Acta Biotheoretica最新文献

Von Uexküll’s Umwelt Concept Revived Von Uexküll 的 "Umwelt "概念再现 : E. Yong, 2022.一个巨大的世界。动物感官如何揭示我们周围隐藏的领域。Bodley Head，伦敦，449 页；ISBN 978-1-847-92609-8。

IF 1.4 4区生物学

Acta Biotheoretica Pub Date : 2024-11-19 DOI: 10.1007/s10441-024-09487-9

Rob Hengeveld

引用次数: 0

From Fine-Grain to Coarse-Grain Modeling: Estimating Kinetic Parameters of DNA Molecules 从细粒度建模到粗粒度建模：估算 DNA 分子的动力学参数。

IF 1.4 4区生物学

Acta Biotheoretica Pub Date : 2024-11-19 DOI: 10.1007/s10441-024-09489-7

Jeremy Curuksu

{"title":"From Fine-Grain to Coarse-Grain Modeling: Estimating Kinetic Parameters of DNA Molecules","authors":"Jeremy Curuksu","doi":"10.1007/s10441-024-09489-7","DOIUrl":"10.1007/s10441-024-09489-7","url":null,"abstract":"<div><p>Coarse-grain models are essential to understand the biological function of DNA molecules because the length and time scales of the sequence-dependent physical properties of DNA are often beyond the reach of experimental and all-atom computational methods. Simulating coarse-grain models of DNA, e.g. using Langevin dynamics, requires the parametrization of both potential and kinetic energy functions. Many studies have shown that the flexibility (i.e., potential energy) of a DNA molecule depends on its sequence. In contrast, little is known about the sequence-dependence of DNA mass parameters required to model its kinetic energy. In this paper, an algebraic expression is derived for the kinetic energy as a function of linear and angular velocities of each DNA base parameterized by its mass, center of mass, and rotational inertia tensor. The parameters of this function are then approximated from a set of fine-grain molecular dynamics simulations representing all combinations of the four DNA base pairs AT, TA, GC, and CG, in different sequence contexts. Compatibility conditions associated with the assumption of each base being modeled as a rigid body were verified to be good approximations. The kinetic parameters were found to be significantly different between the four G, C, A, and T bases, and to not be dependent on the sequence context. This suggests that the effective kinetic parameters of a DNA base may depend only on the base itself, not on its neighbors.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"72 4","pages":""},"PeriodicalIF":1.4,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142666831","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

Susceptible-Infectious-Susceptible Epidemic Model with Symmetrical Fluctuations: Equilibrium States and Stability Analyses for Finite Systems 具有对称波动的易感-传染-易感流行病模型：有限系统的平衡状态和稳定性分析

IF 1.4 4区生物学

Acta Biotheoretica Pub Date : 2024-11-13 DOI: 10.1007/s10441-024-09490-0

Paulo S. Adami, Olavo H. Menin, Alexandre S. Martinez

引用次数: 0

Correction: The Effects of Triiodothyronine on the Free Thyroxine Set Point Position in the Hypothalamus Pituitary Thyroid Axis 更正：三碘甲状腺原氨酸对下丘脑-垂体-甲状腺轴游离甲状腺素设定点位置的影响。

IF 1.4 4区生物学

Acta Biotheoretica Pub Date : 2024-09-19 DOI: 10.1007/s10441-024-09488-8

Simon Lucas Goede, Melvin Khee Shing Leow

引用次数: 0

Improved Mathematical Models of Parkinson's Disease with Hopf Bifurcation and Huntington's Disease with Chaos 帕金森病与霍普夫分岔和亨廷顿病与混沌的改进数学模型。

IF 1.4 4区生物学

Acta Biotheoretica Pub Date : 2024-09-02 DOI: 10.1007/s10441-024-09485-x

M. A. Elfouly

{"title":"Improved Mathematical Models of Parkinson's Disease with Hopf Bifurcation and Huntington's Disease with Chaos","authors":"M. A. Elfouly","doi":"10.1007/s10441-024-09485-x","DOIUrl":"10.1007/s10441-024-09485-x","url":null,"abstract":"<div><p>Using delay differential equations to study mathematical models of Parkinson's disease and Huntington's disease is important to show how important it is for synchronization between basal ganglia loops to work together. We used the delay circuit RLC (resistor, inductor, capacitor) model to show how the direct pathway and the indirect pathway in the basal ganglia excite and inhibit the motor cortex, respectively. A term has been added to the mathematical model without time delay in the case of the hyperdirect pathway. It is proposed to add a non-linear term to adjust the synchronization. We studied Hopf bifurcation conditions for the proposed models. The desynchronization of response times between the direct pathway and the indirect pathway leads to different symptoms of Parkinson's disease. Tremor appears when the response time in the indirect pathway increases at rest. The simulation confirmed that tremor occurs and the motor cortex is in an inhibited state. The direct pathway can increase the time delay in the dopaminergic pathway, which significantly increases the activity of the motor cortex. The hyperdirect pathway regulates the activity of the motor cortex. The simulation showed bradykinesia occurs when we switch from one movement to another that is less exciting for the motor cortex. A decrease of GABA in the striatum or delayed excitation of the substantia nigra from the subthalamus may be a major cause of Parkinson's disease. An increase in the response time delay in one of the pathways results in the chaotic movement characteristic of Huntington's disease.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"72 3","pages":""},"PeriodicalIF":1.4,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142118682","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

The Effects of Triiodothyronine on the Free Thyroxine Set Point Position in the Hypothalamus Pituitary Thyroid Axis 三碘甲状腺原氨酸对下丘脑-垂体-甲状腺轴游离甲状腺素设定点位置的影响

IF 1.4 4区生物学

Acta Biotheoretica Pub Date : 2024-08-29 DOI: 10.1007/s10441-024-09486-w

Simon Lucas Goede, Melvin Khee Shing Leow

{"title":"The Effects of Triiodothyronine on the Free Thyroxine Set Point Position in the Hypothalamus Pituitary Thyroid Axis","authors":"Simon Lucas Goede, Melvin Khee Shing Leow","doi":"10.1007/s10441-024-09486-w","DOIUrl":"10.1007/s10441-024-09486-w","url":null,"abstract":"<div><p>In clinical endocrinology, it is often assumed that the results of thyroid hormone function tests (TFTs) before total thyroidectomy are considered euthyroid when the circulating concentrations of thyrotropin [TSH] and free thyroxine [FT4] are within the normal reference ranges. Postoperative thyroid replacement therapy with levothyroxine (L-T4) is aimed to reproduce the preoperative euthyroid condition. Currently, intra-individual changes in the euthyroid set point before and after total thyroidectomy are only partly understood. After total thyroidectomy, a greater postoperative [FT4] than preoperative [FT4] for equivalent euthyroid [TSH] was found, with differences ranging from 3 to 8 pmol/L. This unexplained difference can be explained by the use of a mathematical model of the hypothalamus-pituitary-thyroid (HPT) axis set point theory. In this article, the postoperative HPT euthyroid set point was calculated using a dataset of total thyroidectomized patients with at least three distinguishable postoperative TFTs. The postoperative [TSH] set point was used as a homeostatic reference for the comparison of preoperative TFTs. The preoperative [FT4] value was equal to the postoperative [FT4] value in 50% of the patients, divided by a factor of ~ 1.25 (within +/- 10%). The factor of 1.25 stems from the lack of postoperative use of thyroidal triiodothyronine (T3). Furthermore, approximately 25% of the patients presented a greater preoperative [FT4] difference than postoperative [FT4]/1.25 combined with a normal [TSH] difference. Based on these observations, the effect of T3 on the value of the [FT4] set point was analyzed and explained from a control theory perspective.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"72 3","pages":""},"PeriodicalIF":1.4,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103301","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

The Geometry of Normal Tissue and Cancer Gene Expression Manifolds 正常组织和癌症基因表达矩阵的几何图形

IF 1.4 4区生物学

Acta Biotheoretica Pub Date : 2024-07-09 DOI: 10.1007/s10441-024-09483-z

Joan Nieves, Augusto Gonzalez

{"title":"The Geometry of Normal Tissue and Cancer Gene Expression Manifolds","authors":"Joan Nieves, Augusto Gonzalez","doi":"10.1007/s10441-024-09483-z","DOIUrl":"10.1007/s10441-024-09483-z","url":null,"abstract":"<div><p>A recent paper shows that in gene expression space the manifold spanned by normal tissues and the manifold spanned by the corresponding tumors are disjoint. The statement is based on a two-dimensional projection of gene expression data. In the present paper, we show that, for the multi-dimensional vectors defining the centers of cloud samples: 1. The closest tumor to a given normal tissue is the tumor developed in that tissue, 2. Two normal tissues define quasi-orthogonal directions, 3. A tumor may have a projection onto its corresponding normal tissue, but it is quasi-orthogonal to all other normal tissues, and 4. The cancer manifold is roughly obtained by translating the normal tissue manifold along an orthogonal direction defined by a global cancer progression axis. These geometrical properties add a new characterization of normal tissues and tumors and may have biological significance. Indeed, normal tissues at the vertices of a high-dimensional simplex could indicate genotype optimization for given tissue functions, and a way of avoiding errors in embryonary development. On the other hand, the cancer progression axis could define relevant pan-cancer genes and seems to be consistent with the atavistic theory of tumors.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"72 3","pages":""},"PeriodicalIF":1.4,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141557694","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

How (not) to Talk to a Plant: An Application of Automata Theory to Plant Communication 如何（不）与植物交谈：自动机理论在植物交流中的应用》。

IF 1.4 4区生物学

Acta Biotheoretica Pub Date : 2024-06-29 DOI: 10.1007/s10441-024-09484-y

Lorenzo Baravalle

引用次数: 0

Paternal Inheritance of Mitochondrial DNA May Lead to Dioecy in Conifers 线粒体 DNA 的父系遗传可能导致针叶树的雌雄异体。

IF 1.4 4区生物学

Acta Biotheoretica Pub Date : 2024-06-13 DOI: 10.1007/s10441-024-09481-1

Tom J. de Jong, Avi Shmida

{"title":"Paternal Inheritance of Mitochondrial DNA May Lead to Dioecy in Conifers","authors":"Tom J. de Jong, Avi Shmida","doi":"10.1007/s10441-024-09481-1","DOIUrl":"10.1007/s10441-024-09481-1","url":null,"abstract":"<div><p>In angiosperms cytoplasmic DNA is typically passed on maternally through ovules. Genes in the mtDNA may cause male sterility. When male-sterile (female) cytotypes produce more seeds than cosexuals, they pass on more copies of their mtDNA and will co-occur with cosexuals with a neutral cytotype. Cytoplasmic gynodioecy is a well-known phenomenon in angiosperms, both in wild and crop plants. In some conifer families (e.g. Pinaceae) mitochondria are also maternally inherited. However in some other families (e.g. Taxaceae and Cupressaceae) mtDNA is paternally inherited through the pollen. With paternal mtDNA inheritance, male cytotypes that produce more pollen than cosexuals are expected to co-occur with cosexuals. This is uncharted territory. An ESS model shows that the presence of male cytotypes selects for more female allocation in the cosexual, i.e. for sexual specialisation. An allele that switches sex from male to female can then invade. This leads to rapid loss of the neutral cytotype of the cosexual, fixation of the male cytotype and dioecy with 50% males and 50% females. The models suggest that paternal inheritance of mtDNA facilitates the evolution dioecy. Consistent with this hypothesis the Pinaceae are 100% monoecious, while dioecy is common in the Taxaceae family and in the genus <i>Juniperus</i> (Cupressaceae). However, no reliable data are yet available on both mode of inheritance of mtDNA and gender variation of the same species. When cosexuals benefit from reproductive assurance (high selfing rate, low inbreeding depression, low fertilisation) they maintain themselves next to males and females. This predicted pattern with three sex types present in the same population is observed in conifers in nature.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"72 2","pages":""},"PeriodicalIF":1.4,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11176109/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141309415","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

Y-chromosome Degeneration due to Speciation and Founder Effect 物种变异和创始人效应导致的 Y 染色体退化。

IF 1.4 4区生物学

Acta Biotheoretica Pub Date : 2024-05-31 DOI: 10.1007/s10441-024-09482-0

Nianqin Zhang, Yongjun Zhang

引用次数: 0