Prediction of the tertiary structure of a protein on a two-dimensional triangular lattice by a hybrid evolutionary algorithm

This work discusses the problem of forecasting the tertiary structure of a protein, based on its primary sequence. The problem is that science, with all its computing power and a set of experimental data, has not learned to build models that describe the process of protein molecule coagulation and predict the tertiary structure of a protein, based on its primary structure. However, it is wrong to assume that nothing is happening in this field of science. The regularities of folding (convolution) of the protein are known, methods for its modelling have been developed. Analysis of the current state of research in the field of these problems indicates the presence of shortcomings associated with the accuracy of forecasting and the time necessary to obtain the optimal solution. Consequently, the development of new computational methods, deprived of these shortcomings, seems relevant. In this work, the authors focused on the lattice model, which is a special case of the known hydrophobic-polar dill. protein conformation according to the chosen model, hybrid algorithms of cloning selection, differential are proposed. Since the processes of protein coagulation have not been fully understood, the researchers proposed several simplified models based on the physical properties of molecules and which leads to problems of combinatorial optimization. A hydrophobic-polar simplified model on the planar triangular lattice is chosen as a protein model. From the point of view of the optimization problem, the problem of protein folding comes down to finding a conformation with minimal energy. In lattice models, the conformation is represented as a non-self-cutting pathway. A hybrid artificial immune system in the form of a combination of clonal selection and differential evolution algorithms is proposed to solve this problem. The paper proposes a hybrid method and algorithm to solve the protein folding problem using the HP model on a planar triangular lattice. In this paper, a hybrid method and algorithm for solving the protein folding problem using the HP model on a planar triangular lattice are proposed. The developed hybrid algorithm uses special methods for encoding and decoding individuals, as well as the affinity function, which allows reducing the number of incorrect conformations (self-cutting solutions). Experimental studies on test hp-sequences were conducted to verify the effectiveness of the algorithm. The results of these experiments showed some advantages of the developed algorithm over other known methods. Experiments have been taught to verify the effectiveness of the proposed approach. The results labelled "Best" show the minimum energy values achieved over 30 runs, while the results labelled "Medium" show the robustness of the algorithm to achieve minima. Regarding robustness, the hybrid algorithm also offers an advantage, showing higher results. A comparative analysis of the performance results of the proposed algorithm on test sequences with similar results of other published methods allows us to conclude the high efficiency of the developed method. In particular, the result is more stable, and, in some cases, conformations with lower energy are obtained. Keywords: protein folding; hydrophobic-polar model; clonal selection; differential evolution; artificial immune systems; hydrophobic-polar model.

Misconceptions about Conception and Other Fallacies: Historical Bias in Reproductive Biology

Natural selection (differential reproduction) is a major tenet of evolutionary theory. In mammals the success of reproduction is primarily controlled by females who provide the majority of offspring care via gestation and lactation. In some species, maternal care also extends post-weaning. This primacy of female reproduction in evolution has not quite crept into our understanding of organismal adaptations in anatomy, physiology, and behavior. This cultural legacy has left its mark and led to misconceptions in our understanding of reproductive biology that are especially prominent in the understanding of reproduction in the general public. Here, I give examples of such misconceptions. I focus on aspects of physiology (the “sperm race,” the “estrous cycle,” the “28-day” menstrual cycle, “sex” hormones, and meiosis) as well as aspects of terminology in morphology and behavior. The issues I raise are not new, but all remain embedded in the teaching of reproductive biology especially at the introductory level. For each issue, I examine the historical bias, the consequences of that bias, and, more importantly, ways to ameliorate that bias going forward.

Pre-Grazing Herbage Mass Affects Grazing Behavior, Herbage Disappearance, and the Residual Nutritive Value of a Pasture during the First Grazing Session

During the first hours after the allocation of a grazing strip (first grazing session, GS), dairy cows eat most of the daily dry matter (DM) available. There are few studies that analyze how the grazing-down process changes the characteristics of the pasture during the first GS. The objective of this study was to evaluate the effect of two pre-grazing herbage masses (HM; medium herbage mass (MHM) and high herbage mass (HHM) on the DM disappearance, grazing behavior of dairy cows, and the residual nutritive value of a pasture during the first GS. Two groups of twelve dairy cows were used to evaluate the grazing-down process, during a period of 62 days. The pre-grazing HM modified the bite rate, bite mass, and dry matter intake during the first GS. The pre-grazing HM affected the process of herbage disappearance of the pasture, especially during the first 60 min of the GS. The nutrient selection differential for acid detergent fiber was greater for HHM compared with MHM (0.93 vs. 0.86). In conclusion, pre-grazing HM affects the structural characteristics and the residual nutritive value of the pasture. The grazing process in the first GS was modified by the HM, affecting the defoliation and the DM disappearance rate of the pasture.

Selection of Caucasian breed sheep to increase their wool productivity

An analysis of the wool productivity in Caucasian breed sheep of various sex and age groups is presented, and the effectiveness of selection in terms of the length, fineness, thickness and yolk of wool is shown. It was revealed that in the CJSC of “Plemzavod named after V.V. Kalyagin, the Hero of Socialist Labor”, the average clip of greasy wool is 5.8 kg when the yield of washed fiber is 59.1%. It has been established that the genetic recourses of the herd enable the farm to receive an average clip of 3.4 kg of washed wool. The selection differential for washed wool clip in animals of different sex and age groups was determined, which has made 0.9-3.3 kg, or 28.8-63.5%. The sheep capita of the Caucasian breed in the breeding plant is characterized by very thick wool (95.7%), which is confirmed by experimental data, where the total thickness of the hair follicles is 59.1 pieces per 1 mm2 of skin. It was established that the selection differential by the length of wool in the context of sex and age groups varies within 1.5-3.5 cm, or 16.7-43.8%. The revealed differentiation of wool fineness in Caucasian breed sheep confirms the consolidation of the herd by this trait, where the 64th quality is the leading fineness. It was experimentally established that the amount of wool fat in greasy non-fatted wool is 8.3%, the amount of wool sweat has made 12.1%, and the amount of diphilic substances is 3.2%. The ratio of wool fat: wool sweat is 0.70. It is noted that animals of the Caucasian breed have a white wool yolk (94.9%) and a sufficient amount of it (95.6%), which indicates a good consolidation of this trait in the sheep capita.

Inheritance and variability of productivity traits in hybrids of spring soft wheat of the first to fourth generations

The effects of genotype-environment interaction of nine spring soft wheat varieties and seven hybrid populations F1 - F4 formed using these varieties were determined under the conditions of the Kirov region. The significant influence of environmental conditions on all studied traits was established. The contribution of the “year” factor to the number of grains per head in varieties and hybrids was 10.9 and 13.9%, respectively; to the mass of 1000 grains – 5.8 and 19.5%; to the yield – 47.3 and 41.1%. The genetic component made a significant contribution to the mass of 1000 grains in varieties and hybrids (81.5 and 58.8%), as well as to the number of grains in varieties (38.4%). There was a higher varietal specificity in the manifestation of traits in parental varieties compared to the hybrids. The analysis was done for two component traits of head productivity in a series of generations against the background of the action of various lim-factors, the shifts in their average values and the influence on yield were predicted and determined. The indicator of phenotypic domination (hp) in the first generation was determined according to the number of grains per head (hp = -5.00...+ 7.82) and 1000 grains mass (hp = + 0.23...+ 12.00), the combinations with a high level of heterosis were picked out (Baganskaya 95 x Novosibirskaya 44 and Baganskaya 95 x Aktjube 3). The calculation of the breeding differential and the effectiveness of the selections in contrasting environmental conditions of the second (2016) and third (2017) hybrid generations was carried out. Under the conditions of 2018, the yield of the initial populations varied within 219.0...789.6 g/m2, while the figures for the selected progenies were 317.0...647.6 g/m2. The average yield increase of the progenies that had been selected in the dry year was 56.8 g/m2 in relation to the initial populations (11.1%); the increase of the progenies, selected in the conditions of excess moisture was 10.8 g/m2 (3.0%). The correlation analysis revealed the average positive relationship between the first-generation hp indicator and the selection differential in subsequent generations according to the «1000 grains mass» (r = 0.18...0.63) and «number of grains per head» (r = 0.35...0.37) traits. The correlation was weak between the level of heterosis and the selection reaction (r = -0.12…0.27). The selection of genotypes with a high level of selection differential according to the number of grains per head was more effective than the selection according to the mass of 1000 grains. The correlation coefficient between the degree of phenotypic dominance of traits in the first generation and average values of traits in the F2-F4 generations varied within r = 0.35...0.68 (significant values at 5% level r = 0.75).

Dominant Cubic Coefficients of the ‘1/3-Rule’ Reduce Contest Domains

Antagonistic exploitation in competition with a cooperative strategy defines a social dilemma, whereby eventually overall fitness of the population decreases. Frequency-dependent selection between two non-mutating strategies in a Moran model of random genetic drift yields an evolutionary rule of biological game theory. When a singleton fixation probability of co-operation exceeds the selectively neutral value being the reciprocal of population size, its relative frequency in the population equilibrates to less than 1/3. Maclaurin series of a singleton type fixation probability function calculated at third order enables the convergent domain of the payoff matrix to be identified. Asymptotically dominant third order coefficients of payoff matrix entries were derived. Quantitative analysis illustrates non-negligibility of the quadratic and cubic coefficients in Maclaurin series with selection being inversely proportional to population size. Novel corollaries identify the domain of payoff matrix entries that determines polarity of second order terms, with either non-harmful or harmful contests. Violation of this evolutionary rule observed with non-harmful contests depends on the normalized payoff matrix entries and selection differential. Significant violations of the evolutionary rule were not observed with harmful contests.

Evaluation of Maize (Zea mays L.) Half Sib Recurrent Families for Expected Response and Percent Gain Per Cycle

Recurrent Selection (RS) or reselection generation after generation is a vital selection scheme for improving the physio-morphic traits and grain yield in maize populations. The objective of the present research was to determine the response of recurrent selection in CIMMYT maize population CZP-132011 for physio-morphic traits and to estimate selection differential, heritability, expected response and percent gain cycle-1 among the half sib recurrent families for morphological traits and grain yield. Sixty four half sib recurrent families were evaluated in 8×8 lattice square design with two replications at Cereal Crops Research Institute (CCRI), Pirsabak during 2017. Results showed highly significant differences among the half sib families for all the studied traits. Selection differential values were negative for days to tasseling (-3.00), anthesis (-3.08), silking (-3.10), anthesis silking interval (-1.14), plant height (-5.07) and ear height (-7.73). High heritability values (h2 ˃ 0.60) were recorded for all traits except plant height (0.55) which exhibited moderate heritability. Based on broad sense heritability and selection differential, expected response were observed negative for days to tasseling (-2.39), anthesis (-2.56), silking (-2.64), anthesis silking interval (-0.79), plant height (-2.81) and ear height (-5.22). After one cycle of recurrent selection using half sib families, the gain cycle-1 values were negative for (-0.39), anthesis (-0.47), silking (-1.44), anthesis silking interval (-3.17), plant height (-2.34) and ear height (-4.90). Based on the findings of current research it could be concluded that recurrent selection method was found effective in improving the CIMMYT maize source population CZP-132011 for physio-morphic traits.