Journal of Genetics and Genomics

2013, 40(1): I-II. doi: 10.1016/S1673-8527(13)00016-7

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Technology-Driven and Evidence-Based Genomic Analysis for Integrated Pediatric and Prenatal Genetics Evaluation

Yuan Wei, Fang Xu, Peining Li

2013, 40(1): 1-14. doi: 10.1016/j.jgg.2012.12.004

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The first decade since the completion of the Human Genome Project has been marked with rapid development of genomic technologies and their immediate clinical applications. Genomic analysis using oligonucleotide array comparative genomic hybridization (aCGH) or single nucleotide polymorphism (SNP) chips has been applied to pediatric patients with developmental and intellectual disabilities (DD/ID), multiple congenital anomalies (MCA) and autistic spectrum disorders (ASD). Evaluation of analytical and clinical validities of aCGH showed > 99% sensitivity and specificity and increased analytical resolution by higher density probe coverage. Reviews of case series, multi-center comparison and large patient-control studies demonstrated a diagnostic yield of 12%–20%; approximately 60% of these abnormalities were recurrent genomic disorders. This pediatric experience has been extended toward prenatal diagnosis. A series of reports indicated approximately 10% of pregnancies with ultrasound-detected structural anomalies and normal cytogenetic findings had genomic abnormalities, and 30% of these abnormalities were syndromic genomic disorders. Evidence-based practice guidelines and standards for implementing genomic analysis and web-delivered knowledge resources for interpreting genomic findings have been established. The progress from this technology-driven and evidence-based genomic analysis provides not only opportunities to dissect disease-causing mechanisms and develop rational therapeutic interventions but also important lessons for integrating genomic sequencing into pediatric and prenatal genetic evaluation.

Genetics of Nonalcoholic Fatty Liver Disease: An Overview

Jharna Puppala, Siva Prasad Siddapuram, Jyothy Akka, Anjana Munshi

2013, 40(1): 15-22. doi: 10.1016/j.jgg.2012.12.001

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Nonalcoholic fatty liver disease (NAFLD) is the most common liver disease in the world today. Its incidence in adults and children is rising rapidly due to the ongoing epidemics of obesity and type 2 diabetes. Hence, it has become a global public health issue. Environmental factors have been found to play a major role in the etiology of NAFLD, especially for genetically susceptible populations. Among these, one of the most important factors is junk food, especially the typical “Western-style” diet rich in simple carbohydrates, saturated fat, and highly processed food materials. Genetic predisposition to NAFLD does occur; however, a precise definition of genetic factors responsible for NAFLD is still lacking. Specific variants of different genes have been shown to present a risk for NAFLD. Genetic studies might be helpful in the management of the disease by developing novel treatment strategies based on individual's genotype.

The Genetic and Molecular Basis of Plant Resistance to Pathogens

Yan Zhang, Thomas Lubberstedt, Mingliang Xu

2013, 40(1): 23-35. doi: 10.1016/j.jgg.2012.11.003

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Plant pathogens have evolved numerous strategies to obtain nutritive materials from their host, and plants in turn have evolved the preformed physical and chemical barriers as well as sophisticated two-tiered immune system to combat pathogen attacks. Genetically, plant resistance to pathogens can be divided into qualitative and quantitative disease resistance, conditioned by major gene(s) and multiple genes with minor effects, respectively. Qualitative disease resistance has been mostly detected in plant defense against biotrophic pathogens, whereas quantitative disease resistance is involved in defense response to all plant pathogens, from biotrophs, hemibiotrophs to necrotrophs. Plant resistance is achieved through interception of pathogen-derived effectors and elicitation of defense response. In recent years, great progress has been made related to the molecular basis underlying host–pathogen interactions. In this review, we would like to provide an update on genetic and molecular aspects of plant resistance to pathogens.

Production of Transgenic Korean Native Cattle Expressing Enhanced Green Fluorescent Protein Using a FIV-Based Lentiviral Vector Injected into MII Oocytes

Yong-Nan Xu, Sang-Jun Uhm, Bon-Chul Koo, Mo-Sun Kwon, Ji-Yeol Roh, Jung-Seok Yang, Hyun-Yong Choi, Young-Tae Heo, Xiang-Shun Cui, Joon-Ho Yoon, Dae-Hwan Ko, Teoan Kim, Nam-Hyung Kim

2013, 40(1): 37-43. doi: 10.1016/j.jgg.2012.11.001

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The potential benefits of generating and using transgenic cattle range from improvements in agriculture to the production of large quantities of pharmaceutically relevant proteins. Previous studies have attempted to produce transgenic cattle and other livestock by pronuclear injection and somatic cell nuclear transfer, but these approaches have been largely ineffective; however, a third approach, lentivirus-mediated transgenesis, has successfully produced transgenic livestock. In this study, we generated transgenic (TG) Korean native cattle using perivitelline space injection of viral vectors, which expressed enhanced green fluorescent protein (EGFP) systemically. Two different types of lentiviral vectors derived from feline immunodeficiency virus (FIV) and human immunodeficiency virus (HIV) carryingEGFP were injected into the perivitelline space of MII oocytes. EGFP expression at 8-cell stage was significantly higher in the FIV group compared to the HIV group (47.5%±2.2% v.s. 22.9%±2.9%). Eight-cell embryos that expressed EGFP were cultured into blastocysts and then transferred into 40 heifers. Ten heifers were successfully impregnated and delivered 10 healthy calves. All of these calves expressed EGFP as detected by in vivo imaging, PCR and Southern blotting. In addition, we established an EGFP-expressing cell line from TG calves, which was followed by nuclear transfer (NT). Recloned 8-cell embryos also expressed EGFP, and there were no differences in the rates of fusion, cleavage and development between cells derived from TG and non-TG calves, which were subsequently used for NT. These results illustrate that FIV-based lentiviruses are useful for the production of TG cattle. Moreover, our established EGFP cell line can be used for additional studies that involve induced pluripotent stem cells.

Recycling Isolation of Plant DNA, A Novel Method

Lingling Zhang, Bo Wang, Lei Pan, Junhua Peng

2013, 40(1): 45-54. doi: 10.1016/j.jgg.2012.10.001

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DNA is one of the most basic and essential genetic materials in the field of molecular biology. To date, isolation of sufficient and good-quality DNA is still a challenge for many plant species, though various DNA extraction methods have been published. In the present paper, a recycling DNA extraction method was proposed. The key step of this method was that a single plant tissue sample was recycled for DNA extraction for up to four times, and correspondingly four DNA precipitations (termed as the 1st, 2nd, 3rd and 4th DNA sample, respectively) were conducted. This recycling step was integrated into the conventional CTAB DNA extraction method to establish a recycling CTAB method. This modified CTAB method was tested in eight plant species, wheat, sorghum, barley, corn, rice, Brachypodium distachyon, Miscanthus sinensis and tung tree. The results showed that high-yield and good-quality DNA samples could be obtained by using this new method in all the eight plant species. The DNA samples were good templates for PCR amplification of both ISSR and SSR markers. The recycling method can be used in multiple plant species and can be integrated with multiple conventional DNA isolation methods, and thus is an effective and universal DNA isolation method.

Rapid Evolution of the Mammalian HILS1 Gene and the Nuclear Condensation Process during Mammalian Spermiogenesis

Yanhua Su, Dongdong Wu, Weiping Zhou, David M. Irwin, Yaping Zhang

2013, 40(1): 55-59. doi: 10.1016/j.jgg.2012.10.003

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2013 Vol. 40, No. 1