, Rahaf Al Ebrahim, Karina Gilizhdinova, Anna Tokmakova, Artem Malomouzh","doi":"10.1159/000529839","DOIUrl":"10.1159/000529839","url":null,"abstract":"<p><p>There are many facts about the possible role of gamma-aminobutyric acid (GABA) in the development and differentiation of cells not only in nervous but also in muscle tissue. In the present study, a primary culture of rat skeletal muscle myocytes was used to evaluate the correlation between the content of GABA in the cytoplasm and the processes of myocyte division and their fusion into myotubes. The effect of exogenous GABA on the processes of culture development was also estimated. Since the classical protocol for working with myocyte cultures involves the use of fetal bovine serum (FBS) to stimulate cell division (growth medium) and horse serum (HS) to activate the differentiation process (differentiation medium), the studies were carried out both in the medium with FBS and with HS. It was found that cells grown in medium supplemented with FBS contain more GABA compared to cultures growing in medium supplemented with HS. Addition of exogeneous GABA leads to a decrease in the number of myotubes formed in both media, while the addition of an amino acid to the medium supplemented with HS had a more pronounced inhibitory effect. Thus, we have obtained data indicating that GABA is able to participate in the early stages of skeletal muscle myogenesis by modulating the fusion process.</p>","PeriodicalId":9717,"journal":{"name":"Cells Tissues Organs","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9083148","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}

{"title":"Erratum.","authors":"","doi":"10.1159/000538569","DOIUrl":"10.1159/000538569","url":null,"abstract":"","PeriodicalId":9717,"journal":{"name":"Cells Tissues Organs","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140850903","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}

{"title":"Coupled Mutual Inhibition and Mutual Activation Motifs as Tools for Cell-Fate Control.","authors":"Burhanuddin Sabuwala, Kishore Hari, Abhishek Shanmuga Vengatasalam, Mohit Kumar Jolly","doi":"10.1159/000529558","DOIUrl":"10.1159/000529558","url":null,"abstract":"<p><p>Multistability is central to biological systems. It plays a crucial role in adaptation, evolvability, and differentiation. The presence of positive feedback loops can enable multistability. The simplest of such feedback loops are (a) a mutual inhibition (MI) loop, (b) a mutual activation (MA) loop, and (c) self-activation. While it is established that all three motifs can give rise to bistability, the characteristic differences in the bistability exhibited by each of these motifs is relatively less understood. Here, we use dynamical simulations across a large ensemble of parameter sets and initial conditions to study the bistability characteristics of these motifs. Furthermore, we investigate the utility of these motifs for achieving coordinated expression through cyclic and parallel coupling amongst them. Our analysis revealed that MI-based architectures offer discrete and robust control over gene expression, multistability, and coordinated expression among multiple genes, as compared to MA-based architectures. We then devised a combination of MI and MA architectures to improve coordination and multistability. Such designs help enhance our understanding of the control structures involved in robust cell-fate decisions and provide a way to achieve controlled decision-making in synthetic systems.</p>","PeriodicalId":9717,"journal":{"name":"Cells Tissues Organs","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9252904","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}

{"title":"Meckel's Diverticulum in Adult Geese (Alopochen egyptiacus): A Comprehensive Study of Structure Using Histological, Electron Microscopy, and Immunohistochemical Methods.","authors":"Fatma M Abdel-Maksoud, Shimaa Ali, Hanan H Abd-Elhafeez, Kamal E H Abdalla","doi":"10.1159/000536210","DOIUrl":"10.1159/000536210","url":null,"abstract":"<p><strong>Introduction: </strong>The intestine plays an important role in mediating between the bird and its nutritional environment. The yolk stalk, also known as Meckel's diverticulum, is a landmark between the jejunum and ileum. This work aimed to investigate the anatomical, histological, and electron microscopical features of cellular components of the Meckel's diverticulum (MD) in adult geese.</p><p><strong>Methods: </strong>The intestine was dissected from the bird's body cavity, and Meckel's diverticulum was exposed and prepared for light and electron microscopical examinations.</p><p><strong>Results: </strong>Our results revealed that the MD mucosa is thrown up into villi and crypts, and the mucosal epithelium is a columnar epithelium with goblet cells as well as intraepithelial lymphocytes. Lymphoid follicles and numerous immune cells were demonstrated within the lamina propria. The mucous glands were also observed within the lamina propria and among the lymphoid follicles. The lining epithelium of MD appeared with different staining affinities: dark cells (electron-dense) and light cells (electron-lucent) contained few mitochondria and more secretory vesicles, while dark cells contained more mitochondria and fewer secretory vesicles. Immunohistochemical analysis of MD revealed positive immunoreactivity for several markers, such as CD117, chromogranin, PLCβ, cytokeratin, MHC II, and S100.</p><p><strong>Conclusion: </strong>Taken together, our findings suggest that MD is considered an immune organ in adult geese.</p>","PeriodicalId":9717,"journal":{"name":"Cells Tissues Organs","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139490984","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}

{"title":"Mild Synovitis Impairs Chondrogenic Joint Environment.","authors":"Sharada Paudel, Tyler Feltham, Lumanti Manandhar, Yi Guo, Lew Schon, Zijun Zhang","doi":"10.1159/000532008","DOIUrl":"10.1159/000532008","url":null,"abstract":"<p><p>The impact of mild synovitis on the chondrogenic environment in the joint pertaining to cartilage repair is often neglected. In this study, 21 synovial samples were collected from foot surgeries for histology and isolation of fibroblast-like synoviocytes (FLSs). Of the 21 samples, 13 were normal and eight were mild synovitis, according to their synovitis scores. In mild synovitis, CD3+ lymphocytes were increased in the sublining layer. When chondrocytes were cultured and treated with the conditioned medium produced by FLSs, their glycosaminoglycan production was negatively correlated with the synovitis scores of the synovium, from which FLSs were isolated. In conclusion, mild synovitis in common joint conditions compromises the process of chondrogenesis, via inhibiting chondrocyte matrix production by FLSs. The results suggest that the concomitant synovitis, even being mild, could significantly alter the joint environment for chondrogenesis and impair the outcome of cartilage repair.</p>","PeriodicalId":9717,"journal":{"name":"Cells Tissues Organs","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11152049/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10286845","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":"Emergence of Spatial Scales and Macroscopic Tissue Dynamics in Active Epithelial Monolayers.","authors":"Padmalochini Selvamani, Raghunath Chelakkot, Amitabha Nandi, Mandar M Inamdar","doi":"10.1159/000528501","DOIUrl":"10.1159/000528501","url":null,"abstract":"<p><p>Migrating cells in tissues are often known to exhibit collective swirling movements. In this paper, we develop an active vertex model with polarity dynamics based on contact inhibition of locomotion (CIL). We show that under this dynamics, the cells form steady-state vortices in velocity, polarity, and cell stress with length scales that depend on polarity alignment rate (ζ), self-motility (v0), and cell-cell bond tension (λ). When the ratio λ/v0 becomes larger, the tissue reaches a near jamming state because of the inability of the cells to exchange their neighbors, and the length scale associated with tissue kinematics increases. A deeper examination of this jammed state provides insights into the mechanism of sustained swirl formation under CIL rule that is governed by the feedback between cell polarities and deformations. To gain additional understanding of how active forcing governed by CIL dynamics leads to large-scale tissue dynamics, we systematically coarse-grain cell stress, polarity, and motility and show that the tissue remains polar even on larger length scales. Overall, we explore the origin of swirling patterns during collective cell migration and obtain a connection between cell-level dynamics and large-scale cellular flow patterns observed in epithelial monolayers.</p>","PeriodicalId":9717,"journal":{"name":"Cells Tissues Organs","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9295460","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}