Conventional Genetic Approaches Research Articles

Hardware implementation of a novel genetic algorithm

This paper introduces a novel genetic algorithm whose features have been purposely designed to be suited to hardware implementation. This is distinct from previous hardware designs that have been realized directly from conventional genetic algorithm approaches. To be suitable for hardware implementation, we propose that a genetic algorithm should attempt to both minimize final layout dimensions and reduce execution time while remaining a valid implementation. Consequently, the new genetic algorithm specifically aims to keep the requisite silicon area to a minimum by incorporating a monogenetic strategy that retains only the optimal individual, resulting in a dramatic reduction in the memory requirement and obviating the need for crossover circuitry. The results given in this paper demonstrate that new approach improves on a number of existing hardware genetic algorithm implementations in terms of the quality of the solution produced, the calculation time and the hardware component requirements.

Virus‐induced gene silencing is an effective tool for assaying gene function in the basal eudicot speciesPapaver somniferum(opium poppy)

Virus-induced gene silencing (VIGS) is an attractive method for assaying gene function in species that are resistant to conventional genetic approaches. However, VIGS has been shown to be effective in only a few, closely related plant species. Tobacco rattle virus (TRV), a bipartite RNA virus, has a wide host range and so in principle could serve as an efficient vector for VIGS in a diverse array of plant species. Here we show that a vector based on TRV sequences is effective at silencing the endogenous phytoene desaturase (PapsPDS) gene in Papaver somniferum (opium poppy). We show that this vector does not compromise the growth or reproduction of poppy and the plants did not display viral symptoms. The silencing of PapsPDS resulted in a significant reduction in PapsPDS mRNA and a concomitant photobleached phenotype. The ability to rapidly assay gene function in P. somniferum will be valuable in manipulation of the opiate pathway in this pharmaceutically important species. We suggest that our vacuum infiltration method used to deliver TRV-based vectors into poppy is a promising approach for expanding VIGS to diverse angiosperm species in which traditional delivery methods fail to induce VIGS. Furthermore, these studies demonstrate the utility of TRV-VIGS for probing gene function in a basal eudicot species that is phylogenetically distant from model plant species.

The potential of new genetic technologies in selecting for stress resistance in pigs

This paper examines the potential for breeding stress resistance in pigs through an understanding of the physiology of the stress response and its associated genetic basis. Pigs reared in commercial units can encounter numerous concurrent stressors that can have a negative impact on performance and welfare. Stress induces physiological and behavioural responses that are multidimensional, consisting of a complex neuroendocrine and immune signalling milieu. Some stress-related genetic parameters have been identified using conventional genetic approaches applied in experimental models. However, these traits do not capture the complexity of the stress response. As a result, the molecular mechanisms underlying the variation associated with stress resistance in pigs in a commercial environment is poorly understood. Gene expression profiling is a powerful tool that can be applied to systematically elucidate stress response pathways and networks. Consequently, gene expression technologies have been applied to identify some putative stress-regulated genes. Further application of these and more traditional technologies will aid in elucidating stress resistance using gene expression as a measure of phenotypic variation at a molecular level. It is envisaged that in the future, tools for selecting for stress resistance could eventually be applied on-farm to enhance production, health and welfare status.

A new structural optimization method based on the harmony search algorithm

Most structural optimization methods are based on mathematical algorithms that require substantial gradient information. The selection of the starting values is also important to ensure that the algorithm converges to the global optimum. This paper describes a new structural optimization method based on the harmony search (HS) meta-heuristic algorithm, which was conceptualized using the musical process of searching for a perfect state of harmony. The HS algorithm does not require initial values and uses a random search instead of a gradient search, so derivative information is unnecessary. Various truss examples with fixed geometries are presented to demonstrate the effectiveness and robustness of the new method. The results indicate that the new technique is a powerful search and optimization method for solving structural engineering problems compared to conventional mathematical methods or genetic algorithm-based approaches.

Performance of a genetic algorithm for the graph partitioning problem

The performance of the genetic algorithm (GA) for the graph partitioning problem (GPP) is investigated by comparison with standard heuristics on well-known benchmark graphs. In general, there is a case where a practical performance of a conventional genetic approach, which performs only simple operations without a local search strategy, is not sufficient. However, it is known that a combination of GA and local search can produce better solutions. From this practice, we incorporate a simple local search algorithm into the GA. In particular, the search ability of the GA is compared with standard heuristics such as multistart local search and simulated annealing, which use the same neighborhood structure of the simple local search, for solving the GPP. Experimental results show that the GA performs better than its competitors.

Genomics of the marA/soxS/rob regulon of Escherichia coli: identification of directly activated promoters by application of molecular genetics and informatics to microarray data.

Microarray analyses are providing a plethora of data concerning transcriptional responses to specific gene regulators and their inducers but do not distinguish between direct and indirect responses. Here, we identify directly activated promoters of the overlapping marA, soxS and rob regulon(s) of Escherichia coli by applying informatics, genomics and molecular genetics to microarray data obtained by others. Those studies found that overexpression of marA, or the treatment of cells with salicylate to derepress marA, or treatment with paraquat to induce soxS, resulted in elevated transcription of 153 genes. However, only 27 out of the promoters showed increased transcription under at least two of the aforementioned conditions and eight of those were previously known to be directly activated. A computer algorithm was used to identify potential activator binding sites located upstream of the remaining 19 promoters of this subset, and conventional genetic and biochemical approaches were applied to test whether these sites are critical for activation by the homologous MarA, SoxS and Rob transcriptional activators. Only seven out of the 19 promoters were found to be activated when fused to lacZ and tested as single lysogens. All seven contained an essential activator binding site. The remaining promoters were insensitive to stimulation by the inducers suggesting that the great majority of elevated microarray transcripts either were misidentified or resulted from indirect effects requiring sequences outside of the promoter region. We estimate that the total number of directly activated promoters in the regulon is less than 40.

Identification of in vivo protein phosphorylation sites with mass spectrometry.

AbstractProtein phosphorylation, principally on Ser, Thr, and Tyr residues, is one of the most common post-translational cellular regulatory mechanisms (1–4). Phosphorylation can modulate enzyme activity, alter its affinity to other proteins, and transmit signals through kinase cascades that often are branched and interactive. To understand the molecular basis of these regulatory mechanisms and to dissect signal-transduction pathways, it is necessary to determine the sites that are phosphorylated in vivo. Mass spectrometry is in the process of becoming the method of choice for the identification of protein phosphorylation sites (5). This mass spectrometric approach offers at least four major advantages over the conventional biochemical and genetic approaches. First, it is accurate. There is no ambiguity once the phosphorylation site is identified through mass spectrometric sequencing of the phosphopeptide. Second, it is fast. The cycle of identifying phosphorylation sites is typically a few days. Third, it does not require prior knowledge of phosphorylation of the protein of interest. Phosphorylation sites can be identified even for proteins that the consensus phosphorylation sites of their up stream kinases are not known. Fourth, it does not require 32P labeling.KeywordsPhosphorylation SitePeptide MixtureDigestion BufferAmmonia BicarbonateDestain SolutionThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Genetic analysis of DNA-protein interactions using a reporter gene assay in yeast.

Understanding the underlying structural and physico-chemical basis for the recognition of specific DNA sequences by regulatory proteins is a central goal of modern biochemical genetics. A method for the rapid identification of mutant molecules altered in the affinity and/or specificity of such interactions could be a powerful tool in the hands of those studying this difficult problem. Conventional genetic approaches for obtaining and analyzing interesting mutant forms of specific DNA-binding proteins are often infeasible because of the genetic intractability of the species being studied or as a result of difficulties in identifying relevant and specific phenotypes associated with alterations in the interaction under investigation. High-resolution genetic analysis of DNA-protein interactions is particularly problematic in metazoans. We have devised an approach that makes use of the modularity in structure and function of eukaryotic transcription factors (1), the power of the polymerase chain reaction (PCR) to generate specific DNA fragments with defined levels of mutagenesis in vitro (2,3), and the recombinogenic potential of S. cerevisiae (2,4) to carry out a high-resolution genetic analysis of the sequence-specific DNA-binding properties of Xenopus transcription factor IIIA (TFIIIA) (5). It seems likely that this approach will be generally applicable to the study of many DNA-protein interactions.

Generation of conditional mutants in higher eukaryotes by switching between the expression of two genes.

A regulatory system for the in-depth study of gene functions in higher eukaryotic cells has been developed. It is based on the tetracycline-controlled transactivators and reverse tTA, which were remodeled to discriminate efficiently between two different promoters. The system permits one to control reversibly the activity of two genes, or two alleles of a gene, in a mutually exclusive way, and also allows one to abrogate the activities of both. This dual regulatory circuit, which can be operated by a single effector substance such as doxycycline, overcomes limitations of conventional genetic approaches. The conditional mutants that can now be generated will be useful for the study of gene function in vitro and in vivo. In addition, the system may be of value for a variety of practical applications, including gene therapy.

A constraint-based genetic algorithm for concurrent engineering

Concurrent engineering is a complex problem in that a large number of considerations have to be brought to bear during the design stage. Compounding this complexity is that concurrent engineering problems are also likely to encompass both numeric and symbolic variables, and constraints that range from simple algebraic constraints, through conditional constraints, to potentially very complex database constraints. Previous approaches have concentrated on finding good solutions to simplified problems or, alternatively, to finding a feasible solution which may not be close to optimal. This paper presents an approach to concurrent engineering problems that extends the conventional genetic algorithm approach to handle the complex variety of variables and constraints that are inherent in a typical concurrent engineering problem. This poses some severe research challenges and this paper describes three genetic operators (the constraint-based initialization, crossover, and mutation operators) that preserve feasibility during initialization, crossover, and mutation. Preserving feasibility is achieved by incorporating local constraint propagation, boundary propagation, and set propagation. This overall approach is called the constraint-based genetic algorithm (CBGA) and aims to determine a near-optimal solution to concurrent engineering problems. The paper describes the background to constraint modelling, and genetic algorithms. The constraint-based initialization, crossover and mutation operators are then detailed, together with a description of the implementation of the CBGA in a system called Comet. Finally an example application is given.

Design of allele-specific inhibitors to probe protein kinase signaling.

Deconvoluting protein kinase signaling pathways using conventional genetic and biochemical approaches has been difficult because of the overwhelming number of closely related kinases. If cell-permeable inhibitors of individual kinases could be designed, the role of each kinase could be systematically assessed. We have devised an approach combining chemistry and genetics to develop the first highly specific cell-permeable inhibitor of the oncogenic tyrosine kinase v-Src. A functionally silent active-site mutation was made in v-Src to distinguish it from all other cellular kinases. A tight-binding cell-permeable inhibitor of this mutant kinase that does not inhibit wild-type kinases was designed and synthesized. In vitro and whole-cell assays established the unique specificity of the mutant v-Src-inhibitor pair. The inhibitor reversed cell transformation by the engineered but not the 'wild type' v-Src, establishing that changes in cellular signaling can be attributed to specific inhibition of the engineered kinase. The generality of the method was tested by engineering another tyrosine kinase, Fyn, to contain the corresponding active-site mutation to the one in v-Src. The same compound that inhibited mutant v-Src could also potently inhibit the engineered Fyn kinase. Allele-specific cell-permeable inhibitors of individual Src family kinases can be rapidly developed in an approach that should be applicable to all kinases. This approach will be useful for the deconvolution of kinase-mediated cellular pathways and for validating novel kinases as good targets for drug discovery both in vitro and in vivo.

The Thom Award address. Industrial mycology and the new genetics.

The genetic investigation of fungi has been extended substantially by DNA-mediated transformation, providing a supplement to more conventional genetic approaches based upon sexual and parasexual processes. Initial transformation studies with the yeast Saccharomyces cerevisiae provided the model for transformation systems in other fungi with regard to methodology, vector construction and selection strategies. There are, however, certain differences between S. cerevisiae and filamentous fungi with regard to type of genomic insertion and the availability of shuttle vectors. Single-site linked insertions are common in yeast due to the high level of homology required for recombination between vectored and genomic sequences, whereas mycelial fungi often show a high frequency of heterologous and unlinked insertions, often in the form of random and multiple-site integrations. While extrachromosomally-maintained or replicative vectors are readily available for use with yeasts, such vectors have been difficult to construct for use with filamentous fungi. The development of vectors for replicative transformation with these fungi awaits further study. It is proposed that replicative vectors may be inherently less efficient for use with mycelial fungi relative to yeasts, since the mycelium, as an extended and semicontinuous network of cells, may delimit an adequate diffusion of the vector carrying the selectable gene, thus leading to a high frequency of abortive or unstable transformants.