Journal of Biological Physics最新文献_第8页

Effect of Joule heating and entropy generation on multi-slip condition of peristaltic flow of Casson nanofluid in an asymmetric channel 焦耳加热和熵生成对非对称通道中卡森纳米流体蠕动流动多滑移条件的影响

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2022-04-28 DOI: 10.1007/s10867-022-09603-1

Asha Kotnurkar, Namrata Kallolikar

{"title":"Effect of Joule heating and entropy generation on multi-slip condition of peristaltic flow of Casson nanofluid in an asymmetric channel","authors":"Asha Kotnurkar, Namrata Kallolikar","doi":"10.1007/s10867-022-09603-1","DOIUrl":"10.1007/s10867-022-09603-1","url":null,"abstract":"<div><p>In the present investigation, the effect of multi-slip condition on peristaltic flow through asymmetric channel with Joule heating effect is considered. We also considered the incompressible non-Newtonian Casson nanofluid model for blood, which is electrically conducting. Second law of thermodynamics is used to examine the entropy generation. Multi-slip condition is used at the boundary of the wall and the analysis is also restricted under the low Reynolds number and long wavelength assumption. The governing equations were transformed into a non-dimensional form by using suitable terms. The reduced non-dimensional highly nonlinear partial differential equations are solved by using the Homotopy Perturbation Sumudu transformation method (HPSTM). The influence of different physical parameters on dimensionless velocity, pressure gradient, temperature, concentration and nanoparticle is graphically presented. From the results, one can understand that the Joule heating effect controls the heat transfer in the system and as the magnetic parameter is increased, there will be decay in the velocity of fluid. The outcomes of the present investigation can be applicable in examining the chyme motion in the gastrointestinal tract and controlling the blood flow during surgery. Present study shows an excellent agreement with the previously available studies in the limiting case. </p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"48 3","pages":"273 - 293"},"PeriodicalIF":1.8,"publicationDate":"2022-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-022-09603-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5063964","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: 3

“Flexible hinge” dynamics in mismatched DNA revealed by fluorescence correlation spectroscopy 荧光相关光谱揭示错配DNA中的“柔性铰链”动力学

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2022-04-22 DOI: 10.1007/s10867-022-09607-x

Timour B. Ten, Viktoriya Zvoda, Manas K. Sarangi, Serguei V. Kuznetsov, Anjum Ansari

{"title":"“Flexible hinge” dynamics in mismatched DNA revealed by fluorescence correlation spectroscopy","authors":"Timour B. Ten, Viktoriya Zvoda, Manas K. Sarangi, Serguei V. Kuznetsov, Anjum Ansari","doi":"10.1007/s10867-022-09607-x","DOIUrl":"10.1007/s10867-022-09607-x","url":null,"abstract":"<div><p>Altered unwinding/bending fluctuations at DNA lesion sites are implicated as plausible mechanisms for damage sensing by DNA-repair proteins. These dynamics are expected to occur on similar timescales as one-dimensional (1D) diffusion of proteins on DNA if effective in stalling these proteins as they scan DNA. We examined the flexibility and dynamics of DNA oligomers containing 3 base pair (bp) mismatched sites specifically recognized in vitro by nucleotide excision repair protein Rad4 (yeast ortholog of mammalian XPC). A previous Forster resonance energy transfer (FRET) study mapped DNA conformational distributions with cytosine analog FRET pair primarily sensitive to DNA twisting/unwinding deformations (Chakraborty et al. Nucleic Acids Res. 46: 1240–1255 (2018)). These studies revealed B-DNA conformations for nonspecific (matched) constructs but significant unwinding for mismatched constructs specifically recognized by Rad4, even in the absence of Rad4. The timescales of these unwinding fluctuations, however, remained elusive. Here, we labeled DNA with Atto550/Atto647N FRET dyes suitable for fluorescence correlation spectroscopy (FCS). With these probes, we detected higher FRET in specific, mismatched DNA compared with matched DNA, reaffirming unwinding/bending deformations in mismatched DNA. FCS unveiled the dynamics of these spontaneous deformations at ~ 300 µs with no fluctuations detected for matched DNA within the ~ 600 ns–10 ms FCS time window. These studies are the first to visualize anomalous unwinding/bending fluctuations in mismatched DNA on timescales that overlap with the < 500 µs “stepping” times of repair proteins on DNA. Such “flexible hinge” dynamics at lesion sites could arrest a diffusing protein to facilitate damage interrogation and recognition.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"48 3","pages":"253 - 272"},"PeriodicalIF":1.8,"publicationDate":"2022-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-022-09607-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4850315","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

Thermodynamics of unfolding mechanisms of mouse mammary tumor virus pseudoknot from a coarse-grained loop-entropy model 基于粗粒度环熵模型的小鼠乳腺肿瘤病毒假结展开机制的热力学研究

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2022-04-20 DOI: 10.1007/s10867-022-09602-2

Ke Tang, Jorjethe Roca, Rong Chen, Anjum Ansari, Jie Liang

{"title":"Thermodynamics of unfolding mechanisms of mouse mammary tumor virus pseudoknot from a coarse-grained loop-entropy model","authors":"Ke Tang, Jorjethe Roca, Rong Chen, Anjum Ansari, Jie Liang","doi":"10.1007/s10867-022-09602-2","DOIUrl":"10.1007/s10867-022-09602-2","url":null,"abstract":"<div><p>Pseudoknotted RNA molecules play important biological roles that depend on their folded structure. To understand the underlying principles that determine their thermodynamics and folding/unfolding mechanisms, we carried out a study on a variant of the mouse mammary tumor virus pseudoknotted RNA (VPK), a widely studied model system for RNA pseudoknots. Our method is based on a coarse-grained discrete-state model and the algorithm of PK3D (pseudoknot structure predictor in three-dimensional space), with RNA loops explicitly constructed and their conformational entropic effects incorporated. Our loop entropy calculations are validated by accurately capturing previously measured melting temperatures of RNA hairpins with varying loop lengths. For each of the hairpins that constitutes the VPK, we identified alternative conformations that are more stable than the hairpin structures at low temperatures and predicted their populations at different temperatures. Our predictions were validated by thermodynamic experiments on these hairpins. We further computed the heat capacity profiles of VPK, which are in excellent agreement with available experimental data. Notably, our model provides detailed information on the unfolding mechanisms of pseudoknotted RNA. Analysis of the distribution of base-pairing probability of VPK reveals a cooperative unfolding mechanism instead of a simple sequential unfolding of first one stem and then the other. Specifically, we find a simultaneous “loosening” of both stems as the temperature is raised, whereby both stems become partially melted and co-exist during the unfolding process.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"48 2","pages":"129 - 150"},"PeriodicalIF":1.8,"publicationDate":"2022-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-022-09602-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4783428","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

Quantification of adaptive forces on SNP rs1010211 due to viral zoonotic pathogens 病毒性人畜共患病原体对SNP rs1010211的适应性的定量分析

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2022-04-15 DOI: 10.1007/s10867-022-09606-y

Daniah Alsufyani, James Lindesay

{"title":"Quantification of adaptive forces on SNP rs1010211 due to viral zoonotic pathogens","authors":"Daniah Alsufyani, James Lindesay","doi":"10.1007/s10867-022-09606-y","DOIUrl":"10.1007/s10867-022-09606-y","url":null,"abstract":"<div><p>Widespread genotyping of human populations in environmental homeostasis has created opportunities to quantify how environmental parameters affect the genomic distribution of variants in healthy populations. This represents an ongoing natural experiment upon the human species that can only be understood through developing models of adaptation. By examining the information dynamics of optimal SNP distributions within such populations, “adaptive forces” on genomic variants can be quantified through comparisons between different populations. To this end, we are performing double-blind scans of SNPs in order to ascertain any potential smooth functional relationships between the frequencies of the variants and changes in quantified environmental parameters. At present, we have sequentially examined more than twenty thousand SNPs (on chromosome 3) of nine homeostatic native populations for potential adaptive flagging of the variants as functions of 15 environmental parameters. Our first significant flag has related rs1010211 to viral pathogens in mammalian hosts. Such pathogens present a significant risk for the emergence of new infectious diseases in humans. This genomic variant is within the gene TNIK, which is a germinal center kinase (GCK). GCKs are participants in both adaptive and innate immune regulation. However, the function of TNIK is not fully understood. We quantify the adaptive force on the C allele due to the pathogens as 0.04 GEU’s/viral species.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"48 2","pages":"227 - 236"},"PeriodicalIF":1.8,"publicationDate":"2022-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-022-09606-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4594050","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: 1

Modulation of free energy landscapes as a strategy for the design of antimicrobial peptides 自由能景观的调节作为抗菌肽设计的一种策略

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2022-04-14 DOI: 10.1007/s10867-022-09605-z

Sergio A. Hassan, Peter J. Steinbach

{"title":"Modulation of free energy landscapes as a strategy for the design of antimicrobial peptides","authors":"Sergio A. Hassan, Peter J. Steinbach","doi":"10.1007/s10867-022-09605-z","DOIUrl":"10.1007/s10867-022-09605-z","url":null,"abstract":"<div><p>Computational design of antimicrobial peptides (AMPs) is a promising area of research for developing novel agents against drug-resistant bacteria. AMPs are present naturally in many organisms, from bacteria to humans, a time-tested mechanism that makes them attractive as effective antibiotics. Depending on the environment, AMPs can exhibit α-helical or β-sheet conformations, a mix of both, or lack secondary structure; they can be linear or cyclic. Prediction of their structures is challenging but critical for rational design. Promising AMP leads can be developed using essentially two approaches: traditional modeling of the physicochemical mechanisms that determine peptide behavior in aqueous and membrane environments and knowledge-based, e.g., machine learning (ML) techniques, that exploit ever-growing AMP databases. Here, we explore the conformational landscapes of two recently ML-designed AMPs, characterize the dependence of these landscapes on the medium conditions, and identify features in peptide and membrane landscapes that mediate protein-membrane association. For both peptides, we observe greater conformational diversity in an aqueous solvent than in a less polar solvent, and one peptide is seen to alter its conformation more dramatically than the other upon the change of solvent. Our results support the view that structural rearrangement in response to environmental changes is central to the mechanism of membrane-structure disruption by linear peptides. We expect that the design of AMPs by ML will benefit from the incorporation of peptide conformational substates as quantified here with molecular simulations.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"48 2","pages":"151 - 166"},"PeriodicalIF":1.8,"publicationDate":"2022-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-022-09605-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4562413","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: 1

Interaction among bovine serum albumin (BSA) molecules in the presence of anions: a small-angle neutron scattering study 阴离子存在下牛血清白蛋白(BSA)分子间的相互作用:小角中子散射研究

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2022-04-13 DOI: 10.1007/s10867-022-09608-w

Subhankar Pandit, Sarathi Kundu, Vinod K. Aswal

引用次数: 1

Investigation of extracellular medium osmolality depending on zinc application and incubation time on A549 cancer cells 锌对A549癌细胞胞外介质渗透压影响的研究

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2022-03-24 DOI: 10.1007/s10867-022-09604-0

Duygu Tarhan, Nural Pastaci Özsobaci, Dilek Düzgün Ergün, Alev Meltem Ercan

{"title":"Investigation of extracellular medium osmolality depending on zinc application and incubation time on A549 cancer cells","authors":"Duygu Tarhan, Nural Pastaci Özsobaci, Dilek Düzgün Ergün, Alev Meltem Ercan","doi":"10.1007/s10867-022-09604-0","DOIUrl":"10.1007/s10867-022-09604-0","url":null,"abstract":"<div><p>Changes in the osmolality of the extracellular medium (ECM) affect cell volume and cellular processes such as cell migration and proliferation. Not only may high concentrations of zinc (Zn) lead to cell death by apoptosis, but Zn is also a physiological suppressor of apoptosis. The aim of our study was to examine whether Zn and regulation of extracellular osmolality had an effect on the lung cancer cell line (A549) and how to be changed in ECM according to elements and osmolality depending on incubation time and Zn application. Our study consisted of four groups: cell-free medium, ECM of cancer cell after 24 h incubation (24hECM), ECM of cancer cell after 48 h incubation (48hECM), and ECM of cancer cell after 48 h incubation with ZnCl<sub>2</sub> (48hECM + Zn). ECM osmolality was measured by using osmometer, and the levels of chromium (Cr), iron (Fe), and magnesium (Mg) elements were analyzed using ICP-OES device for all groups. According to the result of the analysis, a statistically significant difference was found when osmolality and element values of ECM of 24hECM and 48hECM groups were compared with the values of the 48hECM + Zn group. It was observed that there was a decrease in the levels of Cr, Fe, and Mg with Zn application and incubation period in ECM. The regulation of ECM osmolality is a promising method due to biophysical effects on cancer cells. In our study, we speculated that the understanding of the effects of Zn and osmolality with the relationship between ECM and cancer cell might lead to the discovery of biophysical approaches as a novel therapeutic strategy.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"48 2","pages":"215 - 226"},"PeriodicalIF":1.8,"publicationDate":"2022-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-022-09604-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4943552","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

A neurocomputational model for the processing of conflicting information in context-dependent decision tasks 情境依赖决策任务中冲突信息处理的神经计算模型

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2022-03-08 DOI: 10.1007/s10867-021-09601-9

Francisco M. López, Andrés Pomi

{"title":"A neurocomputational model for the processing of conflicting information in context-dependent decision tasks","authors":"Francisco M. López, Andrés Pomi","doi":"10.1007/s10867-021-09601-9","DOIUrl":"10.1007/s10867-021-09601-9","url":null,"abstract":"<div><p>Context-dependent computation is a relevant characteristic of neural systems, endowing them with the capacity of adaptively modifying behavioral responses and flexibly discriminating between relevant and irrelevant information in a stimulus. This ability is particularly highlighted in solving conflicting tasks. A long-standing problem in computational neuroscience, flexible routing of information, is also closely linked with the ability to perform context-dependent associations. Here we present an extension of a context-dependent associative memory model to achieve context-dependent decision-making in the presence of conflicting and noisy multi-attribute stimuli. In these models, the input vectors are multiplied by context vectors via the Kronecker tensor product. To outfit the model with a noisy dynamic, we embedded the context-dependent associative memory in a leaky competing accumulator model, and, finally, we proved the power of the model in the reproduction of a behavioral experiment with monkeys in a context-dependent conflicting decision-making task. At the end, we discuss the neural feasibility of the tensor product and made the suggestive observation that the capacities of tensor context models are surprisingly in alignment with the more recent experimental findings about functional flexibility at different levels of brain organization.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"48 2","pages":"195 - 213"},"PeriodicalIF":1.8,"publicationDate":"2022-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-021-09601-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4346787","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: 1

Study of β-lactam-based drug interaction with albumin protein using optical, sensing, and docking methods 利用光学、传感和对接方法研究β-内酰胺类药物与白蛋白的相互作用

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2022-01-30 DOI: 10.1007/s10867-021-09599-0

Hannaneh Monirinasab, Mostafa Zakariazadeh, Havva Kohestani, Morteza Kouhestani, Farzaneh Fathi

{"title":"Study of β-lactam-based drug interaction with albumin protein using optical, sensing, and docking methods","authors":"Hannaneh Monirinasab, Mostafa Zakariazadeh, Havva Kohestani, Morteza Kouhestani, Farzaneh Fathi","doi":"10.1007/s10867-021-09599-0","DOIUrl":"10.1007/s10867-021-09599-0","url":null,"abstract":"<div><p>The quality and strength of drug and albumin interaction affecting the drug-free concentration and physiological activity are important issues in pharmacokinetic research. In the present study, not only did we evaluate the binding strength of ceftriaxone and ceftizoxime to bovine serum albumin (BSA), but we also investigated the kinetic and thermodynamic parameters including KD, KA, ΔS, and ΔH. We applied in vitro optical fluorescence spectroscopy and surface plasmon resonance (SPR) sensing approaches as well as molecular docking analyses. The kinetic and thermodynamic investigations were done using different concentrations of drugs at three temperatures. Thermodynamic parameters visibly demonstrated that the binding was an exothermic and spontaneous process. The obtained negative values of both enthalpy change (ΔH) and entropy change (ΔS) in fluorescence and SPR and also molecular docking investigations showed that the major binding force involved in the complexation of drugs to BSA was hydrogen bonding. Static quenching was the foremost fluorescence quenching mechanism between them. Furthermore, the results of ΔG and <i>K</i><sub><i>D</i></sub> values proved that the interaction of ceftriaxone-BSA was stronger than ceftizoxime-BSA. Finally, molecular docking confirmed that the preferable binding sites of ceftizoxime and ceftriaxone were site IIA and site IB of albumin, respectively.</p><h3>Graphic abstract</h3>\u0000 <figure><div><div><div><picture><source><img></source></picture></div></div></div></figure>\u0000 </div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"48 2","pages":"177 - 194"},"PeriodicalIF":1.8,"publicationDate":"2022-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-021-09599-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4011815","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: 8

Biological computation: hearts and flytraps 生物计算:心脏和捕蝇器

IF 1.8 4区生物学

Journal of Biological Physics Pub Date : 2022-01-28 DOI: 10.1007/s10867-021-09590-9

Kay L. Kirkpatrick

引用次数: 2