Biophysica最新文献_第9页

Heterogeneous Tau Oligomers as Molecular Targets for Alzheimer’s Disease and Related Tauopathies 异质性Tau寡聚体作为阿尔茨海默病和相关Tau病的分子靶点

Biophysica Pub Date : 2022-11-11 DOI: 10.3390/biophysica2040039

Chih Hung Lo

{"title":"Heterogeneous Tau Oligomers as Molecular Targets for Alzheimer’s Disease and Related Tauopathies","authors":"Chih Hung Lo","doi":"10.3390/biophysica2040039","DOIUrl":"https://doi.org/10.3390/biophysica2040039","url":null,"abstract":"Tauopathies, including Alzheimer’s disease (AD), are a group of neurodegenerative disorders characterized by pathological aggregation of microtubule binding protein tau. The presence of tau neurofibrillary tangles, which are insoluble β-sheet fibrils, in the brain has been the histopathological hallmark of these diseases as their level correlates with the degree of cognitive impairment. However, recent studies suggest that tau oligomers, which are soluble proteins that are formed prior to insoluble fibrils, are the principal toxic species impairing neurons and inducing neurodegeneration. Targeting toxic tau oligomers is challenging, as they are mostly unstructured and adopting multiple conformations. The heterogeneity of tau oligomers is further illustrated by the different oligomeric species formed by various methods. The current models and technologies to study tau oligomerization represent important resources and avenues to push the forefront of elucidating the true toxic tau species. In this review, we will summarize the distinct tau oligomers generated using different strategies and discuss their conformational characteristics, neurotoxicity, relevance to pathological phenotypes, as well as their applications in drug discovery. This information will provide insights to understanding heterogeneous tau oligomers and their role as molecular targets for AD and related tauopathies.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48141220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

The Modification of Polyvinyl Alcohol for Ice Nucleation Based upon the Structures of Antifreeze Glycoproteins Found in Antarctic Fish 基于南极鱼类抗冻糖蛋白结构的聚乙烯醇冰核改性研究

Biophysica Pub Date : 2022-11-03 DOI: 10.3390/biophysica2040037

M. Bleszynski

{"title":"The Modification of Polyvinyl Alcohol for Ice Nucleation Based upon the Structures of Antifreeze Glycoproteins Found in Antarctic Fish","authors":"M. Bleszynski","doi":"10.3390/biophysica2040037","DOIUrl":"https://doi.org/10.3390/biophysica2040037","url":null,"abstract":"Various alternative compounds have been investigated to prevent icing, one of which includes poly(vinyl) alcohol (PVA), which has shown promising anti-freeze effects. However, determining the optimal structures and formulations of PVA for anti-icing applications has remained a challenge. Building upon our previous work, which used molecular dynamics simulations to assess the effects of hydroxyl group separation distance on ice nucleation, in this work, PVA was modified based upon the structures of antifreeze glycoproteins (AFGPs) found in Antarctic fish, and examined as a potential antifreeze compound. Four different PVA samples with different degrees of hydrolysis were fabricated and subsequently examined for their effects on ice crystallization. The results showed that the modified PVA samples with degrees of hydrolysis of 76% and 66% had an effect on ice crystallization, delaying ice crystallization by an average of approximately 20 min, and even preventing ice crystallization altogether in a small portion of the sample. Meanwhile, other samples with degrees of hydrolysis of 100% and 34% either showed no effect on ice crystallization, shortened the ice crystallization time, and appeared to promote ice nucleation.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41829442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Noninvasive Digital Method for Determining Inflammation after Dental Implantation 无创数字方法测定种植牙后炎症

Biophysica Pub Date : 2022-11-01 DOI: 10.3390/biophysica2040036

D. Prikule, V. Kukushkin, V. F. Prikuls

引用次数: 0

Optimizing Mineralization of Bioprinted Bone Utilizing Type-2 Fuzzy Systems 利用2型模糊系统优化生物打印骨矿化

Biophysica Pub Date : 2022-10-28 DOI: 10.3390/biophysica2040035

A. Sedigh, M. Akbarzadeh-T., R. Tomlinson

{"title":"Optimizing Mineralization of Bioprinted Bone Utilizing Type-2 Fuzzy Systems","authors":"A. Sedigh, M. Akbarzadeh-T., R. Tomlinson","doi":"10.3390/biophysica2040035","DOIUrl":"https://doi.org/10.3390/biophysica2040035","url":null,"abstract":"Bioprinting is an emerging tissue engineering method used to generate cell-laden scaffolds with high spatial resolution. Bioprinting parameters, such as pressure, nozzle size, and speed, highly influence the quality of the bioprinted construct. Moreover, cell suspension density and other critical biological parameters directly impact the biological function. Therefore, an approximation model that can be used to find the optimal bioprinting parameter settings for bioprinted constructs is highly desirable. Here, we propose a type-2 fuzzy model to handle the uncertainty and imprecision in the approximation model. Specifically, we focus on the biological parameters, such as the culture period, that can be used to maximize the output value (mineralization volume 21.8 mm3 with the same culture period of 21 days). We have also implemented a type-1 fuzzy model and compared the results with the proposed type-2 fuzzy model using two levels of uncertainty. We hypothesize that the type-2 fuzzy model may be preferred in biological systems due to the inherent vagueness and imprecision of the input data. Our numerical results confirm this hypothesis. More specifically, the type-2 fuzzy model with a high uncertainty boundary (30%) is superior to type-1 and type-2 fuzzy systems with low uncertainty boundaries in the overall output approximation error for bone bioprinting inputs.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47000333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Genotype-to-Protein Map and Collective Adaptation in a Viral Population 病毒群体的基因型-蛋白图谱和集体适应

Biophysica Pub Date : 2022-10-27 DOI: 10.3390/biophysica2040034

Ariadna Villanueva, Henry Secaira-Morocho, L. F. Seoane, E. Lázaro, S. Manrubia

{"title":"Genotype-to-Protein Map and Collective Adaptation in a Viral Population","authors":"Ariadna Villanueva, Henry Secaira-Morocho, L. F. Seoane, E. Lázaro, S. Manrubia","doi":"10.3390/biophysica2040034","DOIUrl":"https://doi.org/10.3390/biophysica2040034","url":null,"abstract":"Viral populations are large and highly heterogeneous. Despite the evolutionary relevance of such heterogeneity, statistical approaches to quantifying the extent to which viruses maintain a high genotypic and/or phenotypic diversity have been rarely pursued. Here, we address this issue by analyzing a nucleotide-to-protein sequence map through deep sequencing of populations of the Qβ phage adapted to high temperatures. Tens of thousands of different sequences corresponding to two fragments of the gene coding for the viral replicase were recovered. A diversity analysis of two independent populations consistently revealed that about 40% of the mutations identified caused changes in protein amino acids, leading to an almost complete exploration of the protein neighborhood of (non-silent) mutants at a distance of one. The functional form of the empirical distribution of phenotype abundance agreed with analytical calculations that assumed random mutations in the nucleotide sequence. Our results concur with the idea that viral populations maintain a high diversity as an efficient adaptive mechanism and support the hypothesis of universality for a lognormal distribution of phenotype abundances in biologically meaningful genotype–phenotype maps, highlighting the relevance of entropic effects in molecular evolution.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45362310","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Gated Ethidium- and Bleomycin-Loading in Phage T4 That Is Subsequently Purified Leak-Free 在T4噬菌体中装载门控乙啶和博莱霉素，随后被纯化为无泄漏

Biophysica Pub Date : 2022-10-26 DOI: 10.3390/biophysica2040033

P. Serwer, E. Wright

{"title":"Gated Ethidium- and Bleomycin-Loading in Phage T4 That Is Subsequently Purified Leak-Free","authors":"P. Serwer, E. Wright","doi":"10.3390/biophysica2040033","DOIUrl":"https://doi.org/10.3390/biophysica2040033","url":null,"abstract":"Chemotherapy-inhibiting tumor cell evolution to drug-resistance is potentially suppressed by using a drug delivery vehicle (DDV) that has gating. Gating would be used to increase tumor-selectivity of delivery of DDV packaged drug. Tumor-selectivity increase would make possible increase in tumor-delivered drug dose, which would suppress opportunities to evolve drug resistance. Currently used DDVs do not have gating but gating is a natural feature of some bacteriophages (phages). Phage T4, which has recently been found highly persistent in murine blood, is a potential gated DDV. Thus, here, we proceed towards a T4-DDV by developing (1) improved procedure for generating high concentrations and amounts of phage T4, (2) elevated temperature-driven gate-opening and ethidium- and bleomycin-loading, and (3) purification of loaded T4 by rate zonal centrifugation. We test for loading by native agarose gel electrophoresis (AGE) with fluorescence detection. We observe loading in both phage T4 and T4 (tail-free) heads. The loaded particles have an openable, closed gate. Stored, mature T4 phages and phage heads do not release ethidium during at least a month at 4 °C and 6 days at 37 and 42 °C. Tumor-specific T4 phage delivery is projected via both the EPR effect and high T4 persistence.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47810379","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Drug–Membrane Interaction as Revealed by Spectroscopic Methods: The Role of Drug Structure in the Example of Rifampicin, Levofloxacin and Rapamycin 光谱法揭示的药物-膜相互作用：药物结构在利福平、左氧氟沙星和雷帕霉素中的作用

Biophysica Pub Date : 2022-10-17 DOI: 10.3390/biophysica2040032

I. Le-Deygen, A. Safronova, P. Mamaeva, I. Kolmogorov, A. Skuredina, E. Kudryashova

{"title":"Drug–Membrane Interaction as Revealed by Spectroscopic Methods: The Role of Drug Structure in the Example of Rifampicin, Levofloxacin and Rapamycin","authors":"I. Le-Deygen, A. Safronova, P. Mamaeva, I. Kolmogorov, A. Skuredina, E. Kudryashova","doi":"10.3390/biophysica2040032","DOIUrl":"https://doi.org/10.3390/biophysica2040032","url":null,"abstract":"We have investigated the nature of the interaction of small organic drug molecules with lipid membranes of various compositions. Using infrared spectroscopy and differential scanning calorimetry methods, we studied the role of the structure of the active molecule in interaction with the membrane using the example of dipalmitoylphosphatidylcholine (DPPC) and dipalmitoylphosphatidylcholine:cardiolipin (DPPC:CL) liposomes. We discovered the key role of the heterocycle in interaction with the polar part of the bilayer and the network of unsaturated bonds in interaction with the hydrophobic part. For rifampicin and levofloxacin, the main binding sites were phosphate and carbonyl groups of lipids, and in the case of anionic liposomes we found a slight penetration of rifampicin into the hydrophobic part of the bilayer. For rapamycin, experimental confirmation of the localization of the molecule in the region of fatty acid chains was obtained, and perturbation in the region of phosphate groups was demonstrated for the first time. The process of phase transition of liposomal forms of rifampicin and levofloxacin was studied. DPPC liposomes accelerate the phase transition when loaded with a drug. DPPC:CL liposomes are less susceptible to changes in the phase transition rate.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48129022","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 9

Data Structures and Algorithms for k-th Nearest Neighbours Conformational Entropy Estimation 第k近邻构象熵估计的数据结构和算法

Biophysica Pub Date : 2022-10-13 DOI: 10.3390/biophysica2040031

Roberto Borelli, A. Dovier, F. Fogolari

引用次数: 2

Supramolecular-Covalent Peptides Self-Assembly: From Design to Regenerative Medicine and Beyond 超分子共价肽自组装：从设计到再生医学及其他

Biophysica Pub Date : 2022-10-11 DOI: 10.3390/biophysica2040030

R. Pugliese

{"title":"Supramolecular-Covalent Peptides Self-Assembly: From Design to Regenerative Medicine and Beyond","authors":"R. Pugliese","doi":"10.3390/biophysica2040030","DOIUrl":"https://doi.org/10.3390/biophysica2040030","url":null,"abstract":"The field of supramolecular peptides self-assembly has undergone outstanding growth since the early 1990s after the serendipitously discovery by Shuguang Zhang of an ionic self-complementary peptide as a repeating segment in a yeast protein. From then on, the field expanded at an accelerating pace and these self-assembled materials have become an integral part of a broad plethora of designer supramolecular nanomaterials useful for different applications ranging from 3D tissue cell cultures, regenerative medicine, up to optoelectronics. However, the supramolecular peptide based-nanomaterials available thus far for regenerative medicine still lack the dynamic complexity found in the biological structures that mediate regeneration. Indeed, self-assembling peptide (SAPs) suffer from poor mechanical stability, losing mechanical properties at low strains. Just like the extracellular matrix (ECM) of living systems, the chemical structure of the SAP-biomaterials should concurrently contain non-covalent and covalent bonds, bringing, respectively, infinite and finite lifetimes of interactions to obtain a reversibly dynamic matrix. In this review, will be highlighted the major advantages and current limitations of SAP-based biomaterials, and it will be discussed the most widely used strategies for precisely tune their mechanical properties (stiffness, resilience, strain-failure, stress resistance), describing recent and promising approaches in tissue engineering, regenerative medicine, and beyond.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44170537","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Non-Contacting Plant Health Monitoring via Ultrasound in Ambient Air 环境空气超声非接触式植物健康监测

Biophysica Pub Date : 2022-09-27 DOI: 10.3390/biophysica2040029

Teng Yang, Yuqi Jin, N. Dahotre, A. Neogi

引用次数: 0