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Is BAC Transgenesis Obsolete? State of the Art in the Era of Designer Nucleases
J. Beil,L. Fairbairn,P. Pelczar,T. Buch
Journal of Biomedicine and Biotechnology , 2012, DOI: 10.1155/2012/308414
Abstract: DNA constructs based on bacterial artificial chromosomes (BACs) are frequently used to generate transgenic animals as they reduce the influence of position effects and allow predictable expression patterns for genes whose regulatory sequences are not fully identified. Despite these advantages BAC transgenics suffer from drawbacks such as complicated vector construction, low efficiency of transgenesis, and some remaining expression variegation. The recent development of transcription activator-like effector nucleases (TALENs) and zinc finger nucleases (ZFNs) has resulted in new transgenic techniques which do not have the drawbacks associated with BAC transgenesis. Initial reports indicate that such designer nucleases (DNs) allow the targeted insertion of transgenes into endogenous loci by direct injection of the targeting vector and mRNA/DNA encoding the predesigned nucleases into oocytes. This results in the transgene being inserted at a specific locus in the mouse genome, thus circumventing the drawbacks associated with BAC transgenesis.
Vasilis Vasiliou
Human Genomics , 2011, DOI: 10.1186/1479-7364-5-4-215
Abstract: Ikediobi and colleagues have characterised the population frequencies of clinically relevant phar-macogenetic traits in two distinct South African population groups residing in the Western Cape (the Xhosa and Cape Mixed Ancestry). Their data indicate diverse allele frequencies of key pharmaco-genetic genes within the African population. In the Update on Gene Completions and Annotations section, Jackson et al. provide an update on aldehyde dehydrogenase (ALDH) genes in several vertebrates and clarify the annotation found in the National Center for Biotechnology Information (NCBI) gene database. They also discuss gene-duplication and gene-loss events that may have occurred in the ALDH gene superfamily. In the Software Review section of the current issue, Lamy and colleagues discuss software for the genotyping of microarray single nucleotide polymorphisms, in particular software for Affymetrix and Illumina arrays. In Genome Databases, Jassal reviews the new version of the Reactome database and uses it to analyse the solute carrier (SLC) class of transporters. His study and the Reactome provide a basis for a number of analyses, which includes interactions, expression data, over-representation analysis and species comparison. Such analyses may provide the basis for further investigations using systems biology.Finally, Dan Nebert reviews the book, Designer Genes: A New Era in the Evolution of Man by Stephen Potter (Random House; 2010).
Evolution enters the genomic era
David A Liberles
Genome Biology , 2001, DOI: 10.1186/gb-2001-2-11-reports4026
Abstract: The congress covered all aspects of evolution, from the molecular and the genomic to the morphological, and only a small sample of the talks will be discussed here. As was apparent in many talks, genomics is starting to bring together research on ecological forces, morphological innovations, and other kinds of phenotype, with molecular genotypes. This convergence was approached from two directions: by starting with phenotypic differences and looking for a genetic cause, and by starting with genomic sequence differences between organisms and searching for either functional effects or for the signatures of adaptation.There were several very different plenary addresses at the meeting. Nancy Moran (University of Arizona, Tuscon, USA) spoke on the genomic evolution of bacterial symbionts. She concluded that the genome reduction often seen in symbionts is driven not by a selective pressure for genome reduction but by a reduction in selection for gene maintenance. She has found large deletions removing many genes, with no evidence for strong selection to increase gene density (the gene density remained similar as the gene number decreased). Michael Donoghue (Yale University, New Haven, USA) spoke on the value of considering phylogeny when examining historical biogeography, in order to understand the evolution of species distributions. Deborah Charlesworth (University of Edinburgh, UK) gave an overview of the importance of polymorphism and classical population genetics in the genome era for addressing questions central to biology.Following the theme that genomics is unifying evolutionary biology, a new US National Science Foundation forum in evolutionary and ecological functional genomics was presented http://pondside.uchicago.edu/~feder/EEFG.html webcite. This forum, bringing together research and researchers in evolution, ecology, functional analysis (for example in vitro biochemistry), and genomics, is intended to promote understanding of the evolutionary origin and func
Origin and evolution of new genes
Xin Li,Shuang Yang,Lixin Peng,Hong Chen,Wen Wang
Chinese Science Bulletin , 2004, DOI: 10.1007/BF03184298
Abstract: Organisms have variable genome sizes and contain different numbers of genes. This difference demonstrates that new gene origination is a fundamental process in evolutionary biology. Though the study of the origination of new genes dated back more than half a century ago, it is not until the 1990s when the first young genejingwei was found that empirical investigation of the molecular mechanisms of origination of new genes became possible. In the recent years, several young genes were identified and the studies on these genes have greatly enriched the knowledge of this field. Yet more details in a general picture of new genes origination are to be clarified. We have developed a systematic approach to searching for young genes at the genomic level, in the hope to summarize a general pattern of the origination and evolution of new genes, such as the rate of new gene appearance, impact of new genes on their host genomes, etc.
International Journal of Genetics , 2011,
Abstract: Nowadays genes are claimed to explain almost everything that is somehow or another connected withmanifestations of the biological life on the Earth, including evolution. It is now clear, however, that major incongruities existand that there is only a weak relationship between biological complexity and the number of protein coding genes. Thegenome can be divided into two main sections, the coding (genes) and non coding portions. Non coding DNAs have beenconsidered as non-functional DNA by many authors. And to determine which of them is the most important in evolutionbased on the input of genes and non coding DNAs into the origin of the basic forms of life and its diversity. Information aboutnon coding DNAs as the main evolving component of the genome is presented. It is supposed that evolution has notstopped on DNA, which is transcribed into RNA which in turn is translated into proteins
Evolution before genes
Vera Vasas, Chrisantha Fernando, Mauro Santos, Stuart Kauffman, E?rs Szathmáry
Biology Direct , 2012, DOI: 10.1186/1745-6150-7-1
Abstract: We cannot confirm previous claims that autocatalytic sets of organic polymer molecules could undergo evolution in any interesting sense by themselves. While we and others have previously imagined inhibition would result in selectability, we found that it produced multiple attractors in an autocatalytic set that cannot be selected for. Instead, we discovered that if general conditions are satisfied, the accumulation of adaptations in chemical reaction networks can occur. These conditions are the existence of rare reactions producing viable cores (analogous to a genotype), that sustains a molecular periphery (analogous to a phenotype).We conclude that only when a chemical reaction network consists of many such viable cores, can it be evolvable. When many cores are enclosed in a compartment there is competition between cores within the same compartment, and when there are many compartments, there is between-compartment competition due to the phenotypic effects of cores and their periphery at the compartment level. Acquisition of cores by rare chemical events, and loss of cores at division, allows macromutation, limited heredity and selectability, thus explaining how a poor man's natural selection could have operated prior to genetic templates. This is the only demonstration to date of a mechanism by which pre-template accumulation of adaptation could occur.This article was reviewed by William Martin and Eugene Koonin.There are two camps in the origin of life. The metabolism-first camp advocates consider improbable that RNA-like self-replicating polymers appeared before natural selection had operated on chemical networks [1-3], whereas genetics-first supporters find implausible the idea that molecular networks without genetic control could have undergone Darwinian evolution [4]. This Gordian knot was obviously cut on Earth around 3.5 billion years ago or even earlier [5]. A solution to the conundrum can be found in general evolutionary principles shared by some chemical
Evolution of trappin genes in mammals
Akira Kato, Alejandro P Rooney, Yutaka Furutani, Shigehisa Hirose
BMC Evolutionary Biology , 2010, DOI: 10.1186/1471-2148-10-31
Abstract: The database analyses revealed that: 1) duplicated trappin multigenes were found recently in the nine-banded armadillo; 2) duplicated two trappin genes had been found in the Afrotherian species (elephant, tenrec, and hyrax) since ancient days; 3) a single trappin-2 gene was found in various eutherians species; and 4) no typical trappin gene has been found in chicken, zebra finch, and opossum. Bayesian analysis estimated the date of the duplication of trappin genes in the Afrotheria, guinea pig, armadillo, cow, and pig to be 244, 35, 11, 13, and 3 million-years ago, respectively. The coding regions of trappin multigenes of almadillo, bovine, and pig evolved much faster than the noncoding exons, introns, and the flanking regions, showing that these genes have undergone accelerated evolution, and positive Darwinian selection was observed in pig-specific trappin paralogs.These results suggest that trappin is an eutherian-specific molecule and eutherian genomes have the potential to form trappin multigenes.Trappins are a family of small secretory proteins that possess an N-terminal transglutaminase-substrate (TGS) domain and a C-terminal whey acidic protein (WAP) domain [1]. The TGS domain consists of repeats of six semi-conserved amino acids, KGQDPV, that act as anchoring regions. In this case, the lysine or glutamine residues of these regions are cross-linked with extracellular-matrix proteins by the action of transglutaminases, which helps trappin molecules to become concentrated at the site of action [2-4]. In contrast, the WAP domain is a four-disulfide core region and is defined by eight conserved cysteine residues. The WAP domain of trappin shows anti-proteolytic [4-6] and antimicrobial [7-9] activities that allow it to act as an innate immune defense molecule. In fact, trappin-2 displays antibacterial activities against Gram-positive and Gram-negative bacteria [7-9]; it also has antifungal activity [9], and the antimicrobial activity is independent of its antipro
Evolution, ecology and the engineered organism: lessons for synthetic biology
Jeffrey M Skerker, Julius B Lucks, Adam P Arkin
Genome Biology , 2009, DOI: 10.1186/gb-2009-10-11-114
Abstract: One of the most powerful and controversial aspects of engineering living organisms is that they reproduce, evolve, and interact with their environment. Humans have been engineering plants and animals since the advent of agriculture approximately 12,000 years ago through breeding and artificial selection for their domestication [1]. The evolution of corn from the small grass teosinte [2], or the transformation of the wolf into 'man's best friend' (the dog) [1] are testaments to the success of this approach. We have even 'domesticated' microorganisms, using yeast and bacteria for the production of beer, wine, cheese and yogurt as well as numerous other products we consume every day [3,4].Although powerful, genetic engineering by classical breeding and selection is slow, and results in a large number of unknown genetic changes that are hard to reconcile and may have unintended secondary effects. What we need is a rational approach to the engineering of biological systems that makes the process fast, cheap and safe, to solve problems in energy, health, agriculture and the environment. First steps towards realizing this aim began with the advent of recombinant DNA technology in the latter half of the 20th century, which created visions of a new era of 'synthetic biology' where novel genes could be designed and constructed for useful purposes [5-7]. Since then we have made incredible advances in our ability to manipulate genes, genomes and organisms, and this has led to a renewed interest in making synthetic biology a reality [8].A number of recent reviews have been written on the principles and practice of synthetic biology [8-11], but here we focus on the interplay between synthetic biology, evolution and ecology. Evolution teaches us about what solutions nature has evolved for biological problems, how to evolve them further, and how robust they are to change. Ecology gives us information on how our engineered systems will perform once they leave the laboratory and ente
The face without man On human identities in postmodern era and on the metamorphoses of the subject  [PDF]
European Academic Research , 2013,
Abstract: Fragmentation of the conceived or imagined reality, perceptive and emotional fragmentation, collages and puzzles of experience pieces: this is the substance of our lives. Some fragments are in harmony and resonance with each other, some others are in conflict or in contradiction. The existence, even the inner existence, became for most of us, extremely heterogeneous, tensed; hard to handle and to bear. We cannot assimilate ourselves well. We cannot gather our being into a unitary image, into a single man, with a unique identity. The individual doesn’t fit us, no more, or we are the misfits, we overpass its essential features. The individual is a procrustean bed for our minds and beings. We stated to brim over. We became collage-people generating faces, once in a while. A face is not an identity but an exchange coin, a vehicle, a transitory state. Between who and who? Between who and what?What is a face and what remains of an individual if, beyond this face or faces, we have no idea what the human kind is? How is the subject related to the individual? Is the ego its only center of gravity?Where we started from? Have we ever been totally, completely human? Or our presumed essence of humanity has always been a collective fiction, a mutual ideal of the species? I will try to explore these issues by following three levels / dimensions of human interferences existing in the actual world: the internet, the media and the social institutions. I will also discuss different types of addiction, dependence and imprisonment that people are submitted to within postmodern societies.
The domestic dog: man's best friend in the genomic era
Adam R Boyko
Genome Biology , 2011, DOI: 10.1186/gb-2011-12-2-216
Abstract: In the 5 years since the publication of the genome sequence of the domestic dog (Canis familiaris) [1], our understanding of dog origins and evolution has improved considerably. Before this genome sequence was available (the breed chosen to sequence was a boxer, sequenced at 7.8 coverage), canine genomic analysis relied on linkage and radiation hybrid maps encompassing at most 3,000 to 4,000 markers, or approximately 1 Mb resolution of the genome [2,3]. Comparing the boxer genome to an earlier 1.5 coverage poodle genome [4] and low-coverage sequencing from nine other dog breeds and wolves, scientists have now cataloged over 2.5 million single nucleotide polymorphisms (SNPs) [1]. Genotyping technology has enabled tens of thousands of these SNPs to be typed at a modest cost (approximately US$200 per sample for a 20,000 to 60,000 marker array), giving unprecedented resolution of canine population genetics [5-7] and leading to the rapid identification of loci underlying complex and Mendelian traits (see Additional file 1).The phenotypic diversity of the world's 350 to 400 dog breeds is mirrored in their genetic diversity. Although most breeds have existed for less than two centuries, the level of diversity (FST ) in dogs is about twice that found in humans (FST averages 0.28 among dog breeds) [6,8]. In an effort to create a perfect companion, dog fanciers have embarked on an 'experiment', faithfully rearing, selecting, breeding and adapting, generation after generation, millions of pedigreed animals with genetically based proclivities and susceptibilities awaiting genomic interrogation. The recent release of the new 170K Illumina HD canine SNP array coupled with an improved genome assembly (canFam3) and advances in targeted and high-throughput DNA and RNA sequencing will surely accelerate the pace of canine genomics in the near future, expanding our understanding of evolution in dogs and their utility as a model genetic system.Because of the incredible diversity of mode
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