Physical biology最新文献_第4页

Calcium storage in multivesicular endo-lysosome. 钙在多泡内溶酶体中的储存。

IF 2 4区生物学

Physical biology Pub Date : 2023-10-17 DOI: 10.1088/1478-3975/acfe6a

Cameron C Scott, Vaibhav Wasnik, Paula Nunes-Hassler, Nicolas Demaurex, Karsten Kruse, Jean Gruenberg

{"title":"Calcium storage in multivesicular endo-lysosome.","authors":"Cameron C Scott, Vaibhav Wasnik, Paula Nunes-Hassler, Nicolas Demaurex, Karsten Kruse, Jean Gruenberg","doi":"10.1088/1478-3975/acfe6a","DOIUrl":"10.1088/1478-3975/acfe6a","url":null,"abstract":"It is now established that endo-lysosomes, also referred to as late endosomes, serve as intracellular calcium store, in addition to the endoplasmic reticulum. While abundant calcium-binding proteins provide the latter compartment with its calcium storage capacity, essentially nothing is known about the mechanism responsible for calcium storage in endo-lysosomes. In this paper, we propose that the structural organization of endo-lysosomal membranes drives the calcium storage capacity of the compartment. Indeed, endo-lysosomes exhibit a characteristic multivesicular ultrastructure, with intralumenal membranes providing a large amount of additional bilayer surface. We used a theoretical approach to investigate the calcium storage capacity of endosomes, using known calcium binding affinities for bilayers and morphological data on endo-lysosome membrane organization. Finally, we tested our predictions experimentally after Sorting Nexin 3 depletion to decrease the intralumenal membrane content. We conclude that the major negatively-charge lipids and proteins of endo-lysosomes serve as calcium-binding molecules in the acidic calcium stores of mammalian cells, while the large surface area of intralumenal membranes provide the necessary storage capacity.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2023-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41131268","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

Seeking and sharing information in collective olfactory search. 在集体嗅觉搜索中寻求和共享信息。

IF 2 4区生物学

Physical biology Pub Date : 2023-10-09 DOI: 10.1088/1478-3975/acfd7a

Emanuele Panizon, Antonio Celani

引用次数: 0

Facilitating cell segmentation with the projection-enhancement network. 利用投影增强网络促进细胞分割。

IF 2 4区生物学

Physical biology Pub Date : 2023-10-09 DOI: 10.1088/1478-3975/acfe53

Christopher Z Eddy, Austin Naylor, Christian T Cunningham, Bo Sun

{"title":"Facilitating cell segmentation with the projection-enhancement network.","authors":"Christopher Z Eddy, Austin Naylor, Christian T Cunningham, Bo Sun","doi":"10.1088/1478-3975/acfe53","DOIUrl":"10.1088/1478-3975/acfe53","url":null,"abstract":"Contemporary approaches to instance segmentation in cell science use 2D or 3D convolutional networks depending on the experiment and data structures. However, limitations in microscopy systems or efforts to prevent phototoxicity commonly require recording sub-optimally sampled data that greatly reduces the utility of such 3D data, especially in crowded sample space with significant axial overlap between objects. In such regimes, 2D segmentations are both more reliable for cell morphology and easier to annotate. In this work, we propose the projection enhancement network (PEN), a novel convolutional module which processes the sub-sampled 3D data and produces a 2D RGB semantic compression, and is trained in conjunction with an instance segmentation network of choice to produce 2D segmentations. Our approach combines augmentation to increase cell density using a low-density cell image dataset to train PEN, and curated datasets to evaluate PEN. We show that with PEN, the learned semantic representation in CellPose encodes depth and greatly improves segmentation performance in comparison to maximum intensity projection images as input, but does not similarly aid segmentation in region-based networks like Mask-RCNN. Finally, we dissect the segmentation strength against cell density of PEN with CellPose on disseminated cells from side-by-side spheroids. We present PEN as a data-driven solution to form compressed representations of 3D data that improve 2D segmentations from instance segmentation networks.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":"20 6","pages":""},"PeriodicalIF":2.0,"publicationDate":"2023-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10586931/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41156771","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

Quantitative insights in tissue growth and morphogenesis with optogenetics. 光遗传学对组织生长和形态发生的定量见解。

IF 2 4区生物学

Physical biology Pub Date : 2023-09-28 DOI: 10.1088/1478-3975/acf7a1

Mayesha Sahir Mim, Caroline Knight, Jeremiah J Zartman

{"title":"Quantitative insights in tissue growth and morphogenesis with optogenetics.","authors":"Mayesha Sahir Mim, Caroline Knight, Jeremiah J Zartman","doi":"10.1088/1478-3975/acf7a1","DOIUrl":"10.1088/1478-3975/acf7a1","url":null,"abstract":"Cells communicate with each other to jointly regulate cellular processes during cellular differentiation and tissue morphogenesis. This multiscale coordination arises through the spatiotemporal activity of morphogens to pattern cell signaling and transcriptional factor activity. This coded information controls cell mechanics, proliferation, and differentiation to shape the growth and morphogenesis of organs. While many of the molecular components and physical interactions have been identified in key model developmental systems, there are still many unresolved questions related to the dynamics involved due to challenges in precisely perturbing and quantitatively measuring signaling dynamics. Recently, a broad range of synthetic optogenetic tools have been developed and employed to quantitatively define relationships between signal transduction and downstream cellular responses. These optogenetic tools can control intracellular activities at the single cell or whole tissue scale to direct subsequent biological processes. In this brief review, we highlight a selected set of studies that develop and implement optogenetic tools to unravel quantitative biophysical mechanisms for tissue growth and morphogenesis across a broad range of biological systems through the manipulation of morphogens, signal transduction cascades, and cell mechanics. More generally, we discuss how optogenetic tools have emerged as a powerful platform for probing and controlling multicellular development.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2023-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10594237/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10181059","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

Universal calcium fluctuations inHydramorphogenesis. 水合形态发生中普遍存在的钙波动。

IF 2 4区生物学

Physical biology Pub Date : 2023-09-22 DOI: 10.1088/1478-3975/acf8a4

Oded Agam, Erez Braun

{"title":"Universal calcium fluctuations inHydramorphogenesis.","authors":"Oded Agam, Erez Braun","doi":"10.1088/1478-3975/acf8a4","DOIUrl":"10.1088/1478-3975/acf8a4","url":null,"abstract":"Understanding the collective physical processes that drive robust morphological transitions in animal development necessitates the characterization of the relevant fields involved in morphogenesis. Calcium (Ca2+) is recognized as one such field. In this study, we demonstrate that the spatial fluctuations of Ca2+duringHydraregeneration exhibit universal characteristics. To investigate this phenomenon, we employ two distinct controls, an external electric field andheptanol, a gap junction-blocking drug. Both lead to the modulation of the Ca2+activity and a reversible halting of the regeneration process. The application of an electric field enhances Ca2+activity in theHydra's tissue and increases its spatial correlations, while the administration ofheptanolinhibits its activity and diminishes the spatial correlations. Remarkably, the statistical characteristics of Ca2+spatial fluctuations, including the coefficient of variation and skewness, manifest universal shape distributions across tissue samples and conditions. We introduce a field-theoretic model, describing fluctuations in a tilted double-well potential, which successfully captures these universal properties. Moreover, our analysis reveals that the Ca2+activity is spatially localized, and theHydra's tissue operates near the onset of bistability, where the local Ca2+activity fluctuates between low and high excited states in distinct regions. These findings highlight the prominent role of the Ca2+field inHydramorphogenesis and provide insights into the underlying mechanisms governing robust morphological transitions.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2023-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10215486","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: 1

EMT induces characteristic changes of Rho GTPases and downstream effectors with a mitosis-specific twist. EMT通过有丝分裂特异性扭曲诱导Rho-GTP酶和下游效应物的特征性变化。

IF 2 4区生物学

Physical biology Pub Date : 2023-09-12 DOI: 10.1088/1478-3975/acf5bd

Kamran Hosseini, Annika Frenzel, Elisabeth Fischer-Friedrich

{"title":"EMT induces characteristic changes of Rho GTPases and downstream effectors with a mitosis-specific twist.","authors":"Kamran Hosseini, Annika Frenzel, Elisabeth Fischer-Friedrich","doi":"10.1088/1478-3975/acf5bd","DOIUrl":"10.1088/1478-3975/acf5bd","url":null,"abstract":"Epithelial-mesenchymal transition (EMT) is a key cellular transformation for many physiological and pathological processes ranging from cancer over wound healing to embryogenesis. Changes in cell migration, cell morphology and cellular contractility were identified as hallmarks of EMT. These cellular properties are known to be tightly regulated by the actin cytoskeleton. EMT-induced changes of actin-cytoskeletal regulation were demonstrated by previous reports of changes of actin cortex mechanics in conjunction with modifications of cortex-associated f-actin and myosin. However, at the current state, the changes of upstream actomyosin signaling that lead to corresponding mechanical and compositional changes of the cortex are not well understood. In this work, we show in breast epithelial cancer cells MCF-7 that EMT results in characteristic changes of the cortical association of Rho-GTPases Rac1, RhoA and RhoC and downstream actin regulators cofilin, mDia1 and Arp2/3. In the light of our findings, we propose that EMT-induced changes in cortical mechanics rely on two hitherto unappreciated signaling paths-i) an interaction between Rac1 and RhoC and ii) an inhibitory effect of Arp2/3 activity on cortical association of myosin II.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":"20 6","pages":""},"PeriodicalIF":2.0,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10222964","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

Quantitative modeling of EGF receptor ligand discrimination via internalization proofreading. 通过内化校对的EGF受体配体识别的定量建模。

IF 2 4区生物学

Physical biology Pub Date : 2023-08-22 DOI: 10.1088/1478-3975/aceecd

Jaleesa A Leblanc, Michael G Sugiyama, Costin N Antonescu, Aidan I Brown

{"title":"Quantitative modeling of EGF receptor ligand discrimination via internalization proofreading.","authors":"Jaleesa A Leblanc, Michael G Sugiyama, Costin N Antonescu, Aidan I Brown","doi":"10.1088/1478-3975/aceecd","DOIUrl":"10.1088/1478-3975/aceecd","url":null,"abstract":"The epidermal growth factor receptor (EGFR) is a central regulator of cell physiology that is stimulated by multiple distinct ligands. Although ligands bind to EGFR while the receptor is exposed on the plasma membrane, EGFR incorporation into endosomes following receptor internalization is an important aspect of EGFR signaling, with EGFR internalization behavior dependent upon the type of ligand bound. We develop quantitative modeling for EGFR recruitment to and internalization from clathrin domains, focusing on how internalization competes with ligand unbinding from EGFR. We develop two model versions: a kinetic model with EGFR behavior described as transitions between discrete states and a spatial model with EGFR diffusion to circular clathrin domains. We find that a combination of spatial and kinetic proofreading leads to enhanced EGFR internalization ratios in comparison to unbinding differences between ligand types. Various stages of the EGFR internalization process, including recruitment to and internalization from clathrin domains, modulate the internalization differences between receptors bound to different ligands. Our results indicate that following ligand binding, EGFR may encounter multiple clathrin domains before successful recruitment and internalization. The quantitative modeling we have developed describes competition between EGFR internalization and ligand unbinding and the resulting proofreading.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":"20 5","pages":""},"PeriodicalIF":2.0,"publicationDate":"2023-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10420722","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

Phase transitions in insect swarms. 昆虫群的相变。

IF 2 4区生物学

Physical biology Pub Date : 2023-08-22 DOI: 10.1088/1478-3975/aceece

Andy M Reynolds

{"title":"Phase transitions in insect swarms.","authors":"Andy M Reynolds","doi":"10.1088/1478-3975/aceece","DOIUrl":"10.1088/1478-3975/aceece","url":null,"abstract":"In contrast with laboratory insect swarms, wild insect swarms display significant coordinated behaviour. It has been hypothesised that the presence of a fluctuating environment drives the formation of transient, local order (synchronized subgroups), and that this local order pushes the swarm into a new state that is robust to environmental perturbations. The hypothesis is supported by observations of swarming mosquitoes. Here I provide numerical evidence that the formation of transient, local order is an accidental by-product of the strengthening of short-range repulsion which is expected in the presence of environmental fluctuations. The results of the numerical simulations reveal that this strengthening of the short-range can drive swarms into a crystalline phase containing subgroups that participate in cooperative ring exchanges-a new putative form of collective animal movement lacking velocity correlation. I thereby demonstrate that the swarm state and structure may be tuneable with environmental noise as a control parameter. Predicted properties of the collective modes are consistent with observations of transient synchronized subgroups in wild mosquito swarms that contend with environmental disturbances. When mutual repulsion becomes sufficiently strong, swarms are, in accordance with observations, predicted to form near stationary crystalline states. The analysis suggests that the many different forms of swarming motions observed across insect species are not distinctly different phenomena but are instead different phases of a single phenomenon.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":"20 5","pages":""},"PeriodicalIF":2.0,"publicationDate":"2023-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10401954","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: 1

Out-of-equilibrium gene expression fluctuations in the presence of extrinsic noise. 在外来噪声存在下的非平衡基因表达波动。

IF 2 4区生物学

Physical biology Pub Date : 2023-08-10 DOI: 10.1088/1478-3975/acea4e

Marta Biondo, Abhyudai Singh, Michele Caselle, Matteo Osella

{"title":"Out-of-equilibrium gene expression fluctuations in the presence of extrinsic noise.","authors":"Marta Biondo, Abhyudai Singh, Michele Caselle, Matteo Osella","doi":"10.1088/1478-3975/acea4e","DOIUrl":"10.1088/1478-3975/acea4e","url":null,"abstract":"Cell-to-cell variability in protein concentrations is strongly affected by extrinsic noise, especially for highly expressed genes. Extrinsic noise can be due to fluctuations of several possible cellular factors connected to cell physiology and to the level of key enzymes in the expression process. However, how to identify the predominant sources of extrinsic noise in a biological system is still an open question. This work considers a general stochastic model of gene expression with extrinsic noise represented as fluctuations of the different model rates, and focuses on the out-of-equilibrium expression dynamics. Combining analytical calculations with stochastic simulations, we characterize how extrinsic noise shapes the protein variability during gene activation or inactivation, depending on the prevailing source of extrinsic variability, on its intensity and timescale. In particular, we show that qualitatively different noise profiles can be identified depending on which are the fluctuating parameters. This indicates an experimentally accessible way to pinpoint the dominant sources of extrinsic noise using time-coarse experiments.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":"20 5","pages":""},"PeriodicalIF":2.0,"publicationDate":"2023-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10680095/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10020854","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: 2

Fundamental insights into the correlation between chromosome configuration and transcription. 对染色体结构和转录之间的相关性的基本见解。

IF 2 4区生物学

Physical biology Pub Date : 2023-08-04 DOI: 10.1088/1478-3975/ace8e5

Swayamshree Senapati, Inayat Ullah Irshad, Ajeet K Sharma, Hemant Kumar

{"title":"Fundamental insights into the correlation between chromosome configuration and transcription.","authors":"Swayamshree Senapati, Inayat Ullah Irshad, Ajeet K Sharma, Hemant Kumar","doi":"10.1088/1478-3975/ace8e5","DOIUrl":"https://doi.org/10.1088/1478-3975/ace8e5","url":null,"abstract":"Eukaryotic chromosomes exhibit a hierarchical organization that spans a spectrum of length scales, ranging from sub-regions known as loops, which typically comprise hundreds of base pairs, to much larger chromosome territories that can encompass a few mega base pairs. Chromosome conformation capture experiments that involve high-throughput sequencing methods combined with microscopy techniques have enabled a new understanding of inter- and intra-chromosomal interactions with unprecedented details. This information also provides mechanistic insights on the relationship between genome architecture and gene expression. In this article, we review the recent findings on three-dimensional interactions among chromosomes at the compartment, topologically associating domain, and loop levels and the impact of these interactions on the transcription process. We also discuss current understanding of various biophysical processes involved in multi-layer structural organization of chromosomes. Then, we discuss the relationships between gene expression and genome structure from perturbative genome-wide association studies. Furthermore, for a better understanding of how chromosome architecture and function are linked, we emphasize the role of epigenetic modifications in the regulation of gene expression. Such an understanding of the relationship between genome architecture and gene expression can provide a new perspective on the range of potential future discoveries and therapeutic research.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":"20 5","pages":""},"PeriodicalIF":2.0,"publicationDate":"2023-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9969063","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: 1