Journal of Biological Physics最新文献_第2页

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

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><p>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.</p></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><p>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.</p></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><p>Motile bacteria in hybrid nanofluids cause bioconvection. <i>Bacillus cereus</i>, <i>Pseudomonas viscosa</i>, <i>Bacillus brevis</i>, <i>Salmonella typhimurium</i>, and <i>Pseudomonas fluorescens</i> 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 Al<sub>2</sub>O<sub>3</sub> and Cu (Cu-Al<sub>2</sub>O<sub>3</sub>/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 <span>({k}_{p}^{*})</span>. Magnetic, radiation, and chemotaxis factors impact bacterial density. The hybrid nanofluid velocity decreases when the magnetic parameter, <i>M</i>, Prandtl number <i>Pr</i> increases, while it increases with the increasing of porosity coefficient, <span>({k}_{p}^{*})</span>, and the hybrid nanoparticle ratio<i> N</i><sub><i>f</i></sub>. The temperature distribution decreases with the increasing of Prandtl number and <i>N</i><sub><i>f</i></sub>. Increasing temperature differential and bacterium diffusivity increases bacterial aggregation.</p></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

Microrheological comparison of melanoma cells by atomic force microscopy 利用原子力显微镜对黑色素瘤细胞进行微流变学比较。

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2024-01-19 DOI: 10.1007/s10867-023-09648-w

M. Manuela Brás, Aureliana Sousa, Tânia B. Cruz, Jonas Michalewski, Marina Leite, Susana R. Sousa, Pedro L. Granja, Manfred Radmacher

{"title":"Microrheological comparison of melanoma cells by atomic force microscopy","authors":"M. Manuela Brás, Aureliana Sousa, Tânia B. Cruz, Jonas Michalewski, Marina Leite, Susana R. Sousa, Pedro L. Granja, Manfred Radmacher","doi":"10.1007/s10867-023-09648-w","DOIUrl":"10.1007/s10867-023-09648-w","url":null,"abstract":"<div><p>Melanoma is one of the most severe cancers due to its great potential to form metastasis. Recent studies showed the importance of mechanical property assessment in metastasis formation which depends on the cytoskeleton dynamics and cell migration. Although cells are considered purely elastic, they are viscoelastic entities. Microrheology atomic force microscopy (AFM) enables the assessment of elasticity and viscous properties, which are relevant to cell behavior regulation. The current work compares the mechanical properties of human neonatal primary melanocytes (HNPMs) with two melanoma cell lines (WM793B and 1205LU cells), using microrheology AFM. Immunocytochemistry of F-actin filaments and phosphorylated focal adhesion kinase (p-FAK) and cell migration assays were performed to understand the differences found in microrheology AFM regarding the tumor cell lines tested. AFM revealed that HNPMs and tumor cell lines had distinct mechanical properties. HNPMs were softer, less viscous, presenting a higher power-law than melanoma cells. Immunostaining showed that metastatic 1205LU cells expressed more p-FAK than WM793B cells. Melanoma cell migration assays showed that WM73B did not close the gap, in contrast to 1205LU cells, which closed the gap at the end of 23 h. These data seem to corroborate the high migratory behavior of 1205LU cells. Microrheology AFM applied to HNPMs and melanoma cells allowed the quantification of elasticity, viscous properties, glassy phase, and power-law properties, which have an impact in cell migration and metastasis formation. AFM study is important since it can be used as a biomarker of the different stages of the disease in melanoma.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"50 1","pages":"55 - 69"},"PeriodicalIF":1.8,"publicationDate":"2024-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10864228/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139490462","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

Roles of astrocytes and prions in Alzheimer’s disease: insights from mathematical modeling 星形胶质细胞和朊病毒在阿尔茨海默病中的作用：数学建模的启示

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2023-12-29 DOI: 10.1007/s10867-023-09652-0

Mitali Maji, Subhas Khajanchi

{"title":"Roles of astrocytes and prions in Alzheimer’s disease: insights from mathematical modeling","authors":"Mitali Maji, Subhas Khajanchi","doi":"10.1007/s10867-023-09652-0","DOIUrl":"10.1007/s10867-023-09652-0","url":null,"abstract":"<div><p>We present a mathematical model that explores the progression of Alzheimer’s disease, with a particular focus on the involvement of disease-related proteins and astrocytes. Our model consists of a coupled system of differential equations that delineates the dynamics of amyloid beta plaques, amyloid beta protein, tau protein, and astrocytes. Amyloid beta plaques can be considered fibrils that depend on both the plaque size and time. We change our mathematical model to a temporal system by applying an integration operation with respect to the plaque size. Theoretical analysis including existence, uniqueness, positivity, and boundedness is performed in our model. We extend our mathematical model by adding two populations, namely prion protein and amyloid beta-prion complex. We characterize the system dynamics by locating biologically feasible steady states and their local stability analysis for both models. The characterization of the proposed model can help inform in advancing our understanding of the development of Alzheimer’s disease as well as its complicated dynamics. We investigate the global stability analysis around the interior equilibrium point by constructing a suitable Lyapunov function. We validate our theoretical analysis with the aid of extensive numerical illustrations.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"50 2","pages":"149 - 179"},"PeriodicalIF":1.8,"publicationDate":"2023-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139064617","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

Base flipping mechanism and binding strength of methyl-damaged DNA during the interaction with AGT 甲基损伤 DNA 与 AGT 相互作用过程中的碱基翻转机制和结合强度。

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2023-12-27 DOI: 10.1007/s10867-023-09649-9

Rajendra Prasad Koirala, Narayan Prasad Adhikari

{"title":"Base flipping mechanism and binding strength of methyl-damaged DNA during the interaction with AGT","authors":"Rajendra Prasad Koirala, Narayan Prasad Adhikari","doi":"10.1007/s10867-023-09649-9","DOIUrl":"10.1007/s10867-023-09649-9","url":null,"abstract":"<div><p>Methyl damage to DNA bases is common in the cell nucleus. O6-alkylguanine-DNA alkyl transferase (AGT) may be a promising candidate for direct damage reversal in methylated DNA (mDNA) at the O6 point of the guanine. Indeed, atomic-level investigations in the contact region of AGT-DNA complex can provide an in-depth understanding of their binding mechanism, allowing to evaluate the silico-drug nature of AGT and its utility in removing methyl damage in DNA. In this study, molecular dynamics (MD) simulation was utilized to examine the flipping of methylated nucleotide, the binding mechanism between mDNA and AGT, and the comparison of binding strength prior and post methyl transfer to AGT. The study reveals that methylation at the O6 atom of guanine weakens the hydrogen bond (H-bond) between guanine and cytosine, permitting for the flipping of such nucleotide. The formation of a H-bond between the base pair of methylated nucleotide (i.e., cytosine) and the intercalated arginine of AGT also forces the nucleotide to rotate. Following that, electrostatics and van der Waals contacts as well as hydrogen bonding contribute to form the complex of DNA and protein. The stronger binding of AGT with DNA before methyl transfer creates the suitable condition to transfer methyl adduct from DNA to AGT.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"50 1","pages":"71 - 87"},"PeriodicalIF":1.8,"publicationDate":"2023-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139039324","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

Generic algebraic conditions for the occurrence of switch-like behavior of a chemical kinetic system of the hypoxia pathway 缺氧通路化学动力学系统出现开关样行为的通用代数条件。

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2023-12-21 DOI: 10.1007/s10867-023-09647-x

Quentin Vanhaelen

{"title":"Generic algebraic conditions for the occurrence of switch-like behavior of a chemical kinetic system of the hypoxia pathway","authors":"Quentin Vanhaelen","doi":"10.1007/s10867-023-09647-x","DOIUrl":"10.1007/s10867-023-09647-x","url":null,"abstract":"<div><p>Weakly reversible chemical reaction networks with zero deficiency associated with mass-action kinetics admit, within each positive stoichiometric compatibility class, one positive steady state which is locally asymptotically stable and this irrespective of the values of the kinetics constants. Networks which do not enjoy these structural properties potentially exhibit more diverse dynamical behaviors. In this article, we consider a chemical reaction network associated with mass-action kinetics which is not weakly reversible and has a deficiency larger than one. The chemical reactions are at most bimolecular, but inflow and outflow reactions are present. Our results are as follows. We establish the existence of positive steady-state solutions and obtain their analytic expressions in the concentration space and in convex coordinates. We show that the system fulfills necessary conditions for a saddle-node and for a bifurcation into a saddle and a node. We apply a constructive approach to obtain a set of numerical values for the state variables and kinetic parameters, not reported previously, such that the reduced Jacobian is characterized by a zero eigenvalue with all other eigenvalues having negative real parts. The bifurcation diagram confirms the presence of the switch-like behavior.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"50 1","pages":"29 - 53"},"PeriodicalIF":1.8,"publicationDate":"2023-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138827587","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