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Genes, Volume 1, Issue 1 (June 2010), Pages 1-142

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Editorial

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Open AccessEditorial Genes: an Open Access Journal
Genes 2010, 1(1), 1-3; doi:10.3390/genes1010001
Received: 29 October 2009 / Published: 2 November 2009
Cited by 1 | PDF Full-text (23 KB) | HTML Full-text | XML Full-text
Abstract
Genes have been in the scientific vocabulary for a hundred years. The term "gene" was proposed by the Danish plant scientist Wilhelm Johannsen in the first decade of the 20th century. For Johannsen, the gene remained an abstract concept, "free of any [...] Read more.
Genes have been in the scientific vocabulary for a hundred years. The term "gene" was proposed by the Danish plant scientist Wilhelm Johannsen in the first decade of the 20th century. For Johannsen, the gene remained an abstract concept, "free of any hypothesis" [1], but others were already pointing to chromosomes as the likely location of genes. The science of genetics was born at that time, and genes were rapidly connected with mutations, with patterns of inheritance, with development, with quantitative traits, with evolution and with biochemical pathways. All this was achieved without knowledge of the physical nature of genes, but this changed in mid-century with the discoveries of molecular biology. DNA was revealed as the genetic material, and the mechanisms were elucidated by which the information was encoded, and propagated, and linked to the phenotype. However, the concept of a "gene" did not become clearer. Quite the reverse, as the units of mutation, of recombination, of inheritance, of expression, of regulation, etc. did not necessarily coincide. [...] Full article
Open AccessEditorial The Secret Lives of Pluripotent Cells: There and Back Again
Genes 2010, 1(1), 4-8; doi:10.3390/genes1010004
Received: 3 March 2010 / Accepted: 4 March 2010 / Published: 9 March 2010
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Abstract Embryonic stem cells (ESCs) and induced pluripotent stem cells (IPSCs) hold great promise for the therapeutic treatment of human diseases, but their functional similarity, their stability and especially the mechanism underlying their derivation are not yet clearly explained. [...] Full article
(This article belongs to the Special Issue Natural and Induced Pluripotency in Stem Cells)

Research

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Open AccessArticle An Examination of KCNE1 Mutations and Common Variants in Chronic Tinnitus
Genes 2010, 1(1), 23-37; doi:10.3390/genes1010023
Received: 29 March 2010 / Revised: 23 April 2010 / Accepted: 27 April 2010 / Published: 28 April 2010
Cited by 5 | PDF Full-text (387 KB) | HTML Full-text | XML Full-text
Abstract
Chronic tinnitus is a highly prevalent and often incapacitating condition frequently associated with sensorineural hearing loss. While its etiology remains incompletely understood there is a growing awareness of genetic factors that predispose to, or aggravate chronic tinnitus. Candidate genes for the disorder [...] Read more.
Chronic tinnitus is a highly prevalent and often incapacitating condition frequently associated with sensorineural hearing loss. While its etiology remains incompletely understood there is a growing awareness of genetic factors that predispose to, or aggravate chronic tinnitus. Candidate genes for the disorder include KCNE1, a potassium channel subunit gene that has been implicated in maturation defects of central vestibular neurons, in Menière's disease, and in noise-induced hearing loss. 201 Caucasian outpatients with a diagnosis of chronic tinnitus were systematically screened for mutations in the KCNE1 open reading frame and in the adjacent sequence by direct sequencing. Allele frequencies were determined for 46 known variants, plus two novel KCNE1 mutations. These comprised one missense substitution (V47I) in the highly conserved region encoding the KCNE1 transmembrane domain, and one rare variant in the gene's 3'UTR. When genotypes were grouped assuming dominance of the minor alleles, no significant genotype or compound genotype effects were observed on tinnitus severity. The newly identified V47I substitution argues in favor of an enlarged spectrum of mutations in hearing disorders. However, with regard to allele frequencies in healthy control populations from earlier studies, more common KCNE1 variants are unlikely to play a major role in chronic tinnitus. Further investigations are invited to address variation in additional channel subunits as possible risk factors in tinnitus. Full article
Open AccessArticle Population Genomics of Secondary Contact
Genes 2010, 1(1), 124-142; doi:10.3390/genes1010124
Received: 11 May 2010 / Revised: 23 June 2010 / Accepted: 23 June 2010 / Published: 25 June 2010
Cited by 3 | PDF Full-text (403 KB) | HTML Full-text | XML Full-text
Abstract
One common form of reticulate evolution arises as a consequence of secondary contact between previously allopatric populations. Using extensive coalescent simulations, we describe the conditions for, and extent of, the introgression of genetic material into the genome of a colonizing population from [...] Read more.
One common form of reticulate evolution arises as a consequence of secondary contact between previously allopatric populations. Using extensive coalescent simulations, we describe the conditions for, and extent of, the introgression of genetic material into the genome of a colonizing population from an endemic population. The simulated coalescent histories are sampled from models that describe the evolution of entire chromosomes, thereby allowing the expected length of introgressed haplotypes to be estimated. The results indicate that our ability to identify reticulate evolution from genetic data is highly variable and depends critically upon the duration of the period of allopatry, the timing of the secondary contact event, as well as the sizes of the populations at the time of contact. One particularly interesting result arises when secondary contact occurs close to the time of a severe founder event, in this case, genetic introgression can be substantially more difficult to detect. However, if secondary contact occurs after such a founding event, when the range of the colonizing population increases, introgression is more readily detectable across the genome. This result may have important implications for our ability to detect introgression between ancestrally bottlenecked modern human populations and archaic hominin species, such as Neanderthals. Full article
(This article belongs to the Special Issue Reticulate Evolution)

Review

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Open AccessReview Asymmetric Introgressive Hybridization Among Louisiana Iris Species
Genes 2010, 1(1), 9-22; doi:10.3390/genes1010009
Received: 2 February 2010 / Revised: 5 March 2010 / Accepted: 11 March 2010 / Published: 15 March 2010
Cited by 18 | PDF Full-text (1267 KB) | HTML Full-text | XML Full-text
Abstract
In this review, we discuss findings from studies carried out over the past 20+ years that document the occurrence of asymmetric introgressive hybridization in a plant clade. In particular, analyses of natural and experimental hybridization have demonstrated the consistent introgression of genes [...] Read more.
In this review, we discuss findings from studies carried out over the past 20+ years that document the occurrence of asymmetric introgressive hybridization in a plant clade. In particular, analyses of natural and experimental hybridization have demonstrated the consistent introgression of genes from Iris fulva into both Iris brevicaulis and Iris hexagona. Furthermore, our analyses have detected certain prezygotic and postzygotic barriers to reproduction that appear to contribute to the asymmetric introgression. Finally, our studies have determined that a portion of the genes transferred apparently affects adaptive traits. Full article
(This article belongs to the Special Issue Reticulate Evolution)
Open AccessReview Next Generation DNA Sequencing and the Future of Genomic Medicine
Genes 2010, 1(1), 38-69; doi:10.3390/genes1010038
Received: 15 April 2010 / Revised: 20 May 2010 / Accepted: 21 May 2010 / Published: 25 May 2010
Cited by 13 | PDF Full-text (526 KB) | HTML Full-text | XML Full-text
Abstract
In the years since the first complete human genome sequence was reported, there has been a rapid development of technologies to facilitate high-throughput sequence analysis of DNA (termed “next-generation” sequencing). These novel approaches to DNA sequencing offer the promise of complete genomic [...] Read more.
In the years since the first complete human genome sequence was reported, there has been a rapid development of technologies to facilitate high-throughput sequence analysis of DNA (termed “next-generation” sequencing). These novel approaches to DNA sequencing offer the promise of complete genomic analysis at a cost feasible for routine clinical diagnostics. However, the ability to more thoroughly interrogate genomic sequence raises a number of important issues with regard to result interpretation, laboratory workflow, data storage, and ethical considerations. This review describes the current high-throughput sequencing platforms commercially available, and compares the inherent advantages and disadvantages of each. The potential applications for clinical diagnostics are considered, as well as the need for software and analysis tools to interpret the vast amount of data generated. Finally, we discuss the clinical and ethical implications of the wealth of genetic information generated by these methods. Despite the challenges, we anticipate that the evolution and refinement of high-throughput DNA sequencing technologies will catalyze a new era of personalized medicine based on individualized genomic analysis. Full article
(This article belongs to the Special Issue Next Generation DNA Sequencing)
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Open AccessReview Next Generation Sequencing of miRNAs – Strategies, Resources and Methods
Genes 2010, 1(1), 70-84; doi:10.3390/genes1010070
Received: 30 April 2010 / Revised: 1 June 2010 / Accepted: 3 June 2010 / Published: 3 June 2010
Cited by 28 | PDF Full-text (651 KB) | HTML Full-text | XML Full-text
Abstract
miRNAs constitute a family of small RNA species that have been demonstrated to play a central role in regulating gene expression in many organisms. With the advent of next generation sequencing, new opportunities have arisen to identify and quantify miRNAs and elucidate [...] Read more.
miRNAs constitute a family of small RNA species that have been demonstrated to play a central role in regulating gene expression in many organisms. With the advent of next generation sequencing, new opportunities have arisen to identify and quantify miRNAs and elucidate their function. The unprecedented sequencing depth reached by next generation sequencing technologies makes it possible to get a comprehensive miRNA landscape but also poses new challenges for data analysis. We provide an overview of strategies used for miRNA sequencing, public miRNA resources, and useful methods and tools that are available for data analysis. Full article
(This article belongs to the Special Issue Next Generation DNA Sequencing)
Open AccessReview The Application of Next Generation Sequencing in DNA Methylation Analysis
Genes 2010, 1(1), 85-101; doi:10.3390/genes1010085
Received: 28 April 2010 / Revised: 1 June 2010 / Accepted: 3 June 2010 / Published: 4 June 2010
Cited by 16 | PDF Full-text (188 KB) | HTML Full-text | XML Full-text
Abstract
DNA methylation is a major form of epigenetic modification and plays essential roles in physiology and disease processes. In the human genome, about 80% of cytosines in the 56 million CpG sites are methylated to 5-methylcytosines. The methylation pattern of DNA is [...] Read more.
DNA methylation is a major form of epigenetic modification and plays essential roles in physiology and disease processes. In the human genome, about 80% of cytosines in the 56 million CpG sites are methylated to 5-methylcytosines. The methylation pattern of DNA is highly variable among cells types and developmental stages and influenced by disease processes and genetic factors, which brings considerable theoretical and technological challenges for its comprehensive mapping. Recently various high-throughput approaches based on bisulfite conversion combined with next generation sequencing have been developed and applied for the genome wide analysis of DNA methylation. These methods provide single base pair resolution, quantitative DNA methylation data with genome wide coverage. We review these methods here and discuss some technical points of special interest like the sequence depth necessary to reach conclusions, the identification of clonal DNA amplification after bisulfite conversion and the detection of non-CpG methylation. Future application of these methods will greatly facilitate the profiling of the DNA methylation in the genomes of different species, individuals and cell types under healthy and disease states. Full article
(This article belongs to the Special Issue Next Generation DNA Sequencing)
Open AccessReview An Infectious Topic in Reticulate Evolution: Introgression and Hybridization in Animal Parasites
Genes 2010, 1(1), 102-123; doi:10.3390/genes1010102
Received: 29 April 2010 / Revised: 7 June 2010 / Accepted: 7 June 2010 / Published: 9 June 2010
Cited by 22 | PDF Full-text (188 KB) | HTML Full-text | XML Full-text
Abstract
Little attention has been given to the role that introgression and hybridization have played in the evolution of parasites. Most studies are host-centric and ask if the hybrid of a free-living species is more or less susceptible to parasite infection. Here we [...] Read more.
Little attention has been given to the role that introgression and hybridization have played in the evolution of parasites. Most studies are host-centric and ask if the hybrid of a free-living species is more or less susceptible to parasite infection. Here we focus on what is known about how introgression and hybridization have influenced the evolution of protozoan and helminth parasites of animals. There are reports of genome or gene introgression from distantly related taxa into apicomplexans and filarial nematodes. Most common are genetic based reports of potential hybridization among congeneric taxa, but in several cases, more work is needed to definitively conclude current hybridization. In the medically important Trypanosoma it is clear that some clonal lineages are the product of past hybridization events. Similarly, strong evidence exists for current hybridization in human helminths such as Schistosoma and Ascaris. There remain topics that warrant further examination such as the potential hybrid origin of polyploid platyhelminths. Furthermore, little work has investigated the phenotype or fitness, and even less the epidemiological significance of hybrid parasites. Full article
(This article belongs to the Special Issue Reticulate Evolution)

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