Journal of Biological Physics最新文献_第2页

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>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.</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>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.</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>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 1H T2-T2 molecular exchange maps. The results were represented by T2-T2 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. T2-T2 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 T2-T2 molecular exchange map being similar to that of non-osteoporotic bone tissue.</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>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 ((Ca^{2+})) and nitric oxide (NO) to maintain their physiological functions and structural stability. Various studies have demonstrated the correlation between NO and the control of (Ca^{2+}) 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 (Ca^{2+})-ATPase (SERCA) pump, and source influx on the regulation and dysregulation of spatiotemporal calcium and NO 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, SERCA pump, and inositol trisphosphate ((IP_3)) receptor, may contribute to deregulation in the calcium and NO 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.</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>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 Apis mellifera 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 Apis mellifera 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.</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

Mathematical modeling of viral infection and the immune response controlled by the circadian clock 昼夜节律控制的病毒感染和免疫反应的数学建模

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2024-04-20 DOI: 10.1007/s10867-024-09655-5

Jiaxin Zhou, Hongli Wang, Qi Ouyang

{"title":"Mathematical modeling of viral infection and the immune response controlled by the circadian clock","authors":"Jiaxin Zhou, Hongli Wang, Qi Ouyang","doi":"10.1007/s10867-024-09655-5","DOIUrl":"10.1007/s10867-024-09655-5","url":null,"abstract":"<div>Time of day affects how well the immune system responds to viral or bacterial infections. While it is well known that the immune system is regulated by the circadian clock, the dynamic origin of time-of-day-dependent immunity remains unclear. In this paper, we studied the circadian control of immune response upon infection of influenza A virus through mathematical modeling. Dynamic simulation analyses revealed that the time-of-day-dependent immunity was rooted in the relative phase between the circadian clock and the pulse of viral infection. The relative phase, which depends on the time the infection occurs, plays a crucial role in the immune response. It can drive the immune system to one of two distinct bistable states, a high inflammatory state with a higher mortality rate or a safe state characterized by low inflammation. The mechanism we found here also explained why the same species infected by different viruses has different time-of-day-dependent immunities. Further, the time-of-day-dependent immunity was found to be abolished when the immune system was regulated by an impaired circadian clock with decreased oscillation amplitude or without oscillations.</div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"50 2","pages":"197 - 214"},"PeriodicalIF":1.8,"publicationDate":"2024-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140626356","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

Automatic classification of seizure and seizure-free EEG signals based on phase space reconstruction features 基于相空间重构特征的癫痫发作和无癫痫发作脑电信号自动分类

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2024-03-11 DOI: 10.1007/s10867-024-09654-6

Shervin Skaria, Sreelatha Karyaveetil Savithriamma

{"title":"Automatic classification of seizure and seizure-free EEG signals based on phase space reconstruction features","authors":"Shervin Skaria, Sreelatha Karyaveetil Savithriamma","doi":"10.1007/s10867-024-09654-6","DOIUrl":"10.1007/s10867-024-09654-6","url":null,"abstract":"<div>Epilepsy is a type of brain disorder triggered by an abrupt electrical imbalance of neuronal networks. An electroencephalogram (EEG) is a diagnostic tool to capture the underlying brain mechanisms and detect seizure onset in epileptic patients. To detect seizures, neurologists need to manually monitor EEG recordings for long periods, which is challenging and susceptible to errors depending on expertise and experience. Therefore, automatic identification of seizure and seizure-free EEG signals becomes essential. This study introduces a method based on the features extracted from the phase space reconstruction for classifying seizure and seizure-free EEG signals. The computed features are derived from the elliptical area and interquartile range of the Euclidean distance by varying percentage values of data points ranging from 50 to 100%. We consider two public datasets and evaluate these features in each EEG epoch that includes the healthy, interictal, preictal, and ictal stages of epileptic subjects, utilizing the K-nearest neighbor classifier for classification. Results show that the features have higher values during the seizure than the seizure-free EEG signals and healthy subjects. Furthermore, the proposed features can effectively discriminate seizure EEG signals from the seizure-free and normal subjects with 100% accuracy, sensitivity, and specificity in both datasets. Likewise, the classification between the preictal stage and seizure EEG signals attains 98% accuracy. Overall, the reconstructed phase space features significantly enhance the accuracy of detecting epileptic EEG signals compared with existing methods. This advancement holds great potential in assisting neurologists in swiftly and accurately diagnosing epileptic seizures from EEG signals.</div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"50 2","pages":"181 - 196"},"PeriodicalIF":1.8,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140097736","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

Retraction Note: Heat transfer analysis for EMHD peristalsis of ionic-nanofluids via curved channel with Joule dissipation and Hall effects 撤稿说明：带有焦耳耗散和霍尔效应的离子纳米流体通过弯曲通道的电磁流体力学蠕动的传热分析。

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2024-02-10 DOI: 10.1007/s10867-024-09653-7

Saba, Fahad Munir Abbasi, Sabir Ali Shehzad

引用次数: 0

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2024-01-23 DOI: 10.1007/s10867-023-09651-1

Samah Mohamed Mabrouk, Mustafa Inc, Ahmed Saad Rashed, Ali Akgül

{"title":"Similarity analysis of bioconvection of unsteady nonhomogeneous hybrid nanofluids influenced by motile microorganisms","authors":"Samah Mohamed Mabrouk, Mustafa Inc, Ahmed Saad Rashed, Ali Akgül","doi":"10.1007/s10867-023-09651-1","DOIUrl":"10.1007/s10867-023-09651-1","url":null,"abstract":"<div>Motile bacteria in hybrid nanofluids cause bioconvection. Bacillus cereus, Pseudomonas viscosa, Bacillus brevis, Salmonella typhimurium, and Pseudomonas fluorescens were used to evaluate their effect and dispersion in the hybrid nanofluid. Using similarity analysis, a two-phase model for mixed bioconvection magnetohydrodynamic flow was developed using hybrid nanoparticles of Al2O3 and Cu (Cu-Al2O3/water). The parametric investigation, covering the magnetic parameter, permeability coefficient, nanoparticle shape factor, temperature ratio, radiation parameter, nanoparticle fraction ratio, Brownian parameter, thermophoresis parameter, motile bacteria diffusivity, chemotaxis parameter, and Nusselt, Reynold, Prandtl, Sherwood numbers, as well as the number of motile microorganisms’, showed significant outcomes. Velocity and shear stresses are sensitive to M, Pr, and ({k}_{p}^{*}). Magnetic, radiation, and chemotaxis factors impact bacterial density. The hybrid nanofluid velocity decreases when the magnetic parameter, M, Prandtl number Pr increases, while it increases with the increasing of porosity coefficient, ({k}_{p}^{*}), and the hybrid nanoparticle ratio Nf. The temperature distribution decreases with the increasing of Prandtl number and Nf. Increasing temperature differential and bacterium diffusivity increases bacterial aggregation.</div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"50 1","pages":"119 - 148"},"PeriodicalIF":1.8,"publicationDate":"2024-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139518996","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