Journal of Genetics and Genome Research publishes articles on all aspects of inheritance and novel insights into the genome biology of all organisms, including advances in genomic medicine. JGGR focuses on Gene Structure and Organization, Gene Expression, Mutation Detection and Analysis, Linkage Analysis and Genetic Mapping, Physical Mapping, Cytogenetics, Genomic Imaging, Genome Structure and Organization, Disease Association Studies, Comparative Genomics, Molecular Evolution, Genome-Scale Quantitative and Population Genetics, Proteomics, Epigenomics and systems biology.
Journal of Genetics and Genome Research is peer-review open access journal that ensures the publication of high quality articles in the form of original work, reviews, commentaries, shorts communications, letters, oral presentations and case studies. JGGR follows a standard peer-review process with the support of its eminent Editorial board members. Two independent review comments followed by editor's decision will be considered to publish the article. JGGR provides the readers with free and immediate access to its content and is a permanent archive of genetic information under open access category serves the scientific community.
Articles Search by Keyword | Journal title | Author name | DOI
Open Access DOI:10.23937/2378-3648/1410037
Ruicheng Yan, Jianfei Luo, Fusheng Lin, Chao Hu, and Shiqiang Shen
Article Type: ORIGINAL RESEARCH | First Published: September 12, 2018
Vitamin K2 and phosphatidylcholine are two common drugs in clinical treatment. Studies carried out in the past several years demonstrated vitamin K2 and phosphatidylcholine could separately inhibit hepatocarcinogenesis. In this study, we sought to investigate the synergy of vitamin K2 and phosphatidylcholine and the potential mechanism. Multiple assays were performed to evaluate the effect of combination administration in vitro and in vivo. Then ...
Open Access DOI:10.23937/2378-3648/1410036
Padmanabhan Priyavathi, Srikakulam Nagesh, Velayudha Vimala Kumar Kavitha, Christdas Johnson and Pandi Gopal
Article Type: Research Article | First Published: August 25, 2018
Abelmoschus esculentus is widely cultivated and consumed across the globe for its nutritional and medicinal purpose. In spite of the growing demand, its cultivation is massively affected by various insects, fungi, nematodes and viruses. Due to lack of genomic and limited transcriptomic resources, genetic manipulation studies concerning the crop improvement against various environmental factors is scarce for this crop. Thereby, the present study aims to develop high quality transcriptome of A. es...
Open Access DOI:10.23937/2378-3648/1410035
Salleh MS, Mazzoni G, Nielsen MO, Lovendahl P and Kadarmideen HN
Article Type: Research Article | First Published: July 16, 2018
Residual feed intake (RFI) is the difference between actual and predicted feed intake and an important factor determining feed efficiency (FE). Recently, 170 candidate genes were associated with RFI, but no expression quantitative trait loci (eQTL) mapping has hitherto been performed on FE related genes in dairy cows. In this study, an integrative systems genetics approach was applied to map eQTLs in Holstein and Jersey cows fed two different die...
Open Access DOI:10.23937/2378-3648/1410034
Zeynep Yegin and Cumhur Avsar
Article Type: Research Article | First Published: June 23, 2018
The genus Aeromonas is widely distributed in aquatic environments and certain strains are serious pathogens in poikilothermic animals and humans. Human infections related with this pathogen include gastroenteritis, urinary tract infections, pneumonia, wound infections and septicemia. In this study, both the correct medical diagnosis with taking advantages of molecular approaches and a brief investigation of the enzymatic activity potential of Aer...
Open Access DOI:10.23937/2378-3648/1410033
Mohammad Reza Zinatizadeh, Zahra Masoumalinejad, Azim Nejatizadeh, Mohammad Shekari, Farzaneh Parnak and Faeghe Zaree
Article Type: Review Article | First Published: May 30, 2018
NF-κB essential modulator (NEMO) syndrome is an immunodeficiency disease. NF-κB proteins, which regulate the expression of genes that moderate important physiological processes, are called regulatory of cell homeostasis. NEMO is a protein in the IKK inhibitor complex that many organ systems normally do not grow. Cells (as well as organ and tissues) do not grow proteins they express proteins....
Open Access DOI:10.23937/2378-3648/1410032
Ying Wang, Zhengwei Zhang, Yifan Dai and Haiyuan Yang
Article Type: Research Article | First Published: October 11, 2017
GLI family zinc finger 3 (GLI3) has been shown to play a critical role in the regulation of Hedgehog signaling, with important implications in embryonic and postnatal development. However, the molecular characteristics of GLI3 gene and its expression profile in pig tissues have yet to be elucidated....
Open Access DOI:10.23937/2378-3648/1410031
Article Type: Review Article | First Published: July 27, 2017
Substitution rate matrices are used to correct multiple hits at the same sites, which requires the derivation of transition probabilities and evolutionary distances from substitution rate matrices. The derivation is essential in molecular phylogenetics and phylogenomics....
Open Access DOI:10.23937/2378-3648/1410030
Timothy G Jenkins, Monis B Shamsi, Emma James, Kenneth I Aston and Douglas T Carrell
Article Type: Research Article | First Published: June 12, 2017
Shipping of various tissues, including sperm, for the purposes of diagnostic testing and/or collaborative scientific pursuits is commonly performed. While many sample attributes are largely stable during the shipping process regardless of shipping environment, some physical factors such as temperature, duration of storage and other handling conditions may affect certain features of these samples including a commonly assessed epigenetic mark, DNA ...
Open Access DOI:10.23937/2378-3648/1410029
Geert R Verheyen, Koen Van Deun and Sabine Van Miert
Article Type: Research Article | First Published: May 15, 2017
All information for the proper development, functioning and reproduction of organisms is coded in the sequence of matched base-pairs of DNA. DNA mutations can result in harmful effects and play a role in genetic disorders and cancer. As mutations can arise through exposure to chemical substances, testing needs to be done on substances that humans and animals can be exposed to....
Open Access DOI:10.23937/2378-3648/1410028
Mohd Helmy Yusof, Sharifah Izwan Tuan Othman, Siti Shuhada Mokhtar, Yushimah Yunus, Abu Thalhah Abdul Aziz and Hoh Boon Peng
Article Type: Original Article | First Published: September 26, 2016
Obtaining sustainable source of cells or DNA from a single individual has always been a constraint in biomedical research. Generation of lymphoblastoid cell lines (LCLs) as a surrogate for replacement of isolated peripheral blood mononuclear cells (PBMCs) has substantially accelerated the process of biological investigations. LCLs can be established by transfection of B lymphocytes from peripheral blood with Epstein Barr Virus (EBV), bearing mino...
Open Access DOI:10.23937/2378-3648/1410027
Article Type: Review Article | First Published: September 15, 2016
Aerobic oxidation of carbohydrates by mitochondria has been a great invention of nature, marking a big step in early evolution. This biological system has greatly multiplied the energy production of the cell by supplying this energy to different metabolic units, with increased temporal and spatial specificities. The numerous mitochondrial functions that have emerged and developed along evolution constitute strong signatures of evolution pressures...
Open Access DOI:10.23937/2378-3648/1410026
W T Farmer, J R Sommer and C E Farin
Article Type: Review Article | First Published: August 22, 2016
Bovine insulin-like growth factor type 2 receptor (IGF2R) is an imprinted gene whose aberrant expression has been implicated in development of abnormal offspring syndrome. Bovine AIRN (AIRN) is expressed in post-implantation fetal tissues coinciding with imprinted expression of IGF2R. Although expression patterns of bovine AIRN have been reported based on PCR analysis, characteristics of this transcript are unknown....
Open Access DOI:10.23937/2378-3648/1410025
Mehmet Sah Ipek and Alper Akin
Article Type: Case Report | First Published: June 02, 2016
Sedaghatian-type spondylometaphyseal dysplasia (SSMD) is a lethal neonatal form of spondylometaphyseal dysplasias that is reported rarely. The case of a female infant demonstrating a clinical phenotype consistent with a diagnosis of SSMD was presented. She died with acute evidence of myocardial injury. In SSMD, certain organ systems including the central nervous, cardiac, and skeletal systems, are clearly involved. Although the exact cause of the...
Open Access DOI:10.23937/2378-3648/1410024
Abir M Zahreddine, Mohamed E Moustafa and Hala A Chamieh
Article Type: Original Article | First Published: May 24, 2016
Oxidative stress has been frequently associated with the development of type 2 diabetes mellitus. Manganese superoxide dismutase (MnSOD) is one of the most important enzymes responsible for the defense against oxidative damage in the mitochondria. A polymorphism in the second exon of the MnSOD at position 16 that changes Ala into Val, induces changes in the structural conformation and mitochondrial transport of MnSOD. This polymorphism affects th...
Open Access DOI:10.23937/2378-3648/1410023
Giulia Fiscon, Giulio Iannello and Paola Paci
Article Type: Review Article | First Published: May 20, 2016
Investigating the RNA structure contributes greatly to understand RNA roles in cellular processes. Indeed, functional RNAs show specific instrumental sub-structures for their interaction with other molecules. The RNA structure prediction will provide fundamental insights into developing hypothesis connecting function to structure, but it is a challenging and unsolved task yet. We aim at discussing the current status of the widespread RNA folding ...
Open Access DOI:10.23937/2378-3648/1410022
Mendoza-Elizalde S, Olivares-Cervantes AL, Zuniga G, Valencia-Mayoral P, Vigueras-Galindo JC and Velazquez-Guadarrama N
Article Type: Review Article | First Published: April 13, 2016
Helicobacter pylori is a bacterium that has evolved with humans, is transmitted from person to person and persistently colonizes the stomach. During its long coexistence with humans, H. Pylori has developed complex strategies to limit the degree and extent of inflammation and damage to the gastric mucosa. It is capable of altering the physiology and immune response of the host, thereby allowing it to persist throughout life. Infection with H. pyl...
Open Access DOI:10.23937/2378-3648/1410020
Fuhai Li and Ming Zhan
Article Type: Review Article | First Published: November 05, 2015
An increasing body of large-scale genomic profiling data has been being generated on many diseases including cancers and on a number of drugs and compounds. The exploration of such big data has led to data-driven biomedical research. The data-driven studies include exploring disease subtypes with distinct molecular patterns, uncovering novel diagnosis biomarkers or treatments, and discovering new indications of drugs along with novel mechanisms o...
Open Access DOI:10.23937/2378-3648/1410021
Luis Souto, Filipa Tavares, Helena Moreira and Fatima Pinheiro
Article Type: Research Article | First Published: December 28, 2015
The analysis of mtDNA in forensic samples is commonly carried out by direct sequencing of the hyper variable regions of the control region, although with limited power of discrimination. Genotyping SNPs in the coding region of mtDNA can provide additional information and increase the discrimination power of mtDNA typing. In this study, we compare two methodologies for the detection of 9 SNPs in the control region of mtDNA: SNaPshot minisequencing...
Open Access DOI:10.23937/2378-3648/1410019
Zhengwei Dong, Hua Dong, Xiaorong Zhong, Zuxiang Peng, Xuehua Zhu, Yun Sun, Yunqin Chen, Changting Liu, Xiaolu Yin, Guanshan Zhu, Hong Zheng and Yi Gu
Article Type: Research Article | First Published: September 28, 2015
Patients with germ line or somatic BRCA1 and BRCA2 mutations are sensitive to PARP inhibitor treatment. However, current clinical testing of BRCA1/2 is limited to germ line mutations in blood samples. In the present study, we have developed and validated a work flow for BRCA1/2 mutation test in patient tumor samples, which can identify both germ line and somatic mutations. Our approach combined targeted capturing with the BRCA MASTR assay and con...
Open Access DOI:10.23937/2378-3648/1410018
Deepali N. Shinde, Jefferey Chen, Soren Fischbach, David J. Salvador, Kelly Farwell, Hsiao-Mei Lu and Sha Tang
Article Type: Research Article | First Published: September 17, 2015
Whole exome sequencing (WES) has been remarkably successful as both a diagnostic and novel gene discovery tool since its introduction to the clinical laboratory in 2011. Where traditional diagnostic methods have been uninformative in discovering the pathogenic etiology in patients, diagnostic exome sequencing (DES) has provided answers for roughly one-third of patients tested, thus contributing to the management of patients' overall healthcare. S...
Open Access DOI:10.23937/2378-3648/1410017
Heather S.L. Jim, Hui-Yi Lin, Jonathan P. Tyrer, Kate Lawrenson, Joe Dennis, Ganna Chornokur, Zhihua Chen, Ann Y. Chen, Jennifer Permuth-Wey, Katja KH. Aben, Hoda Anton-Culver, Natalia Antonenkova, Fiona Bruinsma, Elisa V. Bandera, Yukie T. Bean, Matthias W. Beckmann, Maria Bisogna, Line Bjorge, Natalia Bogdanova, Louise A. Brinton, Angela Brooks-Wilson, Clareann H. Bunker, Ralf Butzow, Ian G. Campbell, Karen Carty, Jenny Chang-Claude, Linda S. Cook, Daniel W. Cramer, Julie M. Cunningham, Cezary
Article Type: Research Article | First Published: September 15, 2015
Disruption in circadian gene expression, whether due to genetic variation or environmental factors (e.g., light at night, shiftwork), is associated with increased incidence of breast, prostate, gastrointestinal and hematologic cancers and gliomas. Circadian genes are highly expressed in the ovaries where they regulate ovulation; circadian disruption is associated with several ovarian cancer risk factors (e.g., endometriosis). However, no studies ...
Open Access DOI:10.23937/2378-3648/1410016
Vinod Yadav, Ved Prakash Dwivedi, Debapriya Bhattacharya, Ashwan
Article Type: Research Article | First Published: June 27, 2015
It was in 1942 when C.H. Waddington first coined the term epigenetics. According to him there is no direct relationship between a gene and its phenotype. He considered epigenetics as a part of development biology and in his opinion many times genotype and phenotype variations are not associated and phenotype differences do not necessarily involve change in genotype. Since 40s epigenetics became the topic of interest among the scientific community...
Open Access DOI:10.23937/2378-3648/1410015
Jianjian Wu, Weisheng Jia, Wei Chen, Feng Zhou, Zhenqiang Fang, Xianglin Hou, Bing Chen, Gang Ye, and Jianwu Dai
Article Type: Research Article | First Published: June 21, 2015
A 5cm long urethra segment near the penis bone was excised surgically. A collagen scaffold seeded with hBMSCs was sutured to two ends of the host urethra for the urethral repair in the experimental group, whereas the unseeded scaffold was used in the control group. Retrograde urethrography was performed before the operation and at 6 months after the surgery. At 6 months postsurgery, the animals were sacrificed, and the reconstructed urethras were...
Open Access DOI:10.23937/2378-3648/1410014
Chunxian Chen, Clive H. Bock, Tom G. Beckman, Bruce W. Wood and William R. Okie
Article Type: Research Article | First Published: May 30, 2015
Efficient utilization of microsatellites in genetic studies remains impeded largely due to the unknown status of their primer reliability, chromosomal location, and allele polymorphism. Discovery and characterization of microsatellite polymorphisms in a taxon will disclose the unknowns and gain new insights into the polymorphic alleles....
Open Access DOI:10.23937/2378-3648/1410013
Renata Santos Tourinho, Camilla Rodrigues de Almeida, Andreza Salvio Lemos, Noemi Rovaris Gardinali, Yasmine Rangel Vieira, Jonas Schmidt-Chanasit and Vanessa Salete de Paula
Article Type: Short Communication | First Published: March 23, 2015
Hepatitis A, which presents a major health problem globally, is caused by hepatitis A virus (HAV). This virus, whose primary site of replication is the liver, is the most common agent causing acute liver disease worldwide. Hepatitis E virus (HEV) is the most recently discovered of the hepatotropic viruses, its genome having been identified in 1991. Despite the similarity with hepatitis A virus in their pathogenesis and transmission form, HEV has ...
Open Access DOI:10.23937/2378-3648/1410012
Wallax Augusto Silva Ferreira, Mariana Diniz Araujo, Nilson Praia Anselmo, Maria Lucia Harada and Barbara do Nascimento Borges
Article Type: Research Article | First Published: February 27, 2015
Astrocytoma is a common aggressive intracranial tumor and a formidable challenge in clinic. Association of the altered DNA methylation pattern of the promoter CpG islands has been found in many human tumors. OCT4 and SOX2 are essential transcription factors for embryonic development and play key roles in determining the fate of stem cells....
Open Access DOI:10.23937/2378-3648/1410011
Carlos G Urzua-Traslavina, Maria G Moreno-Trevino, Denisse A Martinez-Trevino, Hugo A Barrera-Saldana and Rafael BR Leon-Cachon
Article Type: Review Article | First Published: December 16, 2014
Mitochondria are responsible for energy production in unicellular and multicellular eukaryotes. Apart from their major role in metabolism, mitochondria are involved in many other cellular processes. A new paradigm is needed to understand aging, aging-related illnesses, and complex diseases. Because of the long co-evolution of mitochondria with the cells, subtle variations in the function of these organelles could influence many organ systems. Und...
Open Access DOI:10.23937/2378-3648/1410010
Adriana Arita and Max Costa
Article Type: Review Article | First Published: December 15, 2014
Epigenetics refers to the study of the changes in gene expression that occur without changes in the DNA sequence. There is growing evidence that epigenetic modifications such as changes in the levels of DNA methylation or post-translational histone modifications are involved in the pathogenesis of many human diseases including cancer. Oxidative stress as a result of metabolic or environmental factors leads to excessive production of reactive oxyg...
Open Access DOI:10.23937/2378-3648/1410009
Silvia Bresolin, Paola De Filippi, Claudia Cagioni, Simone Cesaro, Annamaria Di Meglio, Anna Leszl, Fiorenza Aprili, Chiara Cugno, Chiara Frasson, Marco Zecca, Cesare Danesino and Geertruyte Kronnie
Article Type: Research Article | First Published: December 14, 2014
Juvenile myelomonocytic leukemia is a rare neoplastic disorder occurring in early childhood often showing an aggressive progression. We report a case of a twin pair with concordant JMML but an extremely different disease course. Both twins presented with somatic aberrations of chromosome 7 and mutations in PTPN11. Analysis of sorted BM and PB cell populations revealed the clonal nature of the disease and indicated that genomic aberrations arise f...
Open Access DOI:10.23937/2378-3648/1410008
Serazhutdin A. Abdullaev and Azhub I. Gaziev
Article Type: Research Article | First Published: December 08, 2014
The transfer of mitochondrial DNA (mtDNA) into the nuclear genome is a dynamic process, resulting in the formation of nuclear mitochondrial (numt) pseudogenes or numt-insertions. Experimental determination of de novo numt-insertions is limited by the extensive homology of mtDNA in the nuclear DNA (nDNA) of eukaryotes. Since chicken nDNA contains only 13 numtpseudogenes, we tried to follow experimentally the induction of numt-insertions de novo in...
Open Access DOI:10.23937/2378-3648/1410007
Nesli Avgan, Heidi G. Sutherland, Lauren K. Spriggens, Astrid J. Rodriguez-Acevedo, Larisa M. Haupt, David H. K. Shum and Lyn R. Griffihs
Article Type: Research Article | First Published: November 12, 2014
Serotonin and its receptors, including the 5-Hydroxytryptamine Receptor 2A encoded by the HTR2A gene, are important for learning and memory in animals and humans.Polymorphic variation in the HTR2A gene, which encodes the 5-HT2Aserotonin receptor, has previously been shown to associate with some memory traits,in particular effecting delayed verbal memory. In the current study we have examined the HTR2A His452Tyr (H452Y) substitution for associatio...
Open Access DOI:10.23937/2378-3648/1410006
Rosa Santacroce, Angelica Leccese, Roberta Trunzo, Giuseppe Lassandro, Paola Giordano, Cosimo Ettorre, Stefano Antoncecchi, Isabella Cantori, Alfredo Dragani, Donata Belvini, Roberta Salviato and Maurizio Margaglione
Article Type: Research Article | First Published: October 14, 2014
Introduction: Haemophilia A (HA) is the most common X-linked recessive genetic disease caused by mutations in the gene coding for coagulation factor VIII (FVIII) resulting in spontaneous bleeding. Aim: The aim of our study is to provide additional information about the genetic causes of HA describing the correlation between the observed mutations and the clinical phenotype in a cohort of 52 patients suffering from HA to different degrees. Met...
Open Access DOI:10.23937/2378-3648/1410005
Perng-Kuang Chang and Leslie L. Scharfenstein
Article Type: Research Article | First Published: October 05, 2014
The availability of a representative Gene Ontology (GO) database is a prerequisite for a successful functional genomics study. Using the online Blast2GO tool we constructed a GO database of Aspergillus flvus, a plant and human pathogen. Of the predicted total 13,485 A. flvus genes 8,987 were annotated with GO terms. The mean GO level was 5.64. Using a low stringency setting of a sequence cut-off number of 10 and a node score of 20, we obtained 1,...
Open Access DOI:10.23937/2378-3648/1410004
Shela Lee, Joy Radecki, Hsiao-Mei Lu, and Aaron M. Elliott
Article Type: Research Article | First Published: October 05, 2014
The clinical implementation of new target enrichment methods and next-generation sequencing (NGS) technology has rapidly transformed genetic testing. Diagnostic labs can now offer a wide variety of large comprehensive multi-gene panels or even full exome sequencing to help clinicians diagnose and treat patients. The unmatched sensitivity, accuracy and throughput of NGS compared to traditional Sanger sequencing make it an ideal technology not only...
Open Access DOI:10.23937/2378-3648/1410003
Tejendra Singh Chauhan, Swayam Prakash, Raj Kumar Sharma and Suraksha Agrawal
Article Type: Research Article | First Published: October 04, 2014
Aim: Immune mechanisms of Cytomegalovirus (CMV) infection suggest a possible relationship between CMV with development of acute graft rejection. Current immune suppression impairs antiviral specifi T-cell immunity in solid organ transplantation. Inhibitory/ activating NK receptor bindings activated by self HLA antigens confront allogeneic cells that lack a ligand for specifi receptor. KIR ligand incompatibility caused due to presence/absence of K...
Open Access DOI:10.23937/2378-3648/1410002
Hassan SM, Al Muslahi M, Al Riyami M, Bakker E, Harteveld CL and Giordano PC
Article Type: Research Article | First Published: September 26, 2014
Objective: To describe the effect of Hydroxyurea (HU) treatment in Omani Sickle Cell Disease (SCD) patients with different beta-globin gene cluster haplotypes. Materials and methods: A total of 52 cases treated with HU were enrolled in this study. Response to the drug was compared between patients with and without the XmnI polymorphism in the different betaglobin gene cluster haplotypes. We have classified our cohort into three categories: good...
Open Access DOI:10.23937/2378-3648/1410001
Nikolay A. Barashkov, Aisen V. Solovyev, Fedor M. Teryutin, Vera G. Pshennikova1, Leonid A. Klarov, Georgii P. Romanov, Sergey S. Nakhodkin, Kyunney E. Savvinova, Nyurgun N. Gotovtsev, Natalya A. Solovyeva, Andrei A. Kozhevnikov, Lena M. Vasilyeva, Elvira E. Fedotova, Maria V. Pak, Sargylana N. Lekhanova, Elena V. Zakharova, Adyum M. Rafailov, Nikolay V. Luginov, Anatoliy N. Alexeev, Olga L. Posukh, Lilya U. Dzhemileva, Elza K. Khusnutdinova and Sardana A. Fedorova
Article Type: Research article | First Published: September 01, 2014
This study presents data on the carrier frequencies of IVS1+1 G>A mutation in GJB2 gene, causing by autosomal recessive form of deafness among various ethno-geographical groups of Yakut population and in a random sample of the Yakuts. 350 DNA samples of hearing individuals from various ethno-geographical groups of Yakut population: Central (n=60), Vilyui (n=60), Northern (n=60) and random samples of Yakuts (n=170) were obtained from the DNA Bank ...
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