Fractal calculus in tumor growth simulations: The proof is in the pudding
Biosystems. 2024 Feb 12;237:105141. doi: 10.1016/j.biosystems.2024.105141. Online ahead of print.ABSTRACTMathematical modeling in oncology has a long history. Recently, mathematical models and their predictions have made inroads into prospective clinical trials with encouraging results. The goal of many such modeling efforts is to make predictions, either to clinician's choice therapy or into "optimal" therapy - often for individual patients. The mathematical oncology community rightfully puts great hope into predictive modeling and mechanistic digital twins - but with this great opportunity comes great responsibility. Mat...
Source: Biosystems - February 14, 2024 Category: Biotechnology Authors: Heiko Enderling Source Type: research
Fractal calculus in tumor growth simulations: The proof is in the pudding
Biosystems. 2024 Feb 12;237:105141. doi: 10.1016/j.biosystems.2024.105141. Online ahead of print.ABSTRACTMathematical modeling in oncology has a long history. Recently, mathematical models and their predictions have made inroads into prospective clinical trials with encouraging results. The goal of many such modeling efforts is to make predictions, either to clinician's choice therapy or into "optimal" therapy - often for individual patients. The mathematical oncology community rightfully puts great hope into predictive modeling and mechanistic digital twins - but with this great opportunity comes great responsibility. Mat...
Source: Biosystems - February 14, 2024 Category: Biotechnology Authors: Heiko Enderling Source Type: research
Elucidation of productive alanine recognition mechanism by Escherichia coli alanyl-tRNA synthetase
In this study, using a malachite green assay, we aimed to elucidate the alanine recognition mechanism of a fragment (AlaRS368N) containing only the amino acid activation domain of Escherichia coli AlaRS. This method quantifies monophosphate by decomposing pyrophosphate generated during aminoacyl-AMP production. AlaRS368N produced far more pyrophosphate when glycine or serine was used as a substrate than when alanine was used. Among several mutants tested, an AlaRS mutant in which the widely conserved aspartic acid at the 235th position (D235) near the active center was replaced with glutamic acid (D235E) increased pyrophos...
Source: Biosystems - February 12, 2024 Category: Biotechnology Authors: Mayu Onoguchi Riku Otsuka Miki Koyama Tadashi Ando Hiromi Mutsuro-Aoki Takuya Umehara Koji Tamura Source Type: research
Accurate phenotypic self-replication as a necessary cause for biological evolution
In this report I use the simple mathematics of evolutionary theory to investigate the dynamics of self-replication accuracy and allelic selection. Results indicate that the degree of self-replication accuracy must be greater than a threshold related to the selection coefficients of the alleles in a population in order for evolution to occur. Accurate replication of cellular phenotype and of the molecules involved in genotype/phenotype linkage is necessary for the origin of evolution and may be considered the fundamental principle of life.PMID:38346554 | DOI:10.1016/j.biosystems.2024.105154 (Source: Biosystems)
Source: Biosystems - February 12, 2024 Category: Biotechnology Authors: Seymour Garte Source Type: research
Single-cell classification, analysis, and its application using deep learning techniques
Biosystems. 2024 Feb 9;237:105142. doi: 10.1016/j.biosystems.2024.105142. Online ahead of print.ABSTRACTSingle-cell analysis (SCA) improves the detection of cancer, the immune system, and chronic diseases from complicated biological processes. SCA techniques generate high-dimensional, innovative, and complex data, making traditional analysis difficult and impractical. In the different cell types, conventional cell sequencing methods have signal transformation and disease detection limitations. To overcome these challenges, various deep learning techniques (DL) have outperformed standard state-of-the-art computer algorithms...
Source: Biosystems - February 10, 2024 Category: Biotechnology Authors: R Premkumar Arthi Srinivasan K G Harini Devi Deepika M Gaayathry E Pramod Jadhav Abhishek Futane Vigneswaran Narayanamurthy Source Type: research
STIM1 regulates pancreatic β-cell behaviour: A modelling study
Biosystems. 2024 Feb 8:105138. doi: 10.1016/j.biosystems.2024.105138. Online ahead of print.ABSTRACTPancreatic β-cells are equipped with the molecular machinery allowing them to respond to high glucose levels in the form of electrical activity and Ca2+ oscillations. These oscillations drive insulin secretion. Two key ionic mechanisms involved in this response are the Store-Operated Current and the current through ATP-dependent K+ channels. Both currents have been shown to be regulated by the protein STIM1, but this dual regulation by STIM1 has not been studied before. In this paper, we use mathematical modelling to gain i...
Source: Biosystems - February 10, 2024 Category: Biotechnology Authors: Hugo Enrique Romero-Campos Genevi ève Dupont Virginia Gonz ález-Vélez Source Type: research
Memory induced-mechanism of noise attenuator of myosin V molecular motors
Biosystems. 2024 Feb 7;237:105139. doi: 10.1016/j.biosystems.2024.105139. Online ahead of print.ABSTRACTDepending on the chemical energy from ATP hydrolysis, myosin V can drive the multistep and continuous coupled cycling process to transport cellular cargo to targeted regions. However, it is still obscure how the molecular memory induced by the multistep coupled transported process could regulate the dynamic behavior of the motor state of myosin V. Here, we propose a novel non-Markovian polymorphic mechanochemical model to investigate the effect of the molecular memory on the mechanic of noise attenuation of myosin V syst...
Source: Biosystems - February 9, 2024 Category: Biotechnology Authors: Xin Zhang Sizhe Wang Jingwen Zhang Haohua Wang Source Type: research
Temporal regulation of gene expression and pathways in chemotherapy-induced senescence in HeLa cervical cancer cell line
Biosystems. 2024 Feb 7;237:105140. doi: 10.1016/j.biosystems.2024.105140. Online ahead of print.ABSTRACTCellular senescence is the state of permanent growth arrest. Chemotherapeutic drugs induce senescence, known as therapy-induced senescence. Although there are studies deciphering processes in senescence, more studies providing detailed information on therapy-induced senescence at the transcriptome level are needed. In order to understand temporal molecular changes of doxorubicin treatment in the course of senescence formation, two data sets from HeLa cells at 16 h and 72 h doxorubicin treatment were analyzed. GO BP enric...
Source: Biosystems - February 9, 2024 Category: Biotechnology Authors: Ceren Sucularli Yaprak Dilber Şimay Demir Aysun Özdemir Mustafa Ark Source Type: research
The tri-flow adaptiveness of codes in major evolutionary transitions
Biosystems. 2024 Feb 7:105133. doi: 10.1016/j.biosystems.2024.105133. Online ahead of print.ABSTRACTLife codes increase in both number and variety with biological complexity. Although our knowledge of codes is constantly expanding, the evolutionary progression of organic, neural, and cultural codes in response to selection pressure remains poorly understood. Greater clarification of the selective mechanisms is achieved by investigating how major evolutionary transitions reduce spatiotemporal and energetic constraints on transmitting heritable code to offspring. Evolution toward less constrained flows is integral to endurin...
Source: Biosystems - February 9, 2024 Category: Biotechnology Authors: Chris Girard Source Type: research
Proton-polarized states in DNA
Biosystems. 2024 Feb 7;237:105125. doi: 10.1016/j.biosystems.2024.105125. Online ahead of print.ABSTRACTWe observed signatures of a phase transition in the double-stranded DNA fragment of known length and sequences using a non-invasive semiconductor-electrolyte interface technique and statistical physics methods. Observations revealed a coherence peak in the electromotive force and a significant decline in calculated dynamic entropy at a critical temperature and pH. This behavior may arise from the dynamic interaction of proton (H+) pairs with opposite momentum and spin, carrying a charge q=2+ under critical conditions.PMI...
Source: Biosystems - February 8, 2024 Category: Biotechnology Authors: Mariusz Pietruszka Marek Marzec Source Type: research
Capsule formation induced by flow
Biosystems. 2024 Feb 5:105137. doi: 10.1016/j.biosystems.2024.105137. Online ahead of print.ABSTRACTPhysical compartments are essential for the origin of life. While lipid vesicles are commonly regarded as precursors of cell membranes, we propose a simpler and more primitive model based on proteinoids. Proteinoids are macromolecules formed by the thermal polymerization of amino acids, mimicking primitive proteins. They self-assemble into spherical microspheres in water. Under a temperature gradient, proteinoid microspheres (PM) dissolve and flow, forming microcapsules with thin shells. The mechanism of this process has not...
Source: Biosystems - February 7, 2024 Category: Biotechnology Authors: Shunsuke Ito Shigeru Sakurazawa Source Type: research
Significance of genetic code module structure in gene expression and GC content enhancement in RNA sequences
Biosystems. 2024 Feb 4;237:105135. doi: 10.1016/j.biosystems.2024.105135. Online ahead of print.ABSTRACTThe existent algebraic models of the genetic code contribute to the understanding of the physio-chemical characteristics of the amino acids. However, the process of translating a gene into a phenotype is highly complex. Moreover, the intricacy of gene expression gets further multiplied due to the biases in the codon usage. This paper explores an algebraic structure called module on the set of codons as well as on that of RNA sequences. We study the potential implications of these structures on gene expression and the GC ...
Source: Biosystems - February 6, 2024 Category: Biotechnology Authors: Devangi Sojitra Minakshi Biswas Hathiwala Gautam Hathiwala Ashok Kumar Bishoyi Source Type: research
A novel approach to encode melodies in DNA
Biosystems. 2024 Feb 3:105136. doi: 10.1016/j.biosystems.2024.105136. Online ahead of print.ABSTRACTDNA data storage has gained more attention last decades. DNA molecules can be used for encoding of non-biological information and as promising carriers due to greater data capacity, higher duration of the storage, and better technical failures stability. Here we propose a new method for encoding of notes and music in DNA. The encoding technique takes into account the duration and tonality of each note, enabling to encode all seven octaves by assigning a nucleotide sequence to each key. A certain set of short sequences is sug...
Source: Biosystems - February 5, 2024 Category: Biotechnology Authors: Olga Yu Kiryanova Ravil R Garafutdinov Irek M Gubaydullin Alexey V Chemeris Source Type: research
Operator model for evolutionary dynamics
Biosystems. 2024 Feb 1;237:105130. doi: 10.1016/j.biosystems.2024.105130. Online ahead of print.ABSTRACTDrift, selection, and mutation are integral evolutionary factors. In this article, operator model is newly suggested to intuitively represent those evolutionary factors into mathematical operators, and to ultimately offer unconventional methodology for understanding evolutionary dynamics. To be specific, each of the drift, selection, and mutation was respectively interpreted as operator which in essence is a random matrix that acts upon the vector which contains population distribution information. The simulation results...
Source: Biosystems - February 3, 2024 Category: Biotechnology Authors: Kangbien Park Yonghee Bae Source Type: research
Coupling and biological free-energy transduction processes as a bridge between physics and life: Molecular-level instantiation of Ervin Bauer's pioneering concepts in biological thermodynamics
Biosystems. 2024 Feb;236:105134. doi: 10.1016/j.biosystems.2024.105134. Epub 2024 Jan 30.ABSTRACTThe nonequilibrium coupled processes of oxidation and ATP synthesis in the biological process of oxidative phosphorylation (OXPHOS) are fundamental to all life on our planet. These steady-state energy transduction processes ‒ coupled by proton and anion/counter-cation concentration gradients in the OXPHOS pathway ‒ generate ∼95 % of the ATP requirement of aerobic systems for cellular function. The rapid energy cycling and homeostasis of metabolites involved in this coupling are shown to be responsible for maintenance and ...
Source: Biosystems - February 1, 2024 Category: Biotechnology Authors: Sunil Nath Source Type: research
