JournalTOCs

Acta Biotheoretica
Journal Prestige (SJR): 0.284

Citation Impact (citeScore): 1
Number of Followers: 3

Hybrid journal (It can contain Open Access articles)
ISSN (Print) 1572-8358 - ISSN (Online) 0001-5342
Published by Springer-Verlag

[2468 journals]

Trypanosomosis and Transhumance: Contributions to Contemporary Conflicts
Between Farmers and Herdsmen Along the Tsetse Fly Belts: Mathematical
Modeling and Systematic Field Analysis Approach
- Free pre-print version: Loading...
  Rate this result: What is this?
  
  Please help us test our new pre-print finding feature by giving the pre-print link a rating.
  A 5 star rating indicates the linked pre-print has the exact same content as the published article.
  
  Abstract: Abstract Conflicts within the tsetse fly belt revealed a strong correlation between the dynamics of bovine trypanosomosis and the insurgency involving farmers and herders in Nigeria and parts of West Africa. This study examined the history, causes and influence of farmers-herdsmen conflicts on banditry, terrorism and food security as it relates to the epidemiology of African animal trypanosomosis (AAT). A combination of literature database searches, semi-structured questionnaires, and mathematical modeling was employed. The study found that transhumance contributes significantly to conflicts between farmers and herdsmen. An average of 6.46 persons per attack were reported between 2005 and 2021. Only 8.4 $\%$ (95 $\%$ CI: 5.0 $-$ 12.9) of farmers and 18.2 $\%$ (95 $\%$ CI: 12.4 $-$ 25.4) of herdsmen have engaged in conflict resolution efforts. The study shows that both conflict and the spread of trypanosomosis can be effectively controlled when $R_0 < 1$ , ensuring that the sub-population remains in the basin of attraction of the trypanosomosis-conflict-free equilibrium ( $T_{0c}$ ). The partial derivative of the basic reproduction number, $R_0$ , with respect to improved conflict resolution, suggests that halting transhumance can prevent a portion of the cattle recruitment rate ( $\Lambda_c$ ) from becoming infected with AAT. Climate change exacerbates these issues, leading to settlement and resettlement strategies within the fly belt regions. The model indicates that the basic reproduction number can only be reduced to less than one ( $R_0 < 1$ ) to become globally asymptotically stable if there is effective conflict resolution involving both farmers and herders. The study advocates for the establishment of ranching in tsetse-free zones with adequate social amenities, improved marketing strategies for animals and animal products led by government agencies through public-private partnerships, the banning of open grazing, and strict enforcement of policies against violators.
  PubDate: 2025-01-15
  DOI: 10.1007/s10441-024-09491-z
From Fine-Grain to Coarse-Grain Modeling: Estimating Kinetic Parameters of
DNA Molecules
- Free pre-print version: Loading...
  Rate this result: What is this?
  
  Please help us test our new pre-print finding feature by giving the pre-print link a rating.
  A 5 star rating indicates the linked pre-print has the exact same content as the published article.
  
  Abstract: Abstract 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.
  PubDate: 2024-11-19
  DOI: 10.1007/s10441-024-09489-7
Von Uexküll’s Umwelt Concept Revived
- Free pre-print version: Loading...
  Rate this result: What is this?
  
  Please help us test our new pre-print finding feature by giving the pre-print link a rating.
  A 5 star rating indicates the linked pre-print has the exact same content as the published article.
  
  PubDate: 2024-11-19
  DOI: 10.1007/s10441-024-09487-9
Susceptible-Infectious-Susceptible Epidemic Model with Symmetrical
Fluctuations: Equilibrium States and Stability Analyses for Finite Systems
- Free pre-print version: Loading...
  Rate this result: What is this?
  
  Please help us test our new pre-print finding feature by giving the pre-print link a rating.
  A 5 star rating indicates the linked pre-print has the exact same content as the published article.
  
  Abstract: Abstract Accurate prediction of epidemic evolution faces challenges such as understanding disease dynamics and inadequate epidemiological data. A recent approach faced these issues by modeling susceptible-infectious-susceptible (SIS) dynamics based on the first two statistical moments. Here, we improve this approach by including finite-size populations and analyzing the stability of the resulting model. Results underscore the influence of uncertainties and population size in the natural history of the epidemic.
  PubDate: 2024-11-13
  DOI: 10.1007/s10441-024-09490-0
Correction: The Effects of Triiodothyronine on the Free Thyroxine Set
Point Position in the Hypothalamus Pituitary Thyroid Axis
- Free pre-print version: Loading...
  Rate this result: What is this?
  
  Please help us test our new pre-print finding feature by giving the pre-print link a rating.
  A 5 star rating indicates the linked pre-print has the exact same content as the published article.
  
  PubDate: 2024-09-19
  DOI: 10.1007/s10441-024-09488-8
Improved Mathematical Models of Parkinson's Disease with Hopf Bifurcation
and Huntington's Disease with Chaos
- Free pre-print version: Loading...
  Rate this result: What is this?
  
  Please help us test our new pre-print finding feature by giving the pre-print link a rating.
  A 5 star rating indicates the linked pre-print has the exact same content as the published article.
  
  Abstract: Abstract 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.
  PubDate: 2024-09-02
  DOI: 10.1007/s10441-024-09485-x
The Effects of Triiodothyronine on the Free Thyroxine Set Point Position
in the Hypothalamus Pituitary Thyroid Axis
- Free pre-print version: Loading...
  Rate this result: What is this?
  
  Please help us test our new pre-print finding feature by giving the pre-print link a rating.
  A 5 star rating indicates the linked pre-print has the exact same content as the published article.
  
  Abstract: Abstract 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.
  PubDate: 2024-08-29
  DOI: 10.1007/s10441-024-09486-w
The Geometry of Normal Tissue and Cancer Gene Expression Manifolds
- Free pre-print version: Loading...
  Rate this result: What is this?
  
  Please help us test our new pre-print finding feature by giving the pre-print link a rating.
  A 5 star rating indicates the linked pre-print has the exact same content as the published article.
  
  Abstract: Abstract 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.
  PubDate: 2024-07-09
  DOI: 10.1007/s10441-024-09483-z
How (not) to Talk to a Plant: An Application of Automata Theory to Plant
Communication
- Free pre-print version: Loading...
  Rate this result: What is this?
  
  Please help us test our new pre-print finding feature by giving the pre-print link a rating.
  A 5 star rating indicates the linked pre-print has the exact same content as the published article.
  
  Abstract: Abstract Plants are capable of a range of complex interactions with the environment. Over the last decade, some authors have used this as evidence to argue that plants are cognitive agents. While there is no consensus on this view, it is certainly interesting to approach the debate from a comparative perspective, trying to understand whether different lineages of plants show different degrees of responsiveness to environmental cues, and how their responses compare with those of animals or humans. In this paper, I suggest that a potentially fruitful approach to these comparative studies is provided by automata theory. Accordingly, I shall present a possible application of this theory to plant communication. Two tentative results will emerge. First, that different lineages may exhibit different levels of complexity in response to similar stimuli. Second, that current evidence does not allow to infer great cognitive sophistication in plants.
  PubDate: 2024-06-29
  DOI: 10.1007/s10441-024-09484-y
Paternal Inheritance of Mitochondrial DNA May Lead to Dioecy in Conifers
- Free pre-print version: Loading...
  Rate this result: What is this?
  
  Please help us test our new pre-print finding feature by giving the pre-print link a rating.
  A 5 star rating indicates the linked pre-print has the exact same content as the published article.
  
  Abstract: Abstract 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 Juniperus (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.
  PubDate: 2024-06-13
  DOI: 10.1007/s10441-024-09481-1
Y-chromosome Degeneration due to Speciation and Founder Effect
- Free pre-print version: Loading...
  Rate this result: What is this?
  
  Please help us test our new pre-print finding feature by giving the pre-print link a rating.
  A 5 star rating indicates the linked pre-print has the exact same content as the published article.
  
  Abstract: Abstract The Y chromosome in the XY sex-determination system is often shorter than its X counterpart, a condition attributed to degeneration after Y recombination ceases. Contrary to the traditional view of continuous, gradual degeneration, our study reveals stabilization within large mating populations. In these populations, we demonstrate that both mutant and active alleles on the Y chromosome can reach equilibrium through a mutation-selection balance. However, the emergence of a new species, particularly through the founder effect, can disrupt this equilibrium. Specifically, if the male founders of a new species carry only a mutant allele for a particular Y-linked gene, this allele becomes fixed, leading to the loss of the corresponding active gene on the Y chromosome. Our findings suggest that the rate of Y-chromosome degeneration may be linked to the frequency of speciation events associated with single-male founder events.
  PubDate: 2024-05-31
  DOI: 10.1007/s10441-024-09482-0
Teleological Functional Explanations: A New Naturalist Synthesis
- Free pre-print version: Loading...
  Rate this result: What is this?
  
  Please help us test our new pre-print finding feature by giving the pre-print link a rating.
  A 5 star rating indicates the linked pre-print has the exact same content as the published article.
  
  Abstract: Abstract The etiological account of teleological function is beset by several difficulties, which I propose to solve by grafting onto the etiological theory a subordinated goal-contribution clause. This approach enables us to ascribe neither too many teleofunctions nor too few; to give a unitary, one-clause analysis that works just as well for teleological functions derived from Darwinian evolution, as for those derived from human intention; and finally, to save the etiological theory from falsification, by explaining how, in spite of appearances, the theory can allow for evolutionary function loss.
  PubDate: 2024-05-16
  DOI: 10.1007/s10441-024-09480-2
Reorienting the Debate on Biological Individuality: Politics and Practices
- Free pre-print version: Loading...
  Rate this result: What is this?
  
  Please help us test our new pre-print finding feature by giving the pre-print link a rating.
  A 5 star rating indicates the linked pre-print has the exact same content as the published article.
  
  Abstract: Abstract Biological individuality is without a doubt a key concept in philosophy of biology. Questions around the individuality of organisms, species, and biological systems can be traced throughout the philosophy of biology since the discipline’s inception, not to mention the sustained attention they have received in biology and philosophy more broadly. It’s high time the topic got its own Cambridge Element. McConwell’s Biological Individuality falls short of an authoritative overview of the debate on biological individuality. However, it sends a welcome message to new and seasoned scholars to reorient the debate towards practically and politically relevant themes.
  PubDate: 2024-02-28
  DOI: 10.1007/s10441-024-09479-9
What Influence Could the Acceptance of Visitors Cause on the Epidemic
Dynamics of a Reinfectious Disease': A Mathematical Model
- Free pre-print version: Loading...
  Rate this result: What is this?
  
  Please help us test our new pre-print finding feature by giving the pre-print link a rating.
  A 5 star rating indicates the linked pre-print has the exact same content as the published article.
  
  Abstract: Abstract The globalization in business and tourism becomes crucial more and more for the economical sustainability of local communities. In the presence of an epidemic outbreak, there must be such a decision on the policy by the host community as whether to accept visitors or not, the number of acceptable visitors, or the condition for acceptable visitors. Making use of an SIRI type of mathematical model, we consider the influence of visitors on the spread of a reinfectious disease in a community, especially assuming that a certain proportion of accepted visitors are immune. The reinfectivity of disease here means that the immunity gained by either vaccination or recovery is imperfect. With the mathematical results obtained by our analysis on the model for such an epidemic dynamics of resident and visitor populations, we find that the acceptance of visitors could have a significant influence on the disease’s endemicity in the community, either suppressive or supportive.
  PubDate: 2024-02-25
  DOI: 10.1007/s10441-024-09478-w
Model of Calcium Dynamics Regulating $$IP_{3}$$ , ATP and Insulin
Production in a Pancreatic $$\beta$$ -Cell
- Free pre-print version: Loading...
  Rate this result: What is this?
  
  Please help us test our new pre-print finding feature by giving the pre-print link a rating.
  A 5 star rating indicates the linked pre-print has the exact same content as the published article.
  
  Abstract: Abstract The calcium signals regulate the production and secretion of many signaling molecules like inositol trisphosphate ( $IP_{3}$ ) and adenosine triphosphate (ATP) in various cells including pancreatic $\beta$ -cells. The calcium signaling mechanisms regulating $IP_{3}$ , ATP and insulin responsible for various functions of $\beta$ -cells are still not well understood. Any disturbance in these mechanisms can alter the functions of $\beta$ -cells leading to diabetes and metabolic disorders. Therefore, a mathematical model is proposed by incorporating the reaction-diffusion equation for calcium dynamics and a system of first-order differential equations for $IP_{3}$ , ATP-production and insulin secretion with initial and boundary conditions. The model incorporates the temporal dependence of $IP_{3}$ -production and degradation, ATP production and insulin secretion on calcium dynamics in a $\beta$ -cell. The piecewise linear finite element method has been used for the spatial dimension and the Crank-Nicolson scheme for the temporal dimension to obtain numerical results. The effect of changes in source influxes and buffers on calcium dynamics and production of $IP_{3}$ , ATP and insulin levels in a $\beta$ -cell has been analyzed. It is concluded that the dysfunction of source influx and buffers can cause significant variations in calcium levels and dysregulation of $IP_{3}$ , ATP and insulin production, which can lead to various metabolic disorders, diabetes, obesity, etc. The proposed model provides crucial information about the changes in mechanisms of calcium dynamics causing proportionate disturbances in $IP_3$ , ATP and insulin levels in pancreatic cells, which can be helpful for devising protocols for diagnosis and treatment of various metabolic diseases.
  PubDate: 2024-02-09
  DOI: 10.1007/s10441-024-09477-x
Integrating Multicellular Systems: Physiological Control and Degrees of
Biological Individuality
- Free pre-print version: Loading...
  Rate this result: What is this?
  
  Please help us test our new pre-print finding feature by giving the pre-print link a rating.
  A 5 star rating indicates the linked pre-print has the exact same content as the published article.
  
  Abstract: Abstract This paper focuses on physiological integration in multicellular systems, a notion often associated with biological individuality, but which has not received enough attention and needs a thorough theoretical treatment. Broadly speaking, physiological integration consists in how different components come together into a cohesive unit in which they are dependent on one another for their existence and activity. This paper argues that physiological integration can be understood by considering how the components of a biological multicellular system are controlled and coordinated in such a way that their activities can contribute to the maintenance of the system. The main implication of this perspective is that different ways of controlling their parts may give rise to multicellular organizations with different degrees of integration. After defining control, this paper analyses how control is realized in two examples of multicellular systems located at different ends of the spectrum of multicellularity: biofilms and animals. It focuses on differences in control ranges, and it argues that a high degree of integration implies control exerted at both medium and long ranges, and that insofar as biofilms lack long-range control (relative to their size) they can be considered as less integrated than other multicellular systems. It then discusses the implication of this account for the debate on physiological individuality and the idea that degrees of physiological integration imply degrees of individuality.
  PubDate: 2023-12-27
  DOI: 10.1007/s10441-023-09476-4
Theoretical Assessment of the Impact of Water Stress on Plants Production:
Case of Banana-Plantain
- Free pre-print version: Loading...
  Rate this result: What is this?
  
  Please help us test our new pre-print finding feature by giving the pre-print link a rating.
  A 5 star rating indicates the linked pre-print has the exact same content as the published article.
  
  Abstract: Abstract The aim of this paper is to investigate the role of water stress on plants production. We propose a mathematical model for the dynamics growth of plants that takes into account the concentration of available water in the soil, water stress, plant production and plants compensation. Sensitivity analysis of the model has been performed in order to determine the impact of related parameters on the dynamics growth of plants. We present the theoretical analysis of the model with and without water stress. More precisely, we show that the full model is well-posedness. For each model, we compute the trivial equilibria and derive two thresholds parameters that determine the outcome of water stress within a plantation. Further, we perform numerical simulation on the case of banana-plantain simulations to support the theory. We found that the Hopf bifurcation occurs for a specific value of the water absorption rate of unstressed plants. The impact of the water stress on the banana-plantain production is also numerically investigated. After, the role of the water stress on the plant production is numerically investigated. We found that the water stress can cause about 68.16% of loss of banana-plantain production within a plantation with 1600 rejets initially planted. This suggests that climate change plays a detrimental role on banana-plantains production.
  PubDate: 2023-11-15
  DOI: 10.1007/s10441-023-09473-7
The First Nucleic Acid Strands May Have Grown on Peptides via Primeval
Reverse Translation
- Free pre-print version: Loading...
  Rate this result: What is this?
  
  Please help us test our new pre-print finding feature by giving the pre-print link a rating.
  A 5 star rating indicates the linked pre-print has the exact same content as the published article.
  
  Abstract: Abstract The central dogma of molecular biology dictates that, with only a few exceptions, information proceeds from DNA to protein through an RNA intermediate. Examining the enigmatic steps from prebiotic to biological chemistry, we take another road suggesting that primordial peptides acted as template for the self-assembly of the first nucleic acids polymers. Arguing in favour of a sort of archaic “reverse translation” from proteins to RNA, our basic premise is a Hadean Earth where key biomolecules such as amino acids, polypeptides, purines, pyrimidines, nucleosides and nucleotides were available under different prebiotically plausible conditions, including meteorites delivery, shallow ponds and hydrothermal vents scenarios. Supporting a protein-first scenario alternative to the RNA world hypothesis, we propose the primeval occurrence of short two-dimensional peptides termed “selective amino acid- and nucleotide-matching oligopeptides” (henceforward SANMAOs) that noncovalently bind at the same time the polymerized amino acids and the single nucleotides dispersed in the prebiotic milieu. In this theoretical paper, we describe the chemical features of this hypothetical oligopeptide, its biological plausibility and its virtues from an evolutionary perspective. We provide a theoretical example of SANMAO’s selective pairing between amino acids and nucleosides, simulating a poly-Glycine peptide that acts as a template to build a purinic chain corresponding to the glycine’s extant triplet codon GGG. Further, we discuss how SANMAO might have endorsed the formation of low-fidelity RNA’s polymerized strains, well before the appearance of the accurate genetic material’s transmission ensured by the current translation apparatus.
  PubDate: 2023-11-10
  DOI: 10.1007/s10441-023-09474-6
On Pattern-Cladistic Analyses Based on Complete Plastid Genome Sequences
- Free pre-print version: Loading...
  Rate this result: What is this?
  
  Please help us test our new pre-print finding feature by giving the pre-print link a rating.
  A 5 star rating indicates the linked pre-print has the exact same content as the published article.
  
  Abstract: Abstract The fundamental Hennigian principle, grouping solely on synapomorphy, is seldom used in modern phylogenetics. In the submitted paper, we apply this principle in reanalyzing five datasets comprising 197 complete plastid genomes (plastomes). We focused on the latter because plastome-based DNA sequence data gained dramatic popularity in molecular systematics during the last decade. We show that pattern-cladistic analyses based on complete plastid genome sequences can successfully resolve affinities between plant taxa, simultaneously simplifying both the genomic and analytical frameworks of phylogenetic studies. We developed “Matrix to Newick” (M2N), a program to represent the standard molecular alignment of plastid genomes in the form of trees or relationships directly. Thus, massive plastome-based DNA sequence data can be successfully represented in a relational form rather than as a standard molecular alignment. Application of methods of median supertree construction (the Average Consensus method has been used as an example in this study) or Maximum Parsimony analysis to relational representations of plastome sequence data may help systematist to avoid the complicated assumption-based frameworks of Maximum Likelihood or Bayesian phylogenetics that are most used today in massive plastid sequence data analyses. We also found that significant amounts of pure genomic information that typically accommodate the majority of current plastid phylogenomic studies can be effectively dropped by systematists if they focus on the pattern-cladistics or relational analyses of plastome-based molecular data. The proposed pattern-cladistic approach is a powerful and straightforward heuristic alternative to modern plastome-based phylogenetics.
  PubDate: 2023-11-03
  DOI: 10.1007/s10441-023-09475-5
Interior Operators and Their Relationship to Autocatalytic Networks
- Free pre-print version: Loading...
  Rate this result: What is this?
  
  Please help us test our new pre-print finding feature by giving the pre-print link a rating.
  A 5 star rating indicates the linked pre-print has the exact same content as the published article.
  
  Abstract: Abstract The emergence of an autocatalytic network from an available set of elements is a fundamental step in early evolutionary processes, such as the origin of metabolism. Given the set of elements, the reactions between them (chemical or otherwise), and with various elements catalysing certain reactions, a Reflexively Autocatalytic F-generated (RAF) set is a subset R $'$ of reactions that is self-generating from a given food set, and with each reaction in R $'$ being catalysed from within R $'$ . RAF theory has been applied to various phenomena in theoretical biology, and a key feature of the approach is that it is possible to efficiently identify and classify RAFs within large systems. This is possible because RAFs can be described as the (nonempty) subsets of the reactions that are the fixed points of an (efficiently computable) interior map that operates on subsets of reactions. Although the main generic results concerning RAFs can be derived using just this property, we show that for systems with at least 12 reactions there are generic results concerning RAFs that cannot be proven using the interior operator property alone.Kindly check and confirm the edit made in the title.I confirm that the edit is fine
  PubDate: 2023-10-27
  DOI: 10.1007/s10441-023-09472-8

HOME > Browse the 73 Subjects covered by JournalTOCs
Subject	Total Journals