Journal of Biological Physics最新文献

Pseudo-trajectory inference for identifying essential regulations and molecules in cell fate decisions 通过伪轨迹推理确定细胞命运决定中的基本规则和分子。

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2024-11-14 DOI: 10.1007/s10867-024-09665-3

Xinyu He, Ruoyu Tang, Jie Lou, Ruiqi Wang

{"title":"Pseudo-trajectory inference for identifying essential regulations and molecules in cell fate decisions","authors":"Xinyu He, Ruoyu Tang, Jie Lou, Ruiqi Wang","doi":"10.1007/s10867-024-09665-3","DOIUrl":"10.1007/s10867-024-09665-3","url":null,"abstract":"<div><p>Cell fate decision is crucial in biological development and plays fundamental roles in normal development and functional maintenance of organisms. By identifying key regulatory interactions and molecules involved in these fate decisions, we can shed light on the intricate mechanisms underlying the cell fates. This understanding ultimately reveals the fundamental principles driving biological development and the origins of various diseases. In this study, we present an overarching framework which integrates pseudo-trajectory inference and differential analysis to determine critical regulatory interactions and molecules during cell fate transitions. To demonstrate feasibility and reliability of the approach, we employ the differentiation networks of hepatobiliary system and embryonic stem cells as representative model systems. By applying pseudo-trajectory inference to biological data, we aim to identify critical regulatory interactions and molecules during the cell fate transition processes. Consistent with experimental observations, the approach can allow us to infer dynamical cell fate decision processes and gain insights into the underlying mechanisms which govern cell state decisions.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"51 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142611682","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

Stochastic model of seed dispersal with homogeneous and non-homogeneous Poisson processes under habitat reduction conditions 栖息地减少条件下种子扩散的同质和非同质泊松过程随机模型。

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2024-11-14 DOI: 10.1007/s10867-024-09666-2

Nevena Marić

引用次数: 0

Exploring the effects of simulated microgravity on esophageal cancer cells: insights into morphological, growth behavior, adhesion, and genetic damage 探索模拟微重力对食管癌细胞的影响：对形态学、生长行为、粘附和遗传损伤的认识

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2024-10-14 DOI: 10.1007/s10867-024-09663-5

Saifaldeen Altaie, Amera Alrawi, Xuexin Duan, Qater Alnada

{"title":"Exploring the effects of simulated microgravity on esophageal cancer cells: insights into morphological, growth behavior, adhesion, and genetic damage","authors":"Saifaldeen Altaie, Amera Alrawi, Xuexin Duan, Qater Alnada","doi":"10.1007/s10867-024-09663-5","DOIUrl":"10.1007/s10867-024-09663-5","url":null,"abstract":"<div><p>The exploration of microgravity has garnered substantial scholarly attention due to its potential to offer unique insights into the behavior of biological systems. This study presents a preliminary investigation into the effects of simulated microgravity on esophageal cancer cells, examining various aspects such as morphology, growth behavior, adhesion, inhibition rate, and DNA damage. To achieve this, a novel microgravity simulator named “Gravity Challenge” was utilized for its effectiveness in minimizing external influences that could compromise microgravity conditions. The international cell line SK-GT-4 was utilized as the focal point of this investigation. Results revealed noticeable alterations in the growth behavior of cancer cells following exposure to simulated microgravity for 24 h, characterized by a loss of adhesion properties compared to control cells. Concurrently, cell viability exhibited a decline, as evidenced by cytotoxicity testing. Furthermore, the comet assay test demonstrated that cells subjected to microgravity simulation experienced a higher incidence of DNA damage compared to their control counterparts. In conclusion, this comprehensive examination of the impact of simulated microgravity on esophageal cancer cells extends beyond morphological changes, delving into genetic implications through observed DNA damage. The diminished vitality of cells under microgravity conditions underscores the multifaceted effects on cellular behavior in response to environmental variations. These findings represent a significant step towards understanding the dynamics of cancer cells, laying the groundwork for future research aimed at identifying potential therapeutic strategies for this disease.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"50 3-4","pages":"351 - 366"},"PeriodicalIF":1.8,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142451140","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

A possible origin of the inverted vertebrate retina revealed by physical modeling 通过物理建模揭示脊椎动物倒置视网膜的可能起源

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2024-08-03 DOI: 10.1007/s10867-024-09662-6

Jan M. M. Oomens

{"title":"A possible origin of the inverted vertebrate retina revealed by physical modeling","authors":"Jan M. M. Oomens","doi":"10.1007/s10867-024-09662-6","DOIUrl":"10.1007/s10867-024-09662-6","url":null,"abstract":"<div><p>The evolutionary origin of the inverted retina in the vertebrate eye is unknown. This paper explores a hypothetical evolutionary scenario that explains the unique orientation of the photoreceptors in the vertebrate retina. The proposed scenario follows the scientific accepted scenario for eye evolution and gradually builds up towards an eye prototype by considering light direction detection and increase in achievable spatial resolution as the driving forces. It suggests that eye retinas developed along two different morphological processes, an evagination process that results in the inverted retina in vertebrate eyes and an invagination process that results in a verted retina in cephalopod eyes. The development of the inverted vertebrate retina and eye prototype morphology is strongly substantiated by physics of vision. The proposed evolutionary sequence for vertebrate eye development is simple and has the full potential to explain the origin of the inverted retina and leads to an eye prototype enabling visual detection and orientation. It allows the emergence of eye structures like, extraocular muscles, tapetum lucidum, biconvex lens, cornea, and pupil. This study supports the suggestion that a primitive inverted retina in the predecessor of vertebrates is of ectodermal origin and available before neurulation occurred.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"50 3-4","pages":"327 - 349"},"PeriodicalIF":1.8,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-024-09662-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141886523","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

Motor domain of condensin and step formation in extruding loop of DNA 冷凝蛋白的马达结构域和 DNA 挤压环中的阶跃形成。

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2024-07-30 DOI: 10.1007/s10867-024-09661-7

Ya-chang Chou

{"title":"Motor domain of condensin and step formation in extruding loop of DNA","authors":"Ya-chang Chou","doi":"10.1007/s10867-024-09661-7","DOIUrl":"10.1007/s10867-024-09661-7","url":null,"abstract":"<div><p>During the asymmetric loop extrusion of DNA by a condensin complex, one domain of the complex stably anchors to the DNA molecule, and another domain reels in the DNA strand into a loop. The DNA strand in the loop is fully relaxed, or there is no tension in the loop. Just outside of the loop, there is a tension that resists the extrusion of DNA. To maintain the extrusion of the DNA loop, the condensin complex must have a domain capable of generating a force to overcome the tension outside of the loop. This study proposes that the groove-shaped HEAT repeat domain Ycg1 plays the role of a molecular motor. A DNA molecule may bind to the groove electrostatically, and the weak binding force facilitates the random thermal motion of DNA molecules. A mechanical model that random collisions between DNA and the nonparallel inner surfaces of the groove may generate a directional force which is required for the loop extrusion to sustain. The hinge domain binds to the DNA molecule and acts as an anchor during asymmetric DNA loop extrusion. When the effects of ATP hydrolysis and the viscous drag of the fluid environment are considered, the motor–anchor model for the condensin complex and the mechanical model might explain the asymmetric loop extrusion, the formation of steps, the step size distribution in the loop extrusion, the tension-dependent extrusion speed, the interaction between coexisting loops on the DNA strand, and untying the knots during extrusion. This model can also explain the observed formation of the Z-loop.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"50 3-4","pages":"307 - 325"},"PeriodicalIF":1.8,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141791622","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

Modelling the effect of cell motility on mixing and invasion in epithelial monolayers 模拟细胞运动对上皮单层混合和侵袭的影响。

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2024-07-20 DOI: 10.1007/s10867-024-09660-8

Faris Saad Alsubaie, Zoltan Neufeld

引用次数: 0

Wave propagation in a light-temperature neural network under adaptive local energy balance 自适应局部能量平衡下光温神经网络中的波传播。

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2024-07-03 DOI: 10.1007/s10867-024-09659-1

Feifei Yang, Qun Guo, Guodong Ren, Jun Ma

{"title":"Wave propagation in a light-temperature neural network under adaptive local energy balance","authors":"Feifei Yang, Qun Guo, Guodong Ren, Jun Ma","doi":"10.1007/s10867-024-09659-1","DOIUrl":"10.1007/s10867-024-09659-1","url":null,"abstract":"<div><p>External electric and mechanical stimuli can induce shape deformation in excitable media because of its intrinsic flexible property. When the signals propagation in the media is described by a neural network, creation of heterogeneity or defect is considered as the effect of shape deformation due to accumulation or release of energy in the media. In this paper, a temperature-light sensitive neuron model is developed from a nonlinear circuit composed of a phototube and a thermistor, and the physical energy is kept in capacitive and inductive terms. Furthermore, the Hamilton energy for this function neuron is obtained in theoretical way. A regular neural network is built on a square array by activating electric synapse between adjacent neurons, and a few of neurons in local area is excited by noisy disturbance, which induces local energy diversity, and continuous coupling enables energy propagation and diffusion. Initially, the Hamilton energy function for a temperature-light sensitive neuron can be obtained. Then, the finite neurons are applied noise to obtain energy diversity to explore the energy spread between neurons in the network. For keeping local energy balance, one intrinsic parameter is regulated adaptively until energy diversity in this local area is decreased greatly. Regular pattern formation indicates that local energy balance creates heterogeneity or defects and a few of neurons show continuous parameter shift for keeping energy balance in a local area, which supports gradient energy distribution for propagating waves in the network.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"50 3-4","pages":"271 - 290"},"PeriodicalIF":1.8,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490431","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

Assessment of bone tissue cytoarchitectonics by 2D 1H NMR relaxometry maps 通过二维 1H NMR 驰豫测量图评估骨组织细胞结构。

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2024-06-27 DOI: 10.1007/s10867-024-09658-2

Emese Orban, Zsuzsanna Pap, Remus Sebastian Sipos, Radu Fechete

{"title":"Assessment of bone tissue cytoarchitectonics by 2D 1H NMR relaxometry maps","authors":"Emese Orban, Zsuzsanna Pap, Remus Sebastian Sipos, Radu Fechete","doi":"10.1007/s10867-024-09658-2","DOIUrl":"10.1007/s10867-024-09658-2","url":null,"abstract":"<div><p>Bone is a complex tissue that fulfills the role of a resistance structure. This quality is most commonly assessed by bone densitometry, but bone strength may not only be related to bone mineral density but also to the preservation of bone cytoarchitectonics. The study included two groups of rats, ovariectomized and non-ovariectomized. Each group was divided into three batches: control, simvastatin-treated, and fenofibrate-treated. In the ovariectomized group, hypolipidemic treatment was instituted at 12 weeks post ovariectomy. One rat from each of the 6 batches was sacrificed 8 weeks after the start of treatment in the group. The experimental study was performed using a Bruker Minispec mq 20 spectrometer operating at a frequency of 20 MHz, subsequently also performed by <sup>1</sup>H <i>T</i><sub>2</sub>-<i>T</i><sub>2</sub> molecular exchange maps. The results were represented by <i>T</i><sub>2</sub>-<i>T</i><sub>2</sub> molecular exchange maps that showed, comparatively, both pore size and their interconnectivity at the level of the femoral epiphysis, being able to evaluate both the effect of estrogen on bone tissue biology and the effect of the lipid-lowering medication, simvastatin, and fenofibrate, in both the presence and absence of estrogen. <i>T</i><sub>2</sub>-<i>T</i><sub>2</sub> molecular exchange maps showed that the absence of estrogen results in an increase in bone tissue pore size and interconnectivity. In the presence of estrogen, lipid-lowering medication, both simvastatin and fenofibrate alter bone tissue cytoarchitectonics by reducing pore interconnectivity. In the absence of estrogen, fenofibrate improves bone tissue cytoarchitectonics, the <i>T</i><sub>2</sub>-<i>T</i><sub>2</sub> molecular exchange map being similar to that of non-osteoporotic bone tissue.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"50 3-4","pages":"255 - 269"},"PeriodicalIF":1.8,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-024-09658-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141454503","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

Regulatory disturbances in the dynamical signaling systems of (Ca^{2+}) and NO in fibroblasts cause fibrotic disorders 成纤维细胞中 C a 2 + 和 NO 的动态信号系统的调节紊乱会导致纤维化疾病。

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2024-05-16 DOI: 10.1007/s10867-024-09657-3

Ankit Kothiya, Neeru Adlakha

{"title":"Regulatory disturbances in the dynamical signaling systems of (Ca^{2+}) and NO in fibroblasts cause fibrotic disorders","authors":"Ankit Kothiya, Neeru Adlakha","doi":"10.1007/s10867-024-09657-3","DOIUrl":"10.1007/s10867-024-09657-3","url":null,"abstract":"<div><p>Studying the calcium dynamics within a fibroblast cell individually has provided only a restricted understanding of its functions. However, research efforts focusing on systems biology approaches for such investigations have been largely neglected by researchers until now. Fibroblast cells rely on signaling from calcium <span>((Ca^{2+}))</span> and nitric oxide (<i>NO</i>) to maintain their physiological functions and structural stability. Various studies have demonstrated the correlation between <i>NO</i> and the control of <span>(Ca^{2+})</span> dynamics in cells. However, there is currently no existing model to assess the disruptions caused by various factors in regulatory dynamics, potentially resulting in diverse fibrotic disorders. A mathematical model has been developed to investigate the effects of changes in parameters such as buffer, receptor, sarcoplasmic endoplasmic reticulum <span>(Ca^{2+})</span>-ATPase (<i>SERCA</i>) pump, and source influx on the regulation and dysregulation of spatiotemporal calcium and <i>NO</i> dynamics in fibroblast cells. This model is based on a system of reaction-diffusion equations, and numerical simulations are conducted using the finite element method. Disturbances in key processes related to calcium and nitric oxide, including source influx, buffer mechanism, <i>SERCA</i> pump, and inositol trisphosphate <span>((IP_3))</span> receptor, may contribute to deregulation in the calcium and <i>NO</i> dynamics within fibroblasts. The findings also provide new insights into the extent and severity of disorders resulting from alterations in various parameters, potentially leading to deregulation and the development of fibrotic disease.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"50 2","pages":"229 - 251"},"PeriodicalIF":1.8,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140943119","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

Magnetite in the abdomen and antennae of Apis mellifera honeybees 蜜蜂腹部和触角中的磁铁矿。

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2024-05-10 DOI: 10.1007/s10867-024-09656-4

Jilder Dandy Peña Serna, Odivaldo Cambraia Alves, Fernanda Abreu, Daniel Acosta-Avalos

{"title":"Magnetite in the abdomen and antennae of Apis mellifera honeybees","authors":"Jilder Dandy Peña Serna, Odivaldo Cambraia Alves, Fernanda Abreu, Daniel Acosta-Avalos","doi":"10.1007/s10867-024-09656-4","DOIUrl":"10.1007/s10867-024-09656-4","url":null,"abstract":"<div><p>The detection of magnetic fields by animals is known as magnetoreception. The ferromagnetic hypothesis explains magnetoreception assuming that magnetic nanoparticles are used as magnetic field transducers. Magnetite nanoparticles in the abdomen of <i>Apis mellifera</i> honeybees have been proposed in the literature as the magnetic field transducer. However, studies with ants and stingless bees have shown that the whole body of the insect contain magnetic material, and that the largest magnetization is in the antennae. The aim of the present study is to investigate the magnetization of all the body parts of honeybees as has been done with ants and stingless bees. To do that, the head without antennae, antennae, thorax, and abdomen obtained from <i>Apis mellifera</i> honeybees were analyzed using magnetometry and Ferromagnetic Resonance (FMR) techniques. The magnetometry and FMR measurements show the presence of magnetic material in all honeybee body parts. Our results present evidence of the presence of biomineralized magnetite nanoparticles in the honeybee abdomen and, for the first time, magnetite in the antennae. FMR measurements permit to identify the magnetite in the abdomen as biomineralized. As behavioral experiments reported in the literature have shown that the abdomen is involved in magnetoreception, new experimental approaches must be done to confirm or discard the involvement of the antennae in magnetoreception.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"50 2","pages":"215 - 228"},"PeriodicalIF":1.8,"publicationDate":"2024-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140896523","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