Genetics Research International http://www.hindawi.com The latest articles from Hindawi Publishing Corporation © 2014 , Hindawi Publishing Corporation . All rights reserved. Application of Microsatellite Markers in Conservation Genetics and Fisheries Management: Recent Advances in Population Structure Analysis and Conservation Strategies Mon, 07 Apr 2014 11:50:03 +0000 http://www.hindawi.com/journals/gri/2014/691759/ Microsatellites are the most popular and versatile genetic marker with myriads of applications in population genetics, conservation biology, and evolutionary biology. These are the arrays of DNA sequences, consisting of tandemly repeating mono-, di-, tri-, and tetranucleotide units, which are distributed throughout the genomes of most eukaryotic species. Microsatellites are codominant in nature, highly polymorphic, easily typed, and Mendelian inherited, all properties which make them very suitable for the study of population structure and pedigree analysis and capable of detecting differences among closely related species. PCR for microsatellites can be automated for identifying simple sequence repeat polymorphism. Small amount of blood samples or alcohol preserved tissue is adequate for analyzing them. Most of the microsatellites are noncoding, and therefore variations are independent of natural selection. These properties make microsatellites ideal genetic markers for conservation genetics and fisheries management. This review addresses the applications of microsatellite markers in conservation genetics and recent advances in population structure analysis in the context of fisheries management. P. M. Abdul-Muneer Copyright © 2014 P. M. Abdul-Muneer. All rights reserved. One-Year Period Prevalence of Oral Aphthous Ulcers and Oral Health-Related Quality of Life in Patients with Behçet’s Disease Sun, 09 Mar 2014 12:38:34 +0000 http://www.hindawi.com/journals/gri/2014/930348/ The aim of this study was to investigate the 1-year period prevalence of oral aphthous ulcers (OAUs) and their association with oral health-related quality of life (OHQOL) in patients with Behçet’s disease (BD) and in the general population. In this cross-sectional study, 675 patients with Behçet’s disease (BD group) and 1,097 males and females in the Japanese general population (control group) completed both questionnaires on their OAU status during the prior year and the General Oral Health Assessment Index (GOHAI). In the BD group, 84% of patients reported experiencing an OAU during the previous year, and the mean number of OAUs/year was 13. In the control group, 31% of individuals experienced an OAU during the previous year, and the mean number of OAUs/year was one. Multivariate analysis indicated that both BD patients (OR, 6.2; 95% CI, 4.8–8.0) and controls (OR, 2.6; 95% CI, 2.0–3.5) who had OAUs at least twice per year were more likely to have GOHAI scores below the norm than were controls who had fewer than two OAUs per year. The association between HLA-B*51 and OAUs remains unknown. The presence of OAUs has a negative effect on the OHQOL of patients with BD. Mariko Naito, Yoshimi Suzukamo, Kenji Wakai, Miki Azechi, Fumio Kaneko, Takeo Nakayama, Nobuyuki Hamajima, and Shunichi Fukuhara Copyright © 2014 Mariko Naito et al. All rights reserved. A New Diagnostic Way for Behcet's Disease: Skin Prick with Self-Saliva Thu, 23 Jan 2014 13:19:35 +0000 http://www.hindawi.com/journals/gri/2014/581468/ Behcet's disease (BD) is a mysterious multisystemic disorder characterized by recurrent involvement of mucocutaneous (including recurrent aphthous stomatitis; RAS), ocular, intestinal, vascular, and/or nervous system organs. Previously, the positivity of “pathergy test”, which is one of the diagnostic examinations, was reported to be related to the possession of HLA-B51 gene in BD patients, even though the positivity is low and different from the countries. Here, instead of the ordinal pathergy test, we would like to propose the prick with self-saliva as a new diagnostic way for patients with RAS of BD based on the genetic intrinsic factors including HLA-B51 and extrinsic triggering factors. BD patients are considered to acquire the hypersensitivity against oral streptococci through the innate immune mechanism in the oral cavity. Bes-1 gene and 65 kD of heat shock protein (HSP-65) derived from oral S. sanguinis are supposed to play important roles as extrinsic factors in BD pathogenesis. Although the prick positivity was not related to the possession of HLA-B51 gene, the method is suggested to be a significant way for BD diagnosis. The results also suggest that BD symptoms are due to the vascular immune responses by monocytes expressed oral streptococcal agents of the patients. Fumio Kaneko, Ari Togashi, Erika Nomura, and Koichiro Nakamura Copyright © 2014 Fumio Kaneko et al. All rights reserved. Expression of Potential Regulatory Genes in Abdominal Adipose Tissue of Broiler Chickens during Early Development Thu, 16 Jan 2014 09:12:26 +0000 http://www.hindawi.com/journals/gri/2014/318304/ The identities of genes that underlie population variation in adipose tissue development in farm animals are poorly understood. Previous studies in our laboratory have suggested that increased fat tissue involves the expression modulation of an array of genes in broiler chickens. Of special interest are eight genes, FGFR3, EPHB2, IGFBP2, GREM1, TNC, COL3A1, ACBD7, and SCD. To understand their expression regulation and response to dietary manipulation, we investigated their mRNA levels after dietary manipulation during early development. Chickens were fed either a recommended standard or a high caloric diet from hatch to eight weeks of age (WOA). The high caloric diet markedly affected bodyweight of the broiler birds. mRNA levels of the eight genes in the abdominal adipose tissue were assayed at 2, 4, 6, and 8 WOA using RT-qPCR. Results indicate that (1) FGFR3 mRNA level was affected significantly by diet, age, and diet:age interaction; (2) COL3A mRNA level was repressed by high caloric diet; (3) mRNA levels of EPHB2, ACBD7, and SCD were affected by age; (4) mRNA level of TNC was modulated by age:diet interaction; (5) changes in GREM1 and IGFBP2 mRNA levels were not statistically different. Ann Bohannon-Stewart, Gary Kelley, Boniface Kimathi, Sri Harsha K. V. Subramanya, Joseph Donkor, Carl Darris, James Tyus, Ashley Payne, Shannon Byers, Dafeng Hui, Samuel Nahashon, Fur-Chi Chen, Michael Ivy, and Xiaofei Wang Copyright © 2014 Ann Bohannon-Stewart et al. All rights reserved. Innate and Adaptive Responses to Heat Shock Proteins in Behcet’s Disease Tue, 31 Dec 2013 09:51:39 +0000 http://www.hindawi.com/journals/gri/2013/249157/ Behcet’s disease (BD) is a systemic, chronic inflammatory disorder with both innate and adaptive immune responses. Heat shock proteins (HSP) are highly conserved molecules in different species with scavenger activity and involved in correct folding of newly synthesized proteins. T and B cell responses against HSPs are observed in BD patients in both and T-cell populations. 60-kD HSP (HSP60) is also shown to be recognized by pattern recognition receptors such as toll-like receptors (TLR) and is suggested to be an endogenous “danger” signal to the immune system with rapid inflammatory cytokine releases and enhancement of adaptive Th1-type responses. Elucidating the exact role of HSPs in BD pathogenesis might pave the way to less toxic therapeutic approaches to BD, such as antibacterial therapies and immunomodulation. H. Direskeneli Copyright © 2013 H. Direskeneli. All rights reserved. Skewed Helper T-Cell Responses to IL-12 Family Cytokines Produced by Antigen-Presenting Cells and the Genetic Background in Behcet’s Disease Mon, 30 Dec 2013 11:51:11 +0000 http://www.hindawi.com/journals/gri/2013/363859/ Behcet’s disease (BD) is a multisystemic inflammatory disease and is characterized by recurrent attacks on eyes, brain, skin, and gut. There is evidence that skewed T-cell responses contributed to its pathophysiology in patients with BD. Recently, we found that Th17 cells, a new helper T (Th) cell subset, were increased in patients with BD, and both Th type 1 (Th1) and Th17 cell differentiation signaling pathways were overactivated. Several researches revealed that genetic polymorphisms in Th1/Th17 cell differentiation signaling pathways were associated with the onset of BD. Here, we summarize current findings on the Th cell subsets, their contribution to the pathogenesis of BD and the genetic backgrounds, especially in view of IL-12 family cytokine production and pattern recognition receptors of macrophages/monocytes. Jun Shimizu, Fumio Kaneko, and Noboru Suzuki Copyright © 2013 Jun Shimizu et al. All rights reserved. Feasibility of Whole RNA Sequencing from Single-Cell mRNA Amplification Mon, 23 Dec 2013 11:39:05 +0000 http://www.hindawi.com/journals/gri/2013/724124/ Single-cell sampling with RNA-seq analysis plays an important role in reference laboratory; cytogenomic diagnosis for specimens on glass-slides or rare cells in circulating blood for tumor and genetic diseases; measurement of sensitivity and specificity in tumor-tissue genomic analysis with mixed-cells; mechanism analysis of differentiation and proliferation of cancer stem cell for academic purpose. Our single- cell RNA-seq technique shows that fragments were 250–450 bp after fragmentation, amplification, and adapter addition. There were 11.6 million reads mapped in raw sequencing reads (19.6 million). The numbers of mapped genes, mapped transcripts, and mapped exons were 31,332, 41,210, and 85,786, respectively. All QC results demonstrated that RNA-seq techniques could be used for single-cell genomic performance. Analysis of the mapped genes showed that the number of genes mapped by RNA-seq (6767 genes) was much higher than that of differential display (288 libraries) among similar specimens which we have developed and published. The single-cell RNA-seq can detect gene splicing using different subtype TGF-beta analysis. The results from using Q-rtPCR tests demonstrated that sensitivity is 76% and specificity is 55% from single-cell RNA-seq technique with some gene expression missing (2/8 genes). However, it will be feasible to use RNA-seq techniques to contribute to genomic medicine at single-cell level. Yunbo Xu, Hongliang Hu, Jie Zheng, and Biaoru Li Copyright © 2013 Yunbo Xu et al. All rights reserved. DNA Methylation Pattern as Important Epigenetic Criterion in Cancer Mon, 23 Dec 2013 09:09:48 +0000 http://www.hindawi.com/journals/gri/2013/317569/ Epigenetic modifications can affect the long-term gene expression without any change in nucleotide sequence of the DNA. Epigenetic processes intervene in the cell differentiation, chromatin structure, and activity of genes since the embryonic period. However, disorders in genes’ epigenetic pattern can affect the mechanisms such as cell division, apoptosis, and response to the environmental stimuli which may lead to the incidence of different diseases and cancers. Since epigenetic changes may return to their natural state, they could be used as important targets in the treatment of cancer and similar malignancies. The aim of this review is to assess the epigenetic changes in normal and cancerous cells, the causative factors, and epigenetic therapies and treatments. Mehrdad Ghavifekr Fakhr, Majid Farshdousti Hagh, Dariush Shanehbandi, and Behzad Baradaran Copyright © 2013 Mehrdad Ghavifekr Fakhr et al. All rights reserved. Arrhythmogenic Right Ventricular Dysplasia/Cardiomyopathy Type 1: A Light on Molecular Mechanisms Thu, 12 Dec 2013 08:36:38 +0000 http://www.hindawi.com/journals/gri/2013/460805/ Arrhythmogenic right ventricular dysplasia/cardiomyopathy (ARVD/C) is an inherited cardiomyopathy associated with cardiac arrhythmias originating in the right ventricle, heart failure, and sudden cardiac death. Development of ARVD/C type 1 has been attributed to differential expression of transforming growth factor beta 3 (TGFβ3). Several mechanisms underlying the molecular basis of ARVD/C type 1 have been proposed. Evaluating previously described mechanisms might elucidate how TGFβ3 contributes to disease progression in ARVD/C type 1. Here we review how TGFβ3 can induce fibrogenesis through Smad and/or β-catenin signaling. Moreover, the role of apoptosis is addressed. Finally the extent to which the immune system has been demonstrated to be a modulating and amplifying agent in the onset and progression of ARVD/C in general is discussed. Koen L. A. Vanderschuren, Tom Sieverink, and Ronald Wilders Copyright © 2013 Koen L. A. Vanderschuren et al. All rights reserved. Lack of TEK Gene Mutation in Patients with Cutaneomucosal Venous Malformations from the North-Western Region of Algeria Mon, 09 Dec 2013 15:53:38 +0000 http://www.hindawi.com/journals/gri/2013/784789/ Background. Venous malformations (VM) result from an error in vascular morphogenesis. The first gene suspected in their development is the TEK gene (tyrosine kinase, endothelial). Mutations of this gene have been identified in several Belgian families with a dominant form of the disease. Therefore, we investigated whether mutations in this TEK gene could explain the MV development in patients of families from Tlemcen region (north-western Algeria). Methods. Genomic DNA was extracted from leucocytes of ten patients. The search for mutations in all the 23 exons and in the 5′ and 3′ intronic sequences flanking the TEK gene was performed using PCR amplification and direct sequencing of amplified genomic DNA. Additionally, a search for somatic mutations of the gene TEK was performed on a biopsy of the venous malformation from one of the ten eligible patients. Results. The sequencing of the 23 exons of the TEK gene revealed neither germinal mutation in our ten patients nor somatic mutation in the tissue of the biopsy. Conclusion. The absence of mutation in the TEK gene in the population studied suggests that the TEK gene is not necessarily involved in the onset of VM; its association with these malformations may differ from one population to another. Nabila Brahami, Mourad Aribi, Badr-Eddine Sari, Philippe Khau Van Kien, Isabelle Touitou, Gérard Lefranc, and Mouna Barat-Houari Copyright © 2013 Nabila Brahami et al. All rights reserved. PCR-SSCP Variation of IGF1 and PIT1 Genes and Their Association with Estimated Breeding Values of Growth Traits in Makooei Sheep Mon, 09 Dec 2013 08:03:19 +0000 http://www.hindawi.com/journals/gri/2013/272346/ Molecular biology techniques genetic improvement by facilitating identification, mapping and analysis of polymorphism of genes by encoding proteins that act on metabolic pathways involved in economically interesting traits. This use of genetic markers can aid identification of those animals with the highest breeding values in sheep. On the basis of sheep genome mapping, information was examined on the ovine IGF1 and PIT1 genes as a possible genetic marker for growth traits in sheep. The current study was designed to estimate the frequencies of putative IGF-1 and PIT-1 genes SNPs and investigate associations with calculated EBVs of growth traits in Makooei sheep. PCR-SSCP analysis of the exon1 of IGF-I gene and include a part of intron2, exon3 and a part of intron3 and PIT-1 gene revealed the following banding patterns; three (AA, AG, GG) and four AA (p1), AB (p2), CC (p3), CD (p4), banding patterns respectively. Results from this study demonstrated higher performance of AA animals in BW and GBW, and AG animal in WW and W6 that may be related to the role of IGF-1 at the pre-puberty and puberty stages. Also higher performance of p3 animals in W9, YW and GSN, and p1 animal in GNY may be related to the PIT-1 role in post-puberty. Masoud Negahdary, Abbas Hajihosseinlo, and Marziyeh Ajdary Copyright © 2013 Masoud Negahdary et al. All rights reserved. Investigation of Genetic Disturbances in Oxygen Sensing and Erythropoietin Signaling Pathways in Cases of Idiopathic Erythrocytosis Mon, 02 Dec 2013 09:19:42 +0000 http://www.hindawi.com/journals/gri/2013/495724/ Background. Idiopathic erythrocytosis is the term reserved for cases with unexplained origins of abnormally increased hemoglobin after initial investigation. Extensive molecular investigation of genes associated with oxygen sensing and erythropoietin signaling pathways, in those cases, usually involves sequencing all of their exons and it may be time consuming. Aim. To perform a strategy for molecular investigation of patients with idiopathic erythrocytosis regarding oxygen sensing and erythropoietin signaling pathways. Methods. Samples of patients with idiopathic erythrocytosis were evaluated for the EPOR, VHL, PHD2, and HIF-2α genes using bidirectional sequencing of their hotspots. Results. One case was associated with HIF-2α mutation. Sequencing did not identify any pathogenic mutation in 4 of 5 cases studied in any of the studied genes. Three known nonpathogenic polymorphisms were found (VHL p.P25L, rs35460768; HIF-2α p.N636N, rs35606117; HIF-2α p.P579P, rs184760160). Conclusion. Extensive molecular investigation of cases considered as idiopathic erythrocytosis does not frequently change the treatment of the patient. However, we propose a complementary molecular investigation of those cases comprising genes associated with erythrocytosis phenotype to meet both academic and genetic counseling purposes. Carla Luana Dinardo, Paulo Caleb Junior Lima Santos, Isolmar Tadeu Schettert, Renata Alonso Gadi Soares, Jose Eduardo Krieger, and Alexandre Costa Pereira Copyright © 2013 Carla Luana Dinardo et al. All rights reserved. Immunopathogenic Role of Herpes Simplex Virus in Behçet’s Disease Sun, 24 Nov 2013 13:39:45 +0000 http://www.hindawi.com/journals/gri/2013/638273/ The role of viral infections, such as herpes simplex virus (HSV) infection, in the pathogenesis of Behçet’s disease (BD) has been investigated for many years. HSV has been detected in peripheral blood leukocytes, saliva, and genital ulcers of patients with BD. Various cell adhesion molecules on cultured endothelial cells have been induced by HSV in a TNF-α dependent manner. In addition, a BD-like animal model was developed by inoculating ICR mouse earlobes with HSV, and antiviral treatment was effective in improving BD-like symptoms in this model. Still, there are several incompletely characterized proteins that possess antiviral properties and are being investigated as mediators of viral infection-related chronic inflammatory reactions. Although the role of HSV in the pathogenesis of BD remains to be fully established, recent research findings regarding HSV in BD have expanded our understanding of the disease and will hopefully lead to the development of more effective therapeutic agents in the near future. Do Young Kim, Suhyun Cho, Min Ju Choi, Seonghyang Sohn, Eun-So Lee, and Dongsik Bang Copyright © 2013 Do Young Kim et al. All rights reserved. Diagnostic Genetics at a Distance: Von Hippel-Lindau Disease and a Novel Mutation Mon, 26 Aug 2013 08:30:04 +0000 http://www.hindawi.com/journals/gri/2013/189196/ Genetic testing at a distance is commonplace where members of a family with a segregating germline mutation are geographically separated. For the most part, this challenge is addressed through the intervention of health professionals in taking and/or processing blood samples for subsequent couriering of DNA to a referral laboratory. In some circumstances, however, the collecting of pivotal clinical material may involve direct patient involvement. We describe such a situation where noninvasive saliva samples were provided by members of a family manifesting Von Hippel-Lindau (VHL) disease. The analysis identified a novel mutation in the VHL gene that was used to exclude other family members as being at risk of VHL disease. Clare Brookes, Debra O. Prosser, Jennifer M. Love, R. J. McKinlay Gardner, and Donald R. Love Copyright © 2013 Clare Brookes et al. All rights reserved. Regression Modeling and Meta-Analysis of Diagnostic Accuracy of SNP-Based Pathogenicity Detection Tools for UGT1A1 Gene Mutation Tue, 13 Aug 2013 08:08:20 +0000 http://www.hindawi.com/journals/gri/2013/546909/ Aims. This review summarized all available evidence on the accuracy of SNP-based pathogenicity detection tools and introduced regression model based on functional scores, mutation score, and genomic variation degree. Materials and Methods. A comprehensive search was performed to find all mutations related to Crigler-Najjar syndrome. The pathogenicity prediction was done using SNP-based pathogenicity detection tools including SIFT, PHD-SNP, PolyPhen2, fathmm, Provean, and Mutpred. Overall, 59 different SNPs related to missense mutations in the UGT1A1 gene, were reviewed. Results. Comparing the diagnostic OR, our model showed high detection potential (diagnostic OR: 16.71, 95% CI: 3.38–82.69). The highest MCC and ACC belonged to our suggested model (46.8% and 73.3%), followed by SIFT (34.19% and 62.71%). The AUC analysis showed a significance overall performance of our suggested model compared to the selected SNP-based pathogenicity detection tool (). Conclusion. Our suggested model is comparable to the well-established SNP-based pathogenicity detection tools that can appropriately reflect the role of a disease-associated SNP in both local and global structures. Although the accuracy of our suggested model is not relatively high, the functional impact of the pathogenic mutations is highlighted at the protein level, which improves the understanding of the molecular basis of mutation pathogenesis. Fakher Rahim, Hamid Galehdari, Javad Mohammadi-asl, and Najmaldin Saki Copyright © 2013 Fakher Rahim et al. All rights reserved. Hidden Y Chromosome Mosaicism in 48 Egyptian Patients with Turner’s Syndrome Sun, 28 Jul 2013 08:57:52 +0000 http://www.hindawi.com/journals/gri/2013/463529/ Background. The presence of Y chromosome material in Turner’s syndrome (TS) patients is a risk factor for the development of gonadoblastoma. Although conventional cytogenetic analysis is the definitive diagnosis of TS, low level Y chromosome mosaicism may be missed. Molecular analysis has demonstrated a higher proportion of mosaicism, but there is controversy regarding the prevalence of Y chromosome-derived material in those patients. Aim and Methods. This study was conducted to investigate the prevalence of hidden Y chromosome mosaicism in 48 TS Egyptian patients using polymerase chain reaction (PCR) for molecular DNA analysis of SRY gene and compare our results with those in the literature. Results. None of TS patients had a cytogenetically obvious Y chromosome; Y chromosome material was detected only at molecular analysis. SRY gene was found in 9 TS patients (18.75%) with the classical 45,X karyotype, whereas all other patients were SRY negative. Conclusion. Cytogenetically undetected Y chromosome mosaicism is common in TS patients; these data reinforce the need for adequate diagnosis of Y chromosome material in those patients. Molecular screening for Y chromosome-derived DNA should be routinely carried out in all TS patients. Mervat M. El-Eshmawy, Sohier Yahia, Faeza A. El-Dahtory, Sahar Hamed, El Hadidy M. El Hadidy, and Mohamed Ragab Copyright © 2013 Mervat M. El-Eshmawy et al. All rights reserved. Molecular Genetic Diversity and Quantitation of Methanogen in Ruminal Fluid of Buffalo (Bubalus bubalis) Fed Ration (Wheat Straw and Concentrate Mixture Diet) Wed, 05 Jun 2013 16:23:56 +0000 http://www.hindawi.com/journals/gri/2013/980191/ High roughage diet causes more methane emissions; however, the total methanogen abundance is not influenced by roughage proportion. Technologies to reduce methane emissions are lacking, and development of inhibitors and vaccines that mitigate rumen-derived methane by targeting methanogens relies on present knowledge of the methanogens. In this work, we have investigated molecular diversity of rumen methanogens of Surti buffalo. DNA from rumen fluid was extracted, and 16S rRNA encoding genes were amplified using methanogen specific primer to generate 16S rDNA clone libraries. Seventy-six clones were randomly selected and analysed by RFLP resulting in 21 operational taxonomic units (OTUs). BLAST analysis with available sequences in database revealed sequences of 13 OTUs (55 clones) showing similarity with Methanomicrobium sp, 3 OTUs (15 clones) with Methanobrevibacter sp. The remaining 5 OTUs (6 clones) belonged to uncultured archaea. The phylogenetic analysis indicated that methanogenic communities found in the library were clustered in the order of Methanomicrobiales (18 OTUs) and Methanobacteriales (3 OTUs). The population of Methanomicrobiales, Methanobacteriales, and Methanococcales were also observed, accounting for 1.94%, 0.72%, and 0.47% of total archaea, respectively. K. M. Singh, A. K. Tripathi, P. R. Pandya, S. Parnerkar, R. K. Kothari, and C. G. Joshi Copyright © 2013 K. M. Singh et al. All rights reserved. Epigenetics in Friedreich's Ataxia: Challenges and Opportunities for Therapy Tue, 19 Feb 2013 11:22:46 +0000 http://www.hindawi.com/journals/gri/2013/852080/ Friedreich's ataxia (FRDA) is an autosomal recessive neurodegenerative disorder caused by homozygous expansion of a GAA·TTC trinucleotide repeat within the first intron of the FXN gene, leading to reduced FXN transcription and decreased levels of frataxin protein. Recent advances in FRDA research have revealed the presence of several epigenetic modifications that are either directly or indirectly involved in this FXN gene silencing. Although epigenetic marks may be inherited from one generation to the next, modifications of DNA and histones can be reversed, indicating that they are suitable targets for epigenetic-based therapy. Unlike other trinucleotide repeat disorders, such as Huntington disease, the large expansions of GAA·TTC repeats in FRDA do not produce a change in the frataxin amino acid sequence, but they produce reduced levels of normal frataxin. Therefore, transcriptional reactivation of the FXN gene provides a good therapeutic option. The present paper will initially focus on the epigenetic changes seen in FRDA patients and their role in the silencing of FXN gene and will be concluded by considering the potential epigenetic therapies. Chiranjeevi Sandi, Sahar Al-Mahdawi, and Mark A. Pook Copyright © 2013 Chiranjeevi Sandi et al. All rights reserved. Community Genetic Services in Iran Wed, 05 Dec 2012 13:34:31 +0000 http://www.hindawi.com/journals/gri/2012/129575/ The aim of the study was to report a description of the primary, secondary, and tertiary level services available for genetic disorders in Iran. For the purpose of this study, essential data were collected from every facility providing community genetic services in Tabriz city of Iran using a prestructured checklist. Technical information was filled in the predesigned forms using diagnostic records of each client/patient. Information was also gathered from community genetic services clients through a face-to-face interview at these facilities to assess the quality of services provided. Primary prevention measures were available in 80 percent of centres in the study population. Diagnostic techniques were fully available in the study area both in public and private sectors. Screening of congenital hypothyroidism and thalassemia has been successfully performed across the country by the Ministry of Health. Other screening programs have also been initiated by the country health authorities for neural tube defects, Down syndrome, and phenylketonuria. The high cost of genetic services at secondary and tertiary levels does not allow many people to get access to these services despite their needs. Governments will therefore need to allocate necessary resources to make the essential genetic services available for everyone needing these in the community. Shirin Atri Barzanjeh, Mozhgan Behshid, Mohammad Bagher Hosseini, Maryam Ezari, Mahdieh Taghizadeh, and Saeed Dastgiri Copyright © 2012 Shirin Atri Barzanjeh et al. All rights reserved. Filling the Silent Void: Genetic Therapies for Hearing Impairment Tue, 04 Dec 2012 14:32:58 +0000 http://www.hindawi.com/journals/gri/2012/748698/ The inner ear cytoarchitecture forms one of the most intricate and delicate organs in the human body and is vulnerable to the effects of genetic disorders, aging, and environmental damage. Owing to the inability of the mammalian cochlea to regenerate sensory hair cells, the loss of hair cells is a leading cause of deafness in humans. Millions of individuals worldwide are affected by the emotionally and financially devastating effects of hearing impairment (HI). This paper provides a brief introduction into the key role of genes regulating inner ear development and function. Potential future therapies that leverage on an improved understanding of these molecular pathways are also described in detail. Joel Sng and Thomas Lufkin Copyright © 2012 Joel Sng and Thomas Lufkin. All rights reserved. The Epigenetics of Emerging and Nonmodel Organisms Wed, 28 Nov 2012 15:43:36 +0000 http://www.hindawi.com/journals/gri/2012/491204/ Vett K. Lloyd, Jennifer A. Brisson, Kathleen A. Fitzpatrick, Lori A. McEachern, and Eveline C. Verhulst Copyright © 2012 Vett K. Lloyd et al. All rights reserved. Mechanistic Roles of Noncoding RNAs in Lung Cancer Biology and Their Clinical Implications Wed, 18 Jul 2012 14:15:04 +0000 http://www.hindawi.com/journals/gri/2012/737416/ Lung cancer biology has traditionally focused on genomic and epigenomic deregulation of protein-coding genes to identify oncogenes and tumor suppressors diagnostic and therapeutic targets. Another important layer of cancer biology has emerged in the form of noncoding RNAs (ncRNAs), which are major regulators of key cellular processes such as proliferation, RNA splicing, gene regulation, and apoptosis. In the past decade, microRNAs (miRNAs) have moved to the forefront of ncRNA cancer research, while the role of long noncoding RNAs (lncRNAs) is emerging. Here we review the mechanisms by which miRNAs and lncRNAs are deregulated in lung cancer, the technologies that can be applied to detect such alterations, and the clinical potential of these RNA species. An improved comprehension of lung cancer biology will come through the understanding of the interplay between deregulation of non-coding RNAs, the protein-coding genes they regulate, and how these interactions influence cellular networks and signalling pathways. Katey S. S. Enfield, Larissa A. Pikor, Victor D. Martinez, and Wan L. Lam Copyright © 2012 Katey S. S. Enfield et al. All rights reserved. Notch Signaling during Oogenesis in Drosophila melanogaster Sun, 10 Jun 2012 15:25:43 +0000 http://www.hindawi.com/journals/gri/2012/648207/ The Notch signaling pathway is an evolutionarily conserved intercellular signaling mechanism that is required for embryonic development, cell fate specification, and stem cell maintenance. Discovered and studied initially in Drosophila melanogaster, the Notch pathway is conserved and functionally active throughout the animal kingdom. In this paper, we summarize the biochemical mechanisms of Notch signaling and describe its role in regulating one particular developmental pathway, oogenesis in Drosophila. Jingxia Xu and Thomas Gridley Copyright © 2012 Jingxia Xu and Thomas Gridley. All rights reserved. Genetics of Deafness Wed, 18 Apr 2012 11:57:32 +0000 http://www.hindawi.com/journals/gri/2012/562848/ Edi Lúcia Sartorato, Karen Friderici, and Ignacio Del Castillo Copyright © 2012 Edi Lúcia Sartorato et al. All rights reserved. Mealybug Chromosome Cycle as a Paradigm of Epigenetics Sun, 08 Apr 2012 12:39:15 +0000 http://www.hindawi.com/journals/gri/2012/867390/ Recently, epigenetics has had an ever-growing impact on research not only for its intrinsic interest but also because it has been implied in biological phenomena, such as tumor emergence and progression. The first epigenetic phenomenon to be described in the early 1960s was chromosome imprinting in some insect species (sciaridae and coccoideae). Here, we discuss recent experimental results to dissect the phenomenon of imprinted facultative heterochromatinization in Lecanoid coccids (mealybugs). In these insect species, the entire paternally derived haploid chromosome set becomes heterochromatic during embryogenesis in males. We describe the role of known epigenetic marks, such as DNA methylation and histone modifications, in this phenomenon. We then discuss the models proposed to explain the noncanonical chromosome cycle of these species. Giorgio Prantera and Silvia Bongiorni Copyright © 2012 Giorgio Prantera and Silvia Bongiorni. All rights reserved. The Epigenetic Repertoire of Daphnia magna Includes Modified Histones Wed, 04 Apr 2012 11:35:46 +0000 http://www.hindawi.com/journals/gri/2012/174860/ Daphnids are fresh water microcrustaceans, many of which follow a cyclically parthenogenetic life cycle. Daphnia species have been well studied in the context of ecology, toxicology, and evolution, but their epigenetics remain largely unexamined even though sex determination, the production of sexual females and males, and distinct adult morphological phenotypes, are determined epigenetically. Here, we report on the characterization of histone modifications in Daphnia. We show that a number of histone H3 and H4 modifications are present in Daphnia embryos and histone H3 dimethylated at lysine 4 (H3K4me2) is present nonuniformly in the nucleus in a cell cycle-dependent manner. In addition, this histone modification, while present in blastula and gastrula cells as well as the somatic cells of adults, is absent or reduced in oocytes and nurse cells. Thus, the epigenetic repertoire of Daphnia includes modified histones and as these epigenetic forces act on a genetically homogeneous clonal population Daphnia offers an exceptional tool to investigate the mechanism and role of epigenetics in the life cycle and development of an ecologically important species. Nicole F. Robichaud, Jeanette Sassine, Margaret J. Beaton, and Vett K. Lloyd Copyright © 2012 Nicole F. Robichaud et al. All rights reserved. Epigenetics in Social Insects: A New Direction for Understanding the Evolution of Castes Wed, 28 Mar 2012 14:26:36 +0000 http://www.hindawi.com/journals/gri/2012/609810/ Epigenetic modifications to DNA, such as DNA methylation, can expand a genome’s regulatory flexibility, and thus may contribute to the evolution of phenotypic plasticity. Recent work has demonstrated the importance of DNA methylation in alternative queen and worker “castes” in social insects, particularly honeybees. Social insects are an excellent system for addressing questions about epigenetics and evolution because: (1) they have dramatic caste polyphenisms that appear to be tied to differential methylation, (2) DNA methylation is widespread in various groups of social insects, and (3) there are intriguing connections between the social environment and DNA methylation in many species, from insects to mammals. In this article, we review research on honeybees, and, when available, other social insects, on DNA methylation and queen and worker caste differences. We outline a conceptual framework for the effects of methylation on caste determination in honeybees that may help guide studies of epigenetic regulation in other polyphenic taxa. Finally, we suggest future paths of study for social insect epigenetic research, including the importance of comparative studies of DNA methylation on a broader range of species, and highlight some key unanswered mechanistic questions about how DNA methylation affects gene regulation. Susan A. Weiner and Amy L. Toth Copyright © 2012 Susan A. Weiner and Amy L. Toth. All rights reserved. Transgenic Epigenetics: Using Transgenic Organisms to Examine Epigenetic Phenomena Tue, 27 Mar 2012 14:48:20 +0000 http://www.hindawi.com/journals/gri/2012/689819/ Non-model organisms are generally more difficult and/or time consuming to work with than model organisms. In addition, epigenetic analysis of model organisms is facilitated by well-established protocols, and commercially-available reagents and kits that may not be available for, or previously tested on, non-model organisms. Given the evolutionary conservation and widespread nature of many epigenetic mechanisms, a powerful method to analyze epigenetic phenomena from non-model organisms would be to use transgenic model organisms containing an epigenetic region of interest from the non-model. Interestingly, while transgenic Drosophila and mice have provided significant insight into the molecular mechanisms and evolutionary conservation of the epigenetic processes that target epigenetic control regions in other model organisms, this method has so far been under-exploited for non-model organism epigenetic analysis. This paper details several experiments that have examined the epigenetic processes of genomic imprinting and paramutation, by transferring an epigenetic control region from one model organism to another. These cross-species experiments demonstrate that valuable insight into both the molecular mechanisms and evolutionary conservation of epigenetic processes may be obtained via transgenic experiments, which can then be used to guide further investigations and experiments in the species of interest. Lori A. McEachern Copyright © 2012 Lori A. McEachern. All rights reserved. Gene Control during Transcription Elongation Sun, 25 Mar 2012 13:48:23 +0000 http://www.hindawi.com/journals/gri/2012/758384/ Sebastián Chávez, David S. Gross, Damien Hermand, and Carlos Suñé Copyright © 2012 Sebastián Chávez et al. All rights reserved. Aphids: A Model for Polyphenism and Epigenetics Wed, 21 Mar 2012 16:11:07 +0000 http://www.hindawi.com/journals/gri/2012/431531/ Environmental conditions can alter the form, function, and behavior of organisms over short and long timescales, and even over generations. Aphid females respond to specific environmental cues by transmitting signals that have the effect of altering the development of their offspring. These epigenetic phenomena have positioned aphids as a model for the study of phenotypic plasticity. The molecular basis for this epigenetic inheritance in aphids and how this type of inheritance system could have evolved are still unanswered questions. With the availability of the pea aphid genome sequence, new genomics technologies, and ongoing genomics projects in aphids, these questions can now be addressed. Here, we review epigenetic phenomena in aphids and recent progress toward elucidating the molecular basis of epigenetics in aphids. The discovery of a functional DNA methylation system, functional small RNA system, and expanded set of chromatin modifying genes provides a platform for analyzing these pathways in the context of aphid plasticity. With these tools and further research, aphids are an emerging model system for studying the molecular epigenetics of polyphenisms. Dayalan G. Srinivasan and Jennifer A. Brisson Copyright © 2012 Dayalan G. Srinivasan and Jennifer A. Brisson. All rights reserved.