trans gene regulation in adaptive evolution: A genetic algorithm model

This is a continuation of earlier studies on the evolution of infinite populations of haploid genotypes within a genetic algorithm framework. We had previously explored the evolutionary consequences of the existence of indeterminate—“plastic”—loci, where a plastic locus had a finite probability in each generation of functioning (being switched “on”) or not functioning (being switched “off”). The relative probabilities of the two outcomes were assigned on a stochastic basis. The present paper examines what happens when the transition probabilities are biased by the presence of regulatory genes. We find that under certain conditions regulatory genes can improve the adaptation of the population and speed up the rate of evolution (on occasion at the cost of lowering the degree of adaptation). Also, the existence of regulatory loci potentiates selection in favour of plasticity. There is a synergistic effect of regulatory genes on plastic alleles: the frequency of such alleles increases when regulatory loci are present. Thus, phenotypic selection alone can be a potentiating factor in a favour of better adaptation.

Genetic analysis of foot-and-mouth disease virus serotype A of Indian origin and detection of positive selection and recombination in leader protease- and capsid-coding regions

The leader protease (L-pro) and capsid-coding sequences (P1) constitute approximately 3 kb of the foot-and-mouth disease virus (FMDV). We studied the phylogenetic relationship of 46 FMDV serotype A isolates of Indian origin collected during the period 1968-2005 and also eight vaccine strains using the neighbour-joining tree and Bayesian tree methods. The viruses were categorized under three major groups - Asian, Euro-South American and European. The Indian isolates formed a distinct genetic group among the Asian isolates. The Indian isolates were further classified into different genetic subgroups (<5% divergence). Post-1995 isolates were divided into two subgroups while a few isolates which originated in the year 2005 from Andhra Pradesh formed a separate group. These isolates were closely related to the isolates of the 1970s. The FMDV isolates seem to undergo reverse mutation or onvergent evolution wherein sequences identical to the ancestors are present in the isolates in circulation. The eight vaccine strains included in the study were not related to each other and belonged to different genetic groups. Recombination was detected in the L-pro region in one isolate (A IND 20/82) and in the VP1 coding 1D region in another isolate (A RAJ 21/96). Positive selection was identified at aa positions 23 in the L-pro (P<0.05; 0.046*) and at aa 171 in the capsid protein VP1 (P<0.01; 0.003**).

The Consequences of Phenotypic Plasticity in Cyclically Varying Environments: A Genetic Algorithm Study

By “phenotypic plasticity” we refer to the capacity of a genotype to exhibit different phenotypes, whether in the same or in different environments. We have previously demonstrated that phenotypic plasticity can improve the degree of adaptation achieved via natural selection (Behera & Nanjundiah, 1995). That result was obtained from a genetic algorithm model of haploid genotypes (idealized as one-dimensional strings of genes) evolving in a fixed environment. Here, the dynamics of evolution is examined under conditions of a cyclically varying environment. We find that the rate of evolution, as well as the extent of adaptation (as measured by mean population fitness) is lowered because of environmental cycling. The decrease is adaptation caused by a varying environment can, however, be partly or wholly compensated by an increase in the degree of plasticity that a genotype is capable of. Also, the reduction of population fitness caused by a variable environment can be partially offset by decreasing the total number of genetic loci. We conjecture that an increase in genome size may have been among the factors responsible for the evolution of phenotypic plasticity.

Characterization of human symptomatic rotavirus isolates MP409 and MP480 having ‘long’ RNA electropherotype and subgroup I specificity, highly related to the P6[1],G8 type bovine rotavirus A5, from Mysore, India

In an epidemiological study of symptomatic human rotaviruses in Mysore, India during 1993 and 1994, isolates MP409 and MP480 were isolated from two children suffering from severe, acute dehydrating diarrhea. Both isolates exhibited 'long' RNA pattern and subgroup I specificity suggesting the likelihood of their animal origin. Both isolates did not react with monoclonal antibodies (MAbs) specific for serotypes G1 to G6 as well as CIO. To determine the genetic origin of these isolates, complete nucleotide sequences of genes encoding the outer capsid proteins VP4 and VP7, nonstructural proteins NSP1 and NSP3 and viral enterotoxin protein NSP4 from MP409 and partial sequences of genes from MP480 were determined. Comparison of the 5' and 3' terminal sequences of 250 nucleotides revealed complete identity of the gene sequences in both strains suggesting that MP409 and MP480 are two different isolates of a single strain. Comparison of the nucleotide and deduced amino acid sequences of VP4, VP7, NSP1 and NSP3 of MP409 with published sequences of strains belonging to different serotypes revealed that both outer capsid proteins VP4 and VP7 and NSP1 are highly related to the respective proteins from the P6[1], G8 type bovine rotavirus A5 isolated from a calf with diarrhoea in Thailand and that the NSP3 is highly homologous to that of bovine rotaviruses. The NSP 1 protein showed greatest sequence identity with NSP4s belonging to the KUN genetic group to which NSP4s from human G2 type strains and bovine rotaviruses belong. MP409 and MP480 likely signify interspecies transmission of P6[1], G8 type strains from cattle to humans and represent the first P6[1] type rotaviruses isolated in humans. These and our previous studies on the asymptomatic neonatal strain I321 are of evolutionary and epidemiological significance in the context of close association of majority of the Indian population with cattle.

Machine-tool selection and operation allocation in FMS: solving a fuzzy goal-programming model using a genetic algorithm

The decision-making process for machine-tool selection and operation allocation in a flexible manufacturing system (FMS) usually involves multiple conflicting objectives. Thus, a fuzzy goal-programming model can be effectively applied to this decision problem. The paper addresses application of a fuzzy goal-programming concept to model the problem of machine-tool selection and operation allocation with explicit considerations given to objectives of minimizing the total cost of machining operation, material handling and set-up. The constraints pertaining to the capacity of machines, tool magazine and tool life are included in the model. A genetic algorithm (GA)-based approach is adopted to optimize this fuzzy goal-programming model. An illustrative example is provided and some results of computational experiments are reported.

Physics beyond Standard Model: Working group 3 report

This is a summary of the beyond the Standard Model (including model building working group of the WHEPP-X workshop held at Chennai from January 3 to 15, 2008.

A self-adaptive migration model genetic algorithm for data mining applications

Data mining involves nontrivial process of extracting knowledge or patterns from large databases. Genetic Algorithms are efficient and robust searching and optimization methods that are used in data mining. In this paper we propose a Self-Adaptive Migration Model GA (SAMGA), where parameters of population size, the number of points of crossover and mutation rate for each population are adaptively fixed. Further, the migration of individuals between populations is decided dynamically. This paper gives a mathematical schema analysis of the method stating and showing that the algorithm exploits previously discovered knowledge for a more focused and concentrated search of heuristically high yielding regions while simultaneously performing a highly explorative search on the other regions of the search space. The effective performance of the algorithm is then shown using standard testbed functions and a set of actual classification datamining problems. Michigan style of classifier was used to build the classifier and the system was tested with machine learning databases of Pima Indian Diabetes database, Wisconsin Breast Cancer database and few others. The performance of our algorithm is better than others.

A Dynamic Migration Model for Self-adaptive Genetic Algorithms

In this paper, we propose a self Adaptive Migration Model for Genetic Algorithms, where parameters of population size, the number of points of crossover and mutation rate for each population are fixed adaptively. Further, the migration of individuals between populations is decided dynamically. This paper gives a mathematical schema analysis of the method stating and showing that the algorithm exploits previously discovered knowledge for a more focused and concentrated search of heuristically high yielding regions while simultaneously performing a highly explorative search on the other regions of the search space. The effective performance of the algorithm is then shown using standard testbed functions, when compared with Island model GA(IGA) and Simple GA(SGA).

A Dynamic Migration Model for self-adaptive Genetic Algorithms

In this paper, we propose a self Adaptive Migration Model for Genetic Algorithms, where parameters of population size, the number of points of crossover and mutation rate for each population are fixed adaptively. Further, the migration of individuals between populations is decided dynamically. This paper gives a mathematical schema analysis of the method stating and showing that the algorithm exploits previously discovered knowledge for a more focused and concentrated search of heuristically high yielding regions while simultaneously performing a highly explorative search on the other regions of the search space. The effective performance of the algorithm is then shown using standard testbed functions, when compared with Island model GA(IGA) and Simple GA(SGA).

A density matrix renormalization group study of low-lying excitations of polythiophene within a Pariser-Parr-Pople model

Symmetrized density-matrix-renormalization-group calculations have been carried out, within Pariser-Parr-Pople Hamiltonian, to explore the nature of the ground and low-lying excited states of long polythiophene oligomers. We have exploited C-2 symmetry and spin parity of the system to obtain excited states of experimental interest, and studied the lowest dipole allowed excited state and lowest dipole forbidden two photon state, for different oligomer sizes. In the long system limit, the dipole allowed excited state always lies below the lowest dipole forbidden two-photon state which implies, by Kasha rule, that polythiophene fluoresces strongly. The lowest triplet state lies below two-photon state as usual in conjugated polymers. We have doped the system with a hole and an electron and obtained the charge excitation gap and the binding energy of the 1(1)B(u)(-) exciton. We have calculated the charge density of the ground, one-photon and two-photon states for the longer system size of 10 thiophene rings to characterize these states. We have studied bond order in these states to get an idea about the equilibrium excited state geometry of the system. We have also studied the charge density distribution of the singly and doubly doped polarons for longer system size, and observe that polythiophenes do not support bipolarons.

Transposable element-medicated evolution of sex: A population genetic model

For a population made up of individuals capable of sexual as well as asexual modes of reproduction, conditions for the spread of a transposable element are explored using a one-locus, two-haplotype model. The analysis is then extended to include the possibility that the transposable element can modulate the probability of sexual reproduction, thus casting Hickey’s (1982,Genetics 101: 519–531) suggestion in a population genetics framework. The model explicitly includes the cost of sexual reproduction, fitness disadvantage to the transposable element, probability of transposition, and the predisposition for sexual reproduction in the presence and absence of the transposable element. The model predicts several kinds of outcome, including initial frequency dependence and stable polymorphism. More importantly, it is seen that for a wide range of parameter values, the transposable element can go to fixation. Therefore it is able to convert the population from a predominantly asexual to a predominantly sexual mode of reproduction. Viewed in conjunction with recent results implicating short stretches of apparently non-coding DNA in sex determination (McCoubreyet al. 1988,Science 242: 1146–1151), the model hints at the important role this mechanism could have played in the evolution of sexuality.

Imaging in vivo Neuronal Transport in Genetic Model Organisms Using Microfluidic Devices

Microfluidic devices have been developed for imaging behavior and various cellular processes in Caenorhabditis elegans, but not subcellular processes requiring high spatial resolution. In neurons, essential processes such as axonal, dendritic, intraflagellar and other long-distance transport can be studied by acquiring fast time-lapse images of green fluorescent protein (GFP)-tagged moving cargo. We have achieved two important goals in such in vivo studies namely, imaging several transport processes in unanesthetized intact animals and imaging very early developmental stages. We describe a microfluidic device for immobilizing C. elegans and Drosophila larvae that allows imaging without anesthetics or dissection. We observed that for certain neuronal cargoes in C. elegans, anesthetics have significant and sometimes unexpected effects on the flux. Further, imaging the transport of certain cargo in early developmental stages was possible only in the microfluidic device. Using our device we observed an increase in anterograde synaptic vesicle transport during development corresponding with synaptic growth. We also imaged Q neuroblast divisions and mitochondrial transport during early developmental stages of C. elegans and Drosophila, respectively. Our simple microfluidic device offers a useful means to image high-resolution subcellular processes in C. elegans and Drosophila and can be readily adapted to other transparent or translucent organisms.

On an exact populationary model of genetic algorithms

Genetic algorithms (GAs) are search methods that are being employed in a multitude of applications with extremely large search spaces. Recently, there has been considerable interest among GA researchers in understanding and formalizing the working of GAs. In an earlier paper, we have introduced the notion of binomially distributed populations as the central idea behind an exact ''populationary'' model of the large-population dynamics of the GA operators for objective functions called ''functions of unitation.'' In this paper, we extend this populationary model of GA dynamics to a more general class of objective functions called functions of unitation variables. We generalize the notion of a binomially distributed population to a generalized binomially distributed population (GBDP). We show that the effects of selection, crossover, and mutation can be exactly modelled after decomposing the population into GBDPs. Based on this generalized model, we have implemented a GA simulator for functions of two unitation variables-GASIM 2, and the distributions predicted by GASIM 2 match with those obtained from actual GA runs. The generalized populationary model of GA dynamics not only presents a novel and natural way of interpreting the workings of GAs with large populations, but it also provides for an efficient implementation of the model as a GA simulator. (C) Elsevier Science Inc. 1997.

Density-matrix renormalization-group study of low-lying excitations of polyacene within a Pariser-Parr-Pople model

We have carried out symmetrized density-matrix renormalization-group calculations to study the nature of excited states of long polyacene oligomers within a Pariser-Parr-Pople Hamiltonian. We have used the C-2 symmetry, the electron-hole symmetry, and the spin parity of the system in our calculations. We find that there is a crossover in the lowest dipole forbidden two-photon state and the lowest dipole allowed excited state with size of the oligomer. In the long system limit, the two-photon state lies below the lowest dipole allowed excited state. The triplet state lies well below the two-photon state and energetically does not correspond to its description as being made up of two triplets. These results are in agreement with the general trends in linear conjugated polymers. However, unlike in linear polyenes wherein the two-photon state is a localized excitation, we find that in polyacenes, the two-photon excitation is spread out over the system. We have doped the systems with a hole and an electron and have calculated the charge excitation gap. Using the charge gap and the optical gap, we estimate the binding energy of the 1(1)B(-) exciton to be 2.09 eV. We have also studied doubly doped polyacenes and find that the bipolaron in these systems, to be composed of two separated polarons, as indicated by the calculated charge-density profile and charge-charge correlation function. We have studied bond orders in various states in order to get an idea of the excited state geometry of the system. We find that the ground state, the triplet state, the dipole allowed state, and the polaron excitations correspond to lengthening of the rung bonds in the interior of the oligomer while the two-photon excitation corresponds to the rung bond lengths having two maxima in the system.