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Genes, Volume 4, Issue 4 (December 2013), Pages 522-665

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Research

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Open AccessArticle Copy Number Variation in Hereditary Non-Polyposis Colorectal Cancer
Genes 2013, 4(4), 536-555; doi:10.3390/genes4040536
Received: 26 July 2013 / Revised: 2 September 2013 / Accepted: 11 September 2013 / Published: 26 September 2013
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Abstract
Hereditary non-polyposis colorectal cancer (HNPCC) is the commonest form of inherited colorectal cancer (CRC) predisposition and by definition describes families which conform to the Amsterdam Criteria or reiterations thereof. In ~50% of patients adhering to the Amsterdam criteria germline variants are identified [...] Read more.
Hereditary non-polyposis colorectal cancer (HNPCC) is the commonest form of inherited colorectal cancer (CRC) predisposition and by definition describes families which conform to the Amsterdam Criteria or reiterations thereof. In ~50% of patients adhering to the Amsterdam criteria germline variants are identified in one of four DNA Mismatch repair (MMR) genes MLH1, MSH2, MSH6 and PMS2. Loss of function of any one of these genes results in a failure to repair DNA errors occurring during replication which can be most easily observed as DNA microsatellite instability (MSI)—a hallmark feature of this disease. The remaining 50% of patients without a genetic diagnosis of disease may harbour more cryptic changes within or adjacent to MLH1, MSH2, MSH6 or PMS2 or elsewhere in the genome. We used a high density cytogenetic array to screen for deletions or duplications in a series of patients, all of whom adhered to the Amsterdam/Bethesda criteria, to determine if genomic re-arrangements could account for a proportion of patients that had been shown not to harbour causative mutations as assessed by standard diagnostic techniques. The study has revealed some associations between copy number variants (CNVs) and HNPCC mutation negative cases and further highlights difficulties associated with CNV analysis. Full article
(This article belongs to the Special Issue Microsatellite Instability)

Review

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Open AccessReview Monogenic Diabetes: A Diagnostic Algorithm for Clinicians
Genes 2013, 4(4), 522-535; doi:10.3390/genes4040522
Received: 15 July 2013 / Revised: 30 August 2013 / Accepted: 2 September 2013 / Published: 26 September 2013
Cited by 4 | PDF Full-text (823 KB) | HTML Full-text | XML Full-text
Abstract
Monogenic forms of beta cell diabetes account for approximately 1%–2% of all cases of diabetes, yet remain underdiagnosed. Overlapping clinical features with common forms of diabetes, make diagnosis challenging. A genetic diagnosis of monogenic diabetes in many cases alters therapy, affects prognosis, [...] Read more.
Monogenic forms of beta cell diabetes account for approximately 1%–2% of all cases of diabetes, yet remain underdiagnosed. Overlapping clinical features with common forms of diabetes, make diagnosis challenging. A genetic diagnosis of monogenic diabetes in many cases alters therapy, affects prognosis, enables genetic counseling, and has implications for cascade screening of extended family members. We describe those types of monogenic beta cell diabetes which are recognisable by distinct clinical features and have implications for altered management; the cost effectiveness of making a genetic diagnosis in this setting; the use of complementary diagnostic tests to increase the yield among the vast majority of patients who will have commoner types of diabetes which are summarised in a clinical algorithm; and the vital role of cascade genetic testing to enhance case finding. Full article
(This article belongs to the Special Issue Genetics of Diabetes)
Open AccessReview Sequencing of Bacterial Genomes: Principles and Insights into Pathogenesis and Development of Antibiotics
Genes 2013, 4(4), 556-572; doi:10.3390/genes4040556
Received: 12 April 2013 / Revised: 24 July 2013 / Accepted: 27 August 2013 / Published: 14 October 2013
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Abstract
The impact of bacterial diseases on public health has become enormous, and is partly due to the increasing trend of antibiotic resistance displayed by bacterial pathogens. Sequencing of bacterial genomes has significantly improved our understanding about the biology of many bacterial pathogens [...] Read more.
The impact of bacterial diseases on public health has become enormous, and is partly due to the increasing trend of antibiotic resistance displayed by bacterial pathogens. Sequencing of bacterial genomes has significantly improved our understanding about the biology of many bacterial pathogens as well as identification of novel antibiotic targets. Since the advent of genome sequencing two decades ago, about 1,800 bacterial genomes have been fully sequenced and these include important aetiological agents such as Streptococcus pneumoniae, Mycobacterium tuberculosis, Escherichia coli O157:H7, Vibrio cholerae, Clostridium difficile and Staphylococcus aureus. Very recently, there has been an explosion of bacterial genome data and is due to the development of next generation sequencing technologies, which are evolving so rapidly. Indeed, the field of microbial genomics is advancing at a very fast rate and it is difficult for researchers to be abreast with the new developments. This highlights the need for regular updates in microbial genomics through comprehensive reviews. This review paper seeks to provide an update on bacterial genome sequencing generally, and to analyze insights gained from sequencing in two areas, including bacterial pathogenesis and the development of antibiotics. Full article
Open AccessReview Pathological and Evolutionary Implications of Retroviruses as Mobile Genetic Elements
Genes 2013, 4(4), 573-582; doi:10.3390/genes4040573
Received: 15 July 2013 / Revised: 27 September 2013 / Accepted: 8 October 2013 / Published: 24 October 2013
Cited by 2 | PDF Full-text (115 KB) | HTML Full-text | XML Full-text
Abstract
Retroviruses, a form of mobile genetic elements, have important roles in disease and primate evolution. Exogenous retroviruses, such as human immunodeficiency virus (HIV), have significant pathological implications that have created a massive public health challenge in recent years. Endogenous retroviruses (ERVs), which [...] Read more.
Retroviruses, a form of mobile genetic elements, have important roles in disease and primate evolution. Exogenous retroviruses, such as human immunodeficiency virus (HIV), have significant pathological implications that have created a massive public health challenge in recent years. Endogenous retroviruses (ERVs), which are the primary focus of this review, can also be pathogenic, as well as being beneficial to a host in some cases. Furthermore, retroviruses may have played a key role in primate evolution that resulted in the incorporation of these elements into the human genome. Retroviruses are mobile genetic elements that have important roles in disease and primate evolution. We will further discuss the pathogenic potential of retroviruses, including their role in cancer biology, and will briefly summarize their evolutionary implications. Full article
Open AccessReview Nickel and Epigenetic Gene Silencing
Genes 2013, 4(4), 583-595; doi:10.3390/genes4040583
Received: 21 May 2013 / Revised: 11 October 2013 / Accepted: 17 October 2013 / Published: 25 October 2013
Cited by 7 | PDF Full-text (181 KB) | HTML Full-text | XML Full-text
Abstract
Insoluble nickel compounds are well-established human carcinogens. Occupational exposure to these compounds leads to increased incidence of lung and nasal cancer in nickel refinery workers. Apart from its weak mutagenic activity and hypoxia mimicking effect there is mounting experimental evidence indicating that [...] Read more.
Insoluble nickel compounds are well-established human carcinogens. Occupational exposure to these compounds leads to increased incidence of lung and nasal cancer in nickel refinery workers. Apart from its weak mutagenic activity and hypoxia mimicking effect there is mounting experimental evidence indicating that epigenetic alteration plays an important role in nickel-induced carcinogenesis. Multiple epigenetic mechanisms have been identified to mediate nickel-induced gene silencing. Nickel ion is able to induce heterochromatinization by binding to DNA-histone complexes and initiating chromatin condensation. The enzymes required for establishing or removing epigenetic marks can be targeted by nickel, leading to altered DNA methylation and histone modification landscapes. The current review will focus on the epigenetic changes that contribute to nickel-induced gene silencing. Full article
(This article belongs to the Special Issue Gene Silencing)
Open AccessReview The Genetics of Diabetic Nephropathy
Genes 2013, 4(4), 596-619; doi:10.3390/genes4040596
Received: 18 July 2013 / Revised: 8 October 2013 / Accepted: 30 October 2013 / Published: 5 November 2013
Cited by 7 | PDF Full-text (415 KB) | HTML Full-text | XML Full-text
Abstract
Up to 40% of patients with type 1 and type 2 diabetes will develop diabetic nephropathy (DN), resulting in chronic kidney disease and potential organ failure. There is evidence for a heritable genetic susceptibility to DN, but despite intensive research efforts the [...] Read more.
Up to 40% of patients with type 1 and type 2 diabetes will develop diabetic nephropathy (DN), resulting in chronic kidney disease and potential organ failure. There is evidence for a heritable genetic susceptibility to DN, but despite intensive research efforts the causative genes remain elusive. Recently, genome-wide association studies have discovered several novel genetic variants associated with DN. The identification of such variants may potentially allow for early identification of at risk patients. Here we review the current understanding of the key molecular mechanisms and genetic architecture of DN, and discuss the merits of employing an integrative approach to incorporate datasets from multiple sources (genetics, transcriptomics, epigenetic, proteomic) in order to fully elucidate the genetic elements contributing to this serious complication of diabetes. Full article
(This article belongs to the Special Issue Genetics of Diabetes)
Open AccessReview Gene Silencing in Crustaceans: From Basic Research to Biotechnologies
Genes 2013, 4(4), 620-645; doi:10.3390/genes4040620
Received: 17 May 2013 / Revised: 14 August 2013 / Accepted: 8 October 2013 / Published: 7 November 2013
Cited by 14 | PDF Full-text (613 KB) | HTML Full-text | XML Full-text
Abstract
Gene silencing through RNA interference (RNAi) is gaining momentum for crustaceans, both in basic research and for commercial development. RNAi has proven instrumental in a growing number of crustacean species, revealing the functionality of novel crustacean genes essential among others to development, [...] Read more.
Gene silencing through RNA interference (RNAi) is gaining momentum for crustaceans, both in basic research and for commercial development. RNAi has proven instrumental in a growing number of crustacean species, revealing the functionality of novel crustacean genes essential among others to development, growth, metabolism and reproduction. Extensive studies have also been done on silencing of viral transcripts in crustaceans, contributing to the understanding of the defense mechanisms of crustaceans and strategies employed by viruses to overcome these. The first practical use of gene silencing in aquaculture industry has been recently achieved, through manipulation of a crustacean insulin-like androgenic gland hormone. This review summarizes the advancements in the use of RNAi in crustaceans, and assesses the advantages of this method, as well as the current hurdles that hinder its large-scale practice. Full article
(This article belongs to the Special Issue Gene Silencing)
Open AccessReview In Vivo RNAi-Based Screens: Studies in Model Organisms
Genes 2013, 4(4), 646-665; doi:10.3390/genes4040646
Received: 29 September 2013 / Revised: 29 October 2013 / Accepted: 14 November 2013 / Published: 25 November 2013
Cited by 2 | PDF Full-text (298 KB) | HTML Full-text | XML Full-text
Abstract
RNA interference (RNAi) is a technique widely used for gene silencing in organisms and cultured cells, and depends on sequence homology between double-stranded RNA (dsRNA) and target mRNA molecules. Numerous cell-based genome-wide screens have successfully identified novel genes involved in various biological [...] Read more.
RNA interference (RNAi) is a technique widely used for gene silencing in organisms and cultured cells, and depends on sequence homology between double-stranded RNA (dsRNA) and target mRNA molecules. Numerous cell-based genome-wide screens have successfully identified novel genes involved in various biological processes, including signal transduction, cell viability/death, and cell morphology. However, cell-based screens cannot address cellular processes such as development, behavior, and immunity. Drosophila and Caenorhabditis elegans are two model organisms whose whole bodies and individual body parts have been subjected to RNAi-based genome-wide screening. Moreover, Drosophila RNAi allows the manipulation of gene function in a spatiotemporal manner when it is implemented using the Gal4/UAS system. Using this inducible RNAi technique, various large-scale screens have been performed in Drosophila, demonstrating that the method is straightforward and valuable. However, accumulated results reveal that the results of RNAi-based screens have relatively high levels of error, such as false positives and negatives. Here, we review in vivo RNAi screens in Drosophila and the methods that could be used to remove ambiguity from screening results. Full article
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