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Hidden Genes Genetic Algorithms
Published in Ossama Abdelkhalik, Algorithms for Variable-Size Optimization, 2021
The design variable n, in Fig. 6.8, is an integer variable that specifies the number of effective variables qi. Maximum value of n is 3. The variable q4 is always computed using Eq. (6.13). The mechanism for specifying the locations of the hidden genes is omitted in this discussion, without loss of generality, to make the presentation simpler. In Fig. 6.8, chromosome 1 represents the optimal solution, where q2 takes the maximum value. Chromosome 2 has q2 as hidden. Chromosome 2, which corresponds to a solution with no inlet at point ‘2’, has poor fitness, and hence will have low probability of being selected for the next generation. A chromosome with effective q2 and a hidden q3 will have higher fitness, and hence higher probability of being selected for the next generation. It is noted here that having a hidden gene is not equivalent to having it effective with a value of zero despite the fact the chromosome fitness is the same in both cases. Each of these two genes has different effects on the subsequent generation. Also, a chromosome with a hidden gene belongs to schema that are different from the schema to which the chromosome belongs to if the gene is effective with a value of zero.
Mathematical Modeling for Advanced PHA Biosynthesis
Published in Martin Koller, The Handbook of Polyhydroxyalkanoates, 2020
Predrag Horvat, Martin Koller, Gerhart Braunegg
Interestingly, one of the first examined PHA producers, R. eutropha (today C. necator), in particular its wild-type strain H16, was not able to utilize glucose, but it was capable of metabolizing fructose and N-acetyl-glucosamine (NAG) [140]. Performed genetic manipulations have yielded mutants (i.e. G+1 and H1G+3) able to utilize glucose [141]. From the genetic point of view, the mentioned R. eutropha H16 genome consists of two individual chromosomes and one separate “megaplasmid pHG1”. A sequence analysis deciphered chromosome 1 (4,052,032 bp), chromosome 2 (2,912,490 bp), and the “megaplasmid” (452,156 bp). These data were the basis for the development of the RehMBEL1391 genomic metabolic model (Park and colleagues [142]) that encompasses 1171 metabolites, 229 transport reactions, and 1391 reactions in total. As reported by the authors, “the metabolic flux distribution and the changes of metabolic fluxes under several perturbed conditions were examined by flux variability”. For that purpose, the metabolic fluxes were varied computationally and the minimal and maximal flux values for each reaction were applied to build an objective function (i.e. maximum cell growth rate, or maximal production rate, for example). Using this procedure (including “metabolic adjustment method” /MOMA/ and quadratic programming /QP/), the authors have discovered the necessary gene knockouts to increase the synthesis of 2-methylcitric acid as well as the strategies leading to enhanced PHB production (optimal pH-value and C/N-source ratio).
Naturally Occurring Polymers—Animals
Published in Charles E. Carraher, Carraher's Polymer Chemistry, 2017
One of the active agents is cyclic AMP. A protein called CREB (for CRE-binding protein; CRE is simply a specific DNA unit, part of a gene, that is called the cyclic AMP response element or site) is activated altering the shape and functioning of the synapse in our brains when exposed to cyclic AMP (10.12) or some related compound in our brains. Genes that are activated are called CRE genes with the name being the initials of cyclic AMP response elements. CREB, when phosphorylated, binds to the CREs near certain genes acting as a transcription factor and turning on or activating the genes. Animals without the CREB-producing gene are able to learn but do not possess long-term memory. It is believed by some that the CREB-related genes are in fact essential to our learning and memory and act as master switches in activating other genes necessary in our learning/memory process. The CREB gene is on chromosome 2. A related and essential gene that helps CREB perform is found on chromosome 16 and is given the name CREBBP.
Advances in characterizing microbial community change and resistance upon exposure to lead contamination: Implications for ecological risk assessment
Published in Critical Reviews in Environmental Science and Technology, 2020
S. Elizabeth George, Yongshan Wan
C. metallidurans strain CH34 harbors additional genes that confer Pb resistance. The pbrR2 (Rmet_2302), cadA, pbrC2 operon is located on chromosome 1 in a genomic island (CMGI-1) and may maintain low cellular Pb(II) concentration (Taghavi et al., 2009). The zntA gene (Zn(II) efflux protein), which is induced by Pb(II) (a Staphylococcus aureus CadA (Cd(II) efflux protein homolog in Escherichia coli induced by Zn(II)/Cd(II)/Pb(II) (Beard et al., 1997; Rensing et al., 1998), is a P-Type ATPase located on chromosome 2. The pbrR3 gene (Rmet_3456; pbrR691) which preferentially binds Pb(II), is located on chromosome 1 (Monsieurs et al., 2011; Taghavi et al., 2009). These genes have been shown to rescue mutations in complementary genes in the C. metallidurans strain CH34 primary Pb resistance operon, pbrUTRABCD (Taghavi et al., 2009). Because the prevalence of host Pb resistance genes, which have the potential to bind Pb(II) and interfere with biosensor Pb detection, minimizing their presence should improve detection.
Digital-twin-based job shop multi-objective scheduling model and strategy
Published in International Journal of Computer Integrated Manufacturing, 2023
Zhuo Zhou, Liyun Xu, Xufeng Ling, Beikun Zhang
During machine crossover, some process loci in parent chromosome 1 are randomly selected, and their processing machines are crossed with the equipment corresponding to the same subprocesses in parent chromosome 2. For the example in Figure 8, if process loci 2 and 7 are selected in parent chromosome 1, they correspond to processes O41 and O22 in parent chromosome 1, which are processed by M3 and M1 in chromosome parent 1 and by M2 and M5 in parent chromosome 2, respectively. After equipment crossover, processes O41 and O22 are processed by M2 and M5 in parent chromosome 1 and by M3 and M1 in parent chromosome 2, respectively.
The unequal area facility layout problem with shortest single-loop AGV path: how material handling method matters
Published in International Journal of Production Research, 2021
Amir Ahmadi-Javid, Amir Ardestani-Jaafari
A crossover probably causes clumsy chromosomes; therefore, the substitution procedure is modified as follows: Step 0. Take a segment of the genes in parent chromosome 2 that must be crossed into parent chromosome 1.Step 1. Initialize the counter as and set as the number of the genes in the input segment.Step 2. Copy parent chromosome 1 in child chromosome 1.Step 3. Set as the position number of the th gene in the given segment in parent chromosome 2.Step 4. In child chromosome 1, find the gene whose value is the same as the th gene in parent chromosome 2, say the th gene.Step 5. Change the values of the th and th genes with each other in child chromosome 1.Step 6. If then and go to step 3, else return child chromosome 1.