A comparative study of immune system based genetic algorithms in dynamic environments

Copyright @ 2006 ACMDiversity and memory are two major mechanisms used in biology to keep the adaptability of organisms in the ever-changing environment in nature. These mechanisms can be integrated into genetic algorithms to enhance their performance for problem optimization in dynamic environments. This paper investigates several GAs inspired by the ideas of biological immune system and transformation schemes for dynamic optimization problems. An aligned transformation operator is proposed and combined to the immune system based genetic algorithm to deal with dynamic environments. Using a series of systematically constructed dynamic test problems, experiments are carried out to compare several immune system based genetic algorithms, including the proposed one, and two standard genetic algorithms enhanced with memory and random immigrants respectively. The experimental results validate the efficiency of the proposed aligned transformation and corresponding immune system based genetic algorithm in dynamic environments

Regeneration and genetic transformation in cowpea

Over the last three decades, sporadic efforts have been made to develop regeneration and transformation systems in cowpea (Vigna unguiculata L. Walp). This paper reviews the progress made to date, including highlights of culture media and explants used for regeneration and chimeric gene constructs employed in transformations. Progress has been slow, mainly due to limited resources, since very few laboratories have been involved. There is an urgent need for more focused and consistent efforts to develop genotype, and tissue-culture dependent and independent approaches for obtaining stable genetic transformation in cowpea

In vitro plant regeneration and Agrobacterium tumefaciens-mediated transformation of Datura stramonium (Solanaceae).

Premise of the Study:Datura stramonium is a pharmacologically and evolutionarily important plant species in the family Solanaceae. Stable transformation methodology of this species would be advantageous for future genetic studies. Methods:In vitro plant regeneration and Agrobacterium tumefaciens-mediated transformation techniques were developed for D. stramonium based on methods reported for tomato. A binary vector containing pAtUBQ10::erGFP was used for transformation. Results:We recovered primary transformants harboring the green fluorescent protein (GFP) transgene that resulted in expression of fluorescence in all tissues analyzed. Transformants were allowed to self-pollinate, and two of five progeny contained the GFP transgene and displayed fluorescence identical to the primary transformants. Discussion:We have demonstrated the first stable transformation in the genus Datura. This is a key first step to study the genetic basis of traits in this evolutionarily interesting species

Exciting Times for Cowpea Genetic Transformation Research

Cowpea represents a major food crop for the poor in Asia and especially in Africa. However, its production is constrained principally by insect pests as well as diseases. Attempts to improve cowpea insect resistance have not yielded significant result till date. This paper reviews biotechnological approaches that have been employed to transfer foreign genes into cowpea with a view to conferring desirable traits on it. The recent advances made in generating cowpea transformants with stable inheritance of trangenes by the progenies heralds exciting times for the genetic transformation research on this erstwhile recalcitrant food crop. As such, this genetic transformation approach could be used to transfer insect resistance traits to the crop species

Plant Cellular and Molecular Biotechnology: Following Mariotti's Steps

This review is dedicated to the memory of Prof. Domenico Mariotti, who significantly contributed to establishing the Italian research community in Agricultural Genetics and carried out the first experiments of Agrobacterium-mediated plant genetic transformation and regeneration in Italy during the 1980s. Following his scientific interests as guiding principles, this review summarizes the recent advances obtained in plant biotechnology and fundamental research aiming to: (i) Exploit in vitro plant cell and tissue cultures to induce genetic variability and to produce useful metabolites; (ii) gain new insights into the biochemical function of Agrobacterium rhizogenes rol genes and their application to metabolite production, fruit tree transformation, and reverse genetics; (iii) improve genetic transformation in legume species, most of them recalcitrant to regeneration; (iv) untangle the potential of KNOTTED1-like homeobox (KNOX) transcription factors in plant morphogenesis as key regulators of hormonal homeostasis; and (v) elucidate the molecular mechanisms of the transition from juvenility to the adult phase in Prunus tree species

Use of somatic embryogenesis as a vehicle for cotton transformation

Cotton has been aptly described as the prosperity plant owing to its unrivalled economic importance as a source of feedstock, food and oil, as well as raw material for diverse industrial applications, ranging from textile and footwear to automobiles, energy, medical and pharmaceutical. As such, over 180 million people of the world depend on its production for livelihood. However, cotton production is grossly hampered, and has long been peaked in many regions where it is being grown. Without prejudice to the genetic improvement already made by conventional breeding with respect to yield and quality over the years, genetic transformation is arguably the last recourse for further development of cotton, especially with respect to the prevailing production constraints of insect pests, weeds, environmental stresses and diseases. This review therefore focuses on the use of somatic embryogenesis as a vehicle for cotton genetic transformation. It indeed attempts to overview the challenges of cotton transformation with respect to narrow genetic base coupled with the recalcitrant nature of the crop species, as well as the research success achieved so far. It then discusses the underlying mechanisms of somatic embryogenesis as well as the current constraints and various strategies being used to overcome them; all with the aim of motivating interest groups to initiate research activities in cotton biotechnology and to strive for its optimization for further genetic improvement

The Regulation of Commodity Options

To outline further genetic mechanisms of transformation from follicular lymphoma (FL) to diffuse large B-cell lymphoma (DLBCL), we have performed whole genome array-CGH in 81 tumors from 60 patients [29 de novo DLBCL (dnDLBCL), 31 transformed DLBCL (tDLBCL), and 21 antecedent FL]. In 15 patients, paired tumor samples (primary FL and a subsequent tDLBCL) were available, among which three possessed more than two subsequent tumors, allowing us to follow specific genetic alterations acquired before, during, and after the transformation. Gain of 2p15-16.1 encompassing, among others, the REL, BCL11A, USP34, COMMD1, and OTX1 genes was found to be more common in the tDLBCL compared with dnDLBCL (P < 0.001). Furthermore, a high-level amplification of 2p15-16.1 was also detected in the FL stage prior to transformation, indicating its importance during the transformation event. Quantitative real-time PCR showed a higher level of amplification of REL, USP34, and COMMD1 (all involved in the NF kappa B-pathway) compared with BCL11A, which indicates that the altered genes disrupting the NF kappa B pathway may be the driver genes of transformation rather than the previously suggested BCL11A. Moreover, a 17q21.33 amplification was exclusively found in tDLBCL, never in FL (P < 0.04) or dnDLBCL, indicating an upregulation of genes of importance during the later phase of transformation. Taken together, our study demonstrates potential genomic markers for disease progression to clinically more aggressive forms. We also confirm the importance of the TP53-, CDKN2A-, and NF kappa B-pathways for the transformation from FL to DLBCL

Nucleosomes affect local transformation efficiency

Genetic transformation is a natural process during which foreign DNA enters a cell and integrates into the genome. Apart from its relevance for horizontal gene transfer in nature, transformation is also the cornerstone of today's recombinant gene technology. Despite its importance, relatively little is known about the factors that determine transformation efficiency. We hypothesize that differences in DNA accessibility associated with nucleosome positioning may affect local transformation efficiency. We investigated the landscape of transformation efficiency at various positions in the Saccharomyces cerevisiae genome and correlated these measurements with nucleosome positioning. We find that transformation efficiency shows a highly significant inverse correlation with relative nucleosome density. This correlation was lost when the nucleosome pattern, but not the underlying sequence was changed. Together, our results demonstrate a novel role for nucleosomes and also allow researchers to predict transformation efficiency of a target region and select spots in the genome that are likely to yield higher transformation efficiency