Searcharxiv⌕ Search

SEARCH · Searcharxiv

Results for “q-bio.OT”

Search indexed arXiv papers on artificial intelligence, large language models, computer vision and robotics. Read source abstracts and follow links to arXiv.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources
arXiv2018

Genetic Code as a Harmonic System: three Supplements

The paper represents three supplements to the source paper, q-bio/0610044 [q-bio.OT], with three new series of harmonic structures of the genetic code, determined by Gauss arithmetical algorithm; by Table of Minimal Adding, as in (Rakocevic, 2011a: Table 4; 2011b: Table 4); all structures in relation to Binary-code tree (Rakocevic, 1998). The determination itself is realized through atom and nucleon number balancing and nuancing of molekular polarity. In the first supplement the word is about some additional harmonic structures in relation to a previous our paper (Rakocevic, 2004); in the second one about the relation that structures with the polarity of protein amino acids. In the third supplement we give new ideas about the genetic code by an inclusion of the notions cipher of the genetic code and the key of that cipher.

q-bio.OT↗
arXiv2019

Genetic Code: Four-Codon and Non-Four-Codon Degeneracy

In this work it is shown that 20 canonical amino acids (AAs) within genetic code appear to be a whole system with strict distinction in Genetic Code Table (GCT) into some different quantums: 20, 23, 61 amino acid molecules. These molecules distinction is followed by specific balanced atom number and/or nucleon number distinctions within those molecules. In this second version two appendices are added; also a new version of Periodic system of numbers, whose first verson is given in arXiv:1107.1998 [q-bio.OT].

q-bio.BM↗
arXiv2022

It is useful to analyze correlation graphs

In 1987, we analyzed the changes in correlation graphs between various features of the organism during stress and adaptation. After 33 years of research of many authors, discoveries and rediscoveries, we can say with complete confidence: It is useful to analyze correlation graphs. In addition, we should add that the concept of adaptability ('adaptation energy') introduced by Selye is useful, especially if it is supplemented by 'adaptation entropy' and free energy, as well as an analysis of limiting factors. Our review of these topics, Dynamic and Thermodynamic Adaptation Models" (Phys Life Rev, 2021, arXiv:2103.01959 [q-bio.OT]), attracted many comments from leading experts, with new ideas and new problems, from the dynamics of aging and the training of athletes to single-cell omics. Methodological backgrounds, like free energy analysis, were also discussed in depth. In this article, we provide an analytical overview of twelve commenting papers and some related publications.

q-bio.TO↗
arXiv2007

Non-coding DNA programs express adaptation and its universal law

Significant fraction (98.5% in humans) of most animal genomes is non- coding dark matter. Its largely unknown function (1-5) is related to programming (rather than to spontaneous mutations) of accurate adaptation to rapidly changing environment. Programmed adaptation to the same universal law for non-competing animals from anaerobic yeast to human is revealed in the study of their extensively quantified mortality (6-21). Adaptation of animals with removed non-coding DNA fractions may specify their contribution to genomic programming. Emergence of new adaptation programs and their (non-Mendelian) heredity may be studied in antibiotic mini-extinctions (22-24). On a large evolutionary scale rapid universal adaptation was vital for survival, and evolved, in otherwise lethal for diverse species major mass extinctions (25-28). Evolutionary and experimental data corroborate these conclusions (6-21, 29-32). Universal law implies certain biological universality of diverse species, thus quantifies applicability of animal models to humans). Genomic adaptation programming calls for unusual approach to its study and implies unanticipated perspectives, in particular, directed biological changes.

q-bio.GN↗
arXiv2007

Evolving inductive generalization via genetic self-assembly

We propose that genetic encoding of self-assembling components greatly enhances the evolution of complex systems and provides an efficient platform for inductive generalization, i.e. the inductive derivation of a solution to a problem with a potentially infinite number of instances from a limited set of test examples. We exemplify this in simulations by evolving scalable circuitry for several problems. One of them, digital multiplication, has been intensively studied in recent years, where hitherto the evolutionary design of only specific small multipliers was achieved. The fact that this and other problems can be solved in full generality employing self-assembly sheds light on the evolutionary role of self-assembly in biology and is of relevance for the design of complex systems in nano- and bionanotechnology.

q-bio.PE↗
arXiv2007

Swimming with a friend at low Reynolds number

We investigate the hydrodynamic interactions between microorganisms swimming at low Reynolds number. By considering simple model swimmers, and combining analytic and numerical approaches, we investigate the time-averaged flow field around a swimmer. At short distances the swimmer behaves like a pump. At large distances the velocity field depends on whether the swimming stroke is invariant under a combined time-reversal and parity transformation. We then consider two swimmers and find that the interaction between them consists of two parts; a dead term, independent of the motion of the second swimmer, which takes the expected dipolar form and a live term resulting from the simultaneous swimming action of both swimmers which does not. We argue that, in general, the latter dominates. The swimmer--swimmer interaction is a complicated function of their relative displacement, orientation and phase, leading to motion that can be attractive, repulsive or oscillatory.

cond-mat.soft↗
arXiv2007

A successive sub-grouping method for multiple sequence alignments analysis

A novel approach to protein multiple sequence alignment is discussed: substantially this method counterparts with substitution matrix based methods (like Blosum or PAM based methods), and implies a more deterministic approach to chemical/physical sub-grouping of amino acids . Amino acids (aa) are divided into sub-groups with successive derivations, that result in a clustering based on the considered property. The properties can be user defined or chosen between default schemes, like those used in the analysis described here. Starting from an initial set of the 20 naturally occurring amino acids, they are successively divided on the basis of their polarity/hydrophobic index, with increasing resolution up to four level of subdivision. Other schemes of subdivision are possible: in this thesis work it was employed also a scheme based on physical/structural properties (solvent exposure, lateral chain mobility and secondary structure tendency), that have been compared to the chemical scheme with testing purposes. In the method described in this chapter, the total score for each position in the alignment accounts for different degree of similarity between amino acids. The scoring value result form the contribution of each level of selectivity for every individual property considered. Simply the method (called M_Al) analyse the n sequence alignment position per position and assigns a score which have contributes by aa identity plus a composed valuation of the chemical or of the structural affinity between the n aligned amino acids. This method has been implemented in a series of programs written in python language; these programs have been tested in some biological cases, with benchmark purposes.

q-bio.OT↗
arXiv2007

The Light Quanta Modulated Physiological Response of Brassica Juncea Seedlings Subjected to Ni(II) Stress

This work is a study of the inter-relationship between parameters that principally affect metal up-take in the plant. The relationships between the concentration of metal in the growth medium, Cs, the concentration of metal absorbed by the plant, Cp, and the total biomass achieved, M, all of which are factors relevant to the efficiency of phytoremediation of the plant, have been investigated via the macro-physiological response of Brassica juncea seedlings to Ni(II) stress. The factorial growth experiments treated the Ni(II) concentration in the agar gel and the diurnal light quanta (DLQ) as independently variable parameters. Observations included the evidence of light enhancement of Ni toxicity at the root as well as at the whole plant level, the shoot mass index as a possible indicator of shoot metal sequestration in B. juncea, the logarithmic variation of Cp with Cs and the power-law dependence of M on Cp. The sum total of these observations indicate that for the metal accumulator B. juncea with regard to its capacity to accumulate Ni, the overall metabolic nature of the plant is important; neither rapid biomass increase nor a high metal concentration capability favor the removal of high metal mass from the medium, but rather the plant with the moderate photosynthetically driven biomass growth and moderate metal concentrations demonstrated the ability to remove the maximum mass of metal from the medium. The implications of these observations in the context of the perceived need in phytoremediation engineering to maximize Cp and M simultaneously in the same plant, are discussed.

q-bio.OT↗
arXiv2008

Influence of experimental context on the development of anhedonia in male mice imposed to chronic social stress

Anhedonia is one of the key symptoms of depression in humans. Consumption of 1% sucrose solution supplemented with 0.2% vanillin was studied in two experimental contexts in male mice living under chronic social stress induced by daily experience of defeats in agonistic interactions and leading to development of depression. In the first experiment, vanillin sucrose solution was made available as an option of water during 10 days to mice living in group home cages. Then the mice were subjected to social defeat stress and during stress exposure they were provided with both vanillin sucrose solution and water using a free two bottles choice paradigm. In the other experiment, vanillin sucrose solution were first offered to mice after 8 days of exposure to social defeat stress. Males familiar with vanillin sucrose solution showed vanillin sucrose preference while experiencing defeat stress: consumption of vanillin sucrose solution was about 70% of total liquid consumption. However, the consumption of vanillin sucrose solution per gram of body weight in mice imposed to social stress during 20 days was significantly lower than in control males. In the second experiment, males after 8 days of social defeat stress were found to consume significantly less vanillin sucrose solution as compared with control males. On average during two weeks of measurements, vanillin sucrose solution intake was less than 20% of total liquid consumption in males with symptoms of depression and anxiety. Consumption per gram of body weight also appeared to be significantly lower than in control group. Influence of the experimental context on the development of anhedonia, which was measured by the reduction in sucrose solution intake by chronically stressed male mice, has been discussed.

q-bio.OT↗
arXiv2007

Unique mechanisms from finite two-state trajectories

Single molecule data made of on and off events are ubiquitous. Famous examples include enzyme turnover, probed via fluorescence, and opening and closing of ion-channel, probed via the flux of ions. The data reflects the dynamics in the underlying multi-substate on-off kinetic scheme (KS) of the process, but the determination of the underlying KS is difficult, and sometimes even impossible, due to the loss of information in the mapping of the mutli-dimensional KS onto two dimensions. A way to deal with this problem considers canonical (unique) forms. (Unique canonical form is constructed from an infinitely long trajectory, but many KSs.) Here we introduce canonical forms of reduced dimensions that can handle any KS (i.e. also KSs with symmetry and irreversible transitions). We give the mapping of KSs into reduced dimensions forms, which is based on topology of KSs, and the tools for extracting the reduced dimensions form from finite data. The canonical forms of reduced dimensions constitute a powerful tool in discriminating between KSs.

q-bio.QM↗
arXiv2007

On the Gompertzian dynamics of growth and self-organization

Comment on the Waliszewski's article "A principle of fractal-sto-chastic dualism and Gompertzian dynamics of growth and self-organization" (BioSystems 82 (2005)61-73) is presented. It has been proved that the main idea of this work that Gompertzian dynamics is governed by the Schrödinger-like equation including anharmonic Morse potential has been already introduced by Molski and Konarski in 2003. Some inconsistencies and mathematical errors in the Waliszewski's model are also pointed out.

q-bio.OT↗
arXiv2007

On the Classification Scheme for Phenomenological Universalities in Growth Problems in Physics and Other Sciences

Comment on "Classification Scheme for Phenomenological Universalities in Growth Problems in Physics and Other Sciences" by P. Castorina, P. P. Delsanto and C. Guiot, Phys. Rev. Lett. {\bf 96}, 188701 (2006) is presented. It has been proved that the West-like function of growth derived by the authors is incorrect and the approach does not take into account the growth of the biological systems undergoing atrophy or demographic and economic systems undergoing involution or regression. A simple extension of the model, which permits derivation of the so far unknown involuted Gompertz function of growth is proposed.

q-bio.OT↗
arXiv2008

New method for the study of psychotropic drug effects under simulated clinical conditions

The sensory contact model allows forming different psychopathological states (anxious depression, catalepsy, social withdrawal, pathological aggression, hypersensitivity, cognition disturbances, anhedonia, alcoholism etc.) produced by repeated agonistic interactions in male mice and investigating the therapeutic and preventive properties of any drug as well as its efficiency under simulated clinical conditions. This approach can be useful for a better understanding of the drugs' action in different stages of disease development in individuals. It is suggested that this pharmacological approach may be applied for the screening of different novel psychotropic drugs.

q-bio.OT↗
arXiv2007

Partition test and sexual motivation in male mice

Theoretical analysis of own and literature investigations of sexual motivation with the use of the partition test [Kudryavtseva, 1987, 1994] in male mice was carried out. It has been shown that appearance of a receptive female in the neighboring compartment of common cage separated by perforated transparent partition produces the enhancement of testosterone level in blood and stimulates the behavioral activity near partition as a reaction to the receptive female in naive males. In many studies this behavioral activity is considered as sexual motivation, arising in this experimental context in male mice. The lack of correlation between behavioral parameters and gonad reaction of males on receptive female, uninterconnected changes of these two parameters as well as the lack of sexual behavior between naive male and female when partition is removed cast doubt on this data interpretation. It has been supposed that in naive males behavioral reaction to a receptive female is induced by positive incentive - odor of the female associated with nursing and warmth from mother and other females which look after posterity. Short-term increase of the level of testosterone (possessing rewarding properties) is innate stimulus-response reaction which stimulates and prolongs behavioral interest of male to receptive female. It has been supposed that after sexual experience female odor is associated in experienced males with sexual behavior directed to the sexual partner and resulted in the formation of sexual motivation. The data are considered also in the light of the theory of motivated behavior including "liking", "wanting" and "learning" [Robinson and Berridge, 1993, 2000].

q-bio.OT↗
arXiv2007

Darwinian Dynamics Implies Developmental Ascendency

A tendency in biological theorizing is to formulate principles above or equal to Evolution by Variation and Selection of Darwin and Wallace. In this letter I analyze one such recent proposal which did so for the developmental ascendency. I show that though the idea of developmental ascendency is brilliant, this is in wrong order in the hierarchical structure of biological theories and can easily generate confusing. Several other examples are also briefly discussed in the note added.

q-bio.PE↗